[med-svn] [Git][med-team/resfinder][upstream] New upstream version 4.4.2
Andreas Tille (@tille)
gitlab at salsa.debian.org
Tue Jan 16 07:06:35 GMT 2024
Andreas Tille pushed to branch upstream at Debian Med / resfinder
Commits:
014c078b by Andreas Tille at 2024-01-16T07:24:05+01:00
New upstream version 4.4.2
- - - - -
20 changed files:
- + .pdm-python
- CHANGELOG.md
- Dockerfile_no_dbs
- bitbucket-pipelines.yml
- dockerfile
- + dockerfile_EFSA_2022
- src/resfinder/__init__.py
- src/resfinder/cge/output/gene_result.py
- src/resfinder/cge/output/std_results.py
- src/resfinder/cge/phenotype2genotype/isolate.py
- src/resfinder/cge/phenotype2genotype/res_profile.py
- src/resfinder/cge/pointfinder.py
- src/resfinder/cge/resfinder.py
- src/resfinder/run_resfinder.py
- + tests/data/test_isolate_12.fa
- + tests/data/test_isolate_14.fa
- + tests/data/test_isolate_14_1.fq
- + tests/data/test_isolate_14_2.fq
- tests/resfinder/cge/output/test_gene_result.md
- tests/resfinder/cge/output/test_phenotype_result.md
Changes:
=====================================
.pdm-python
=====================================
@@ -0,0 +1 @@
+/Users/rolf/workcloud/Scripts-CGE/resfinder/.venv/bin/python
\ No newline at end of file
=====================================
CHANGELOG.md
=====================================
@@ -5,6 +5,50 @@ All notable changes to this project will be documented in this file.
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+## [4.4.2] - 2023-11-27
+
+### Fixed
+
+- Issue where mutations in promoters that are not indels (i.e. substitutions) could be missed as they were uncorrectly registered as unknown mutations.
+
+## [4.4.1] - 2023-11-02
+
+### Fixed
+
+- Issue where mutations in promoters could be missed if using fastq files as input. Issue continues to persist for PointFinder database versions < 4.0.1
+
+## [4.4.0] - 2023-10-27
+
+### Fixed
+
+- Issue where application crashed with a "KeyError: 'var_aa'", when finding mutation in promoters.
+- Issue where PointFinder database reference sequence names containing "promoter-size-\d+bp" would be missed. Issue continues to persist for PointFinder database versions < 4.0.0
+- Spelling error in json output "ref_seq_lenght". It is now "ref_seq_length"
+
+## [4.3.3] - 2023-08-22
+
+### Fixed
+
+- Issue where ResFinder crashed with the error: "UnboundLocalError: local variable \'hit_class\' referenced before assignment'" if the flag '--output_aln' was enabled along with FASTQ input
+
+## [4.3.2] - 2023-05-31
+
+### Fixed
+
+- Issue where PointFinder part crashed with the error: "NameError: name 'combined_id' is not defined"
+
+## [4.3.1] - 2023-03-03
+
+### Removed
+
+- Overlap warning from pointfinder (message was only intended for testing)
+
+### Fixed
+
+- dockerfile, so that it works with NextFlow
+- Issue with alignment output in json
+- Issue with reporting concatenated gene hits in PointFinder
+
## [4.3.0] - 2023-02-09
### Added
=====================================
Dockerfile_no_dbs
=====================================
@@ -8,19 +8,20 @@ RUN apt-get update -qq; \
wget \
ncbi-blast+ \
libz-dev \
+ procps \
; \
rm -rf /var/cache/apt/* /var/lib/apt/lists/*;
# Install KMA
RUN cd /usr/src/; \
- git clone --depth 1 -b 1.4.3 https://bitbucket.org/genomicepidemiology/kma.git; \
+ git clone --depth 1 -b 1.4.11 https://bitbucket.org/genomicepidemiology/kma.git; \
cd kma && make; \
mv kma /usr/bin/; \
cd ..; \
rm -rf kma/;
# Install ResFinder
-RUN pip install --no-cache-dir resfinder==4.3.0
+RUN pip install --no-cache-dir resfinder==4.3.1
# Setup environment
RUN cd /; \
=====================================
bitbucket-pipelines.yml
=====================================
@@ -1,10 +1,15 @@
# Testing ResFinder
-
+clone:
+ depth: full
image: python:3.10
pipelines:
custom:
- test-and-build:
+ mirror-to-github:
+ - step:
+ script:
+ - git push --mirror git at github.com:genomicepidemiology/resfinder
+ test-and-build:
- step:
name: Test
caches:
@@ -29,4 +34,4 @@ pipelines:
- export PATH=/root/.local/bin:$PATH
- pdm install
- pdm run test
- - pdm build
+ - pdm build
\ No newline at end of file
=====================================
dockerfile
=====================================
@@ -9,6 +9,7 @@ RUN apt-get update -qq; \
wget \
ncbi-blast+ \
libz-dev \
+ procps \
; \
rm -rf /var/cache/apt/* /var/lib/apt/lists/*;
@@ -20,7 +21,7 @@ RUN cd /usr/src/; \
cd ..; \
rm -rf kma/;
-ENV RESFINDER_VERSION 4.3.0
+ENV RESFINDER_VERSION 4.4.2
# Install ResFinder
RUN pip install --no-cache-dir resfinder==$RESFINDER_VERSION
=====================================
dockerfile_EFSA_2022
=====================================
@@ -0,0 +1,60 @@
+FROM --platform=linux/amd64 python:3.10-slim-bullseye
+
+ENV INSIDE_DOCKER true
+ENV DEBIAN_FRONTEND noninteractive
+
+RUN apt-get update -qq; \
+ apt-get install --no-install-recommends -y -qq git \
+ build-essential \
+ wget \
+ ncbi-blast+ \
+ libz-dev \
+ procps \
+ ; \
+ rm -rf /var/cache/apt/* /var/lib/apt/lists/*;
+
+# Install python dependencies
+RUN pip3 install --upgrade pip
+RUN pip3 install -U tabulate===0.8.9 cgecore==1.5.6 cgelib==0.7.3 pandas==1.4.2 \
+ biopython==1.79 gitpython==3.1.27 python-dateutil==2.8.2;
+
+# Install KMA
+# Note: In future versions remove kma_index as it is only needed in old versions of pointfinder
+RUN cd /usr/src/; \
+ git clone --depth 1 -b 1.4.11 https://bitbucket.org/genomicepidemiology/kma.git; \
+ cd kma && make; \
+ mv kma /usr/bin/; \
+ mv kma_index /usr/bin/; \
+ cd ..; \
+ rm -rf kma/;
+
+# Install BLAST
+RUN cd /usr/src/; \
+ wget "https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.13.0/ncbi-blast-2.13.0+-x64-linux.tar.gz"; \
+ tar -xf ncbi-blast-2.13.0+-x64-linux.tar.gz; \
+ mv ncbi-blast-2.13.0+/bin/* /usr/bin/;
+
+ENV RESFINDER_VERSION EFSA_2022
+
+# Install ResFinder
+RUN cd /usr/src/; \
+ git clone -b $RESFINDER_VERSION --depth 1 https://bitbucket.org/genomicepidemiology/resfinder.git;
+
+# Install databases
+RUN cd /usr/src/resfinder; \
+ git clone -b $RESFINDER_VERSION --depth 1 https://git@bitbucket.org/genomicepidemiology/resfinder_db.git db_resfinder; \
+ git clone -b $RESFINDER_VERSION --depth 1 https://git@bitbucket.org/genomicepidemiology/pointfinder_db.git db_pointfinder; \
+ cd /usr/src/resfinder/db_resfinder; \
+ python INSTALL.py; \
+ rm -rf .git; \
+ cd /usr/src/resfinder/db_pointfinder; \
+ python INSTALL.py; \
+ rm -rf .git;
+
+# Setup environment
+RUN cd /; \
+ mkdir app;
+WORKDIR /app
+
+# Execute program when running the container
+ENTRYPOINT ["python", "/usr/src/resfinder/run_resfinder.py"]
=====================================
src/resfinder/__init__.py
=====================================
@@ -1 +1 @@
-__version__ = '4.3.0'
+__version__ = "4.4.2"
=====================================
src/resfinder/cge/output/gene_result.py
=====================================
@@ -30,7 +30,7 @@ class GeneResult(dict):
self["ref_database"] = [res_collection.get_db_key(db_name)[0]]
self["identity"] = res["perc_ident"]
self["alignment_length"] = res["HSP_length"]
- self["ref_seq_lenght"] = res["sbjct_length"]
+ self["ref_seq_length"] = res["sbjct_length"]
self["depth"] = res.get("depth", None)
self["ref_start_pos"] = res["sbjct_start"]
self["ref_end_pos"] = res["sbjct_end"]
@@ -41,12 +41,7 @@ class GeneResult(dict):
self["notes"] = []
if conf and conf.output_aln:
- for ab_class, hits in alignments.gene_align_query.items():
- ab_class_keys = list(hits.keys())
- hit_key = next(key for key in ab_class_keys
- if key.startswith(self["ref_id"]))
- hit_class = ab_class
- break
+ hit_class, hit_key = self.get_hit_class(alignments.gene_align_query)
self["query_string"] = alignments.gene_align_query[hit_class][
hit_key]
@@ -56,19 +51,53 @@ class GeneResult(dict):
# BLAST coverage formatted results
coverage = res.get("coverage", None)
- if(coverage is None):
+ if (coverage is None):
# KMA coverage formatted results
coverage = res["perc_coverage"]
else:
coverage = float(coverage) * 100
self["coverage"] = coverage
- self["grade"] = GeneResult.calc_gene_grade(coverage=self["coverage"], identity=self["identity"])
+ self["grade"] = GeneResult.calc_gene_grade(
+ coverage=self["coverage"], identity=self["identity"])
self.remove_NAs()
uniqueness = self._get_unique_gene_key(res_collection)
self["key"] = uniqueness
+ def get_hit_class(self, gene_align_query):
+ """
+ Input:
+ gene_align_query: Dict from either FinderResult (KMA) or
+ Blaster (BLAST)
+ Output:
+ hit_class: Name of AB class
+ hit_key: Key used for query (hit)
+
+ Method looks through all the queries that align to a reference and
+ finds the query (hit) that matches the GeneResult object.
+ For BLAST hits the query is named after the coresponding contig
+ header (query_id), but for KMA the query key is named after the
+ reference it aligns to (ref_id).
+ """
+ lookup_key = self["query_id"]
+ if self["depth"] is not None:
+ lookup_key = self["ref_id"]
+
+ for ab_class, hits in gene_align_query.items():
+ if hits:
+ hits_keys = list(hits.keys())
+ hit_key = next((key for key in hits_keys
+ if key.startswith(lookup_key)), None)
+ if hit_key is None:
+ continue
+ hit_class = ab_class
+ break
+ else:
+ continue
+
+ return hit_class, hit_key
+
@staticmethod
def calc_gene_grade(coverage: float, identity: float) -> int:
if coverage == 100.0 and identity == 100.0:
@@ -87,7 +116,7 @@ class GeneResult(dict):
"""
na_keys = []
for key, val in self.items():
- if(val == "NA" or val is None):
+ if (val == "NA" or val is None):
na_keys.append(key)
for key in na_keys:
del self[key]
@@ -107,7 +136,7 @@ class GeneResult(dict):
If gene_key is found in res_collection. Creates a unique key by
appending a random string ton minimum_gene_key.
"""
- while(gene_key in res_collection["seq_regions"]):
+ while (gene_key in res_collection["seq_regions"]):
rnd_str = GeneResult.random_string(str_len=4)
gene_key = ("{key}{deli}{rnd}"
.format(key=minimum_gene_key, deli=delimiter,
@@ -143,7 +172,7 @@ class GeneResult(dict):
sbjct = header.split("_")
template = sbjct[0]
- if(len(sbjct) > 1):
+ if (len(sbjct) > 1):
variant = sbjct[1]
acc = "_".join(sbjct[2:])
else:
@@ -180,7 +209,7 @@ class GeneResult(dict):
query_id = self.get("query_id", "NA")
# Query id == "NA" when FASTQ
- if(query_id == "NA"):
+ if (query_id == "NA"):
res_collection["seq_regions"][gene_key]["ref_database"].extend(
self["ref_database"])
gene_key = None
=====================================
src/resfinder/cge/output/std_results.py
=====================================
@@ -2,6 +2,7 @@
import random
import string
import json
+import re
from ..phenotype2genotype.res_profile import PhenoDB
from ..phenotype2genotype.feature import ResGene, ResMutation
@@ -11,6 +12,7 @@ from .gene_result import GeneResult
from .seq_variation_result import SeqVariationResult
from .phenotype_result import PhenotypeResult
+from ..pointfinder import PointFinder
def add_gene_result_if_key_not_None(gene_result, res_collection):
'''
@@ -190,3 +192,27 @@ class PointFinderResultHandler():
res_collection, mismatch, gene_results, ref_db_name)
res_collection.add_class(cl="seq_variations",
**seq_var_result)
+
+ @staticmethod
+ def rename_promoter_results(results, method):
+ if method == PointFinder.TYPE_BLAST:
+ PointFinderResultHandler._rename_blast_promoter_results(results)
+ else:
+ PointFinderResultHandler._rename_kma_promoter_results(results)
+
+ def _rename_blast_promoter_results(results):
+ promoter_keys = [k for k in results if re.search(r"promoter-size", k)]
+ for promoter_key in promoter_keys:
+ val_dict = results.pop(promoter_key)
+ new_promoter_key = PhenoDB.if_promoter_gene_rename(promoter_key)
+ results[new_promoter_key] = val_dict
+
+ def _rename_kma_promoter_results(results):
+ promoter_keys = set()
+
+ for inner_dict in results.values():
+ promoter_keys = [k for k in inner_dict if re.search(r"promoter-size", k)]
+ for promoter_key in promoter_keys:
+ val_dict = inner_dict.pop(promoter_key)
+ new_promoter_key = PhenoDB.if_promoter_gene_rename(promoter_key)
+ inner_dict[new_promoter_key] = val_dict
=====================================
src/resfinder/cge/phenotype2genotype/isolate.py
=====================================
@@ -234,7 +234,7 @@ class Isolate(dict):
f"_{feat_res_dict['nuc_change']}")
aa_format = (f"{feat_res_dict['seq_regions'][0]}"
f"_{feat_res_dict['ref_start_pos']}"
- f"_{feat_res_dict['var_aa']}")
+ f"_{var_aa}") # var_aa can be None
return nuc_format, aa_format
# Amino acid mutation
else:
@@ -395,7 +395,7 @@ class Isolate(dict):
hit = DBHit(name=gene_info["name"],
identity=gene_info["identity"],
match_length=gene_info["alignment_length"],
- ref_length=gene_info["ref_seq_lenght"],
+ ref_length=gene_info["ref_seq_length"],
start_ref=gene_info["ref_start_pos"],
end_ref=gene_info["ref_end_pos"],
acc=gene_info["ref_acc"],
@@ -481,7 +481,7 @@ class Isolate(dict):
elif(feature.hit.match_category > best_match):
best_match = feature.hit.match_category
- output_str += "\t" + str(best_match)
+ output_str += "\t" + str(best_match)
gene_list = ab.get_gene_namewacc(tostring=True)
mut_list = ab.get_mut_namewannot(tostring=True)
=====================================
src/resfinder/cge/phenotype2genotype/res_profile.py
=====================================
@@ -610,6 +610,22 @@ class PhenoDB(dict):
return out_string
+ @staticmethod
+ def if_promoter_gene_rename(s):
+ """
+ Needed instead of if_promoter_rename() when only gene name is
+ present without variant number and acc no
+ """
+ out_string = s
+
+ regex = r"^(.+-promoter)-size-\d+bp$"
+ promoter_match = re.search(regex, s)
+
+ if promoter_match:
+ out_string = f"{promoter_match.group(1)}"
+
+ return out_string
+
@staticmethod
def get_csv_tuple(csv_string, sep=",", lower=True):
""" Takes a string containing a comma seperated list, makes it all
=====================================
src/resfinder/cge/pointfinder.py
=====================================
@@ -43,6 +43,7 @@ class PointFinder(CGEFinder):
PHENOTYPE_FILE = "phenotypes.txt"
# Deprecated variable, use phenotype (kept for legacy dbs)
RES_OVERVIEW_FILE = "resistens-overview.txt"
+ PROMOTER_REGEX = r"(.+promoter)-size-(\d+)(?:bp)"
def __init__(self, db_path, species, gene_list=None, ignore_indels=False,
ignore_stop_codons=False):
@@ -57,6 +58,8 @@ class PointFinder(CGEFinder):
self.gene_list = PointFinder.get_file_content(
f"{self.specie_path}/{self.GENE_FILE}")
+ self.promoters = PointFinder.load_promoters(self.gene_list)
+
if os.path.isfile(f"{self.specie_path}/{self.RNA_GENE_FILE}"):
self.RNA_gene_list = PointFinder.get_file_content(
f"{self.specie_path}/{self.RNA_GENE_FILE}")
@@ -82,6 +85,19 @@ class PointFinder(CGEFinder):
"the '{self.RES_OVERVIEW_FILE}' file "
"(legacy database)")
+ @staticmethod
+ def load_promoters(gene_file_list):
+ promoters = {}
+
+ for gene_filename in gene_file_list:
+ promoter_match = re.search(PointFinder.PROMOTER_REGEX, gene_filename)
+ if promoter_match:
+ promoter_key = promoter_match.group(1)
+ promoter_length = promoter_match.group(2)
+ promoters[promoter_key] = int(promoter_length)
+
+ return promoters
+
def get_user_defined_gene_list(self, gene_list):
genes_specified = []
for gene in gene_list:
@@ -255,12 +271,7 @@ class PointFinder(CGEFinder):
for gene, hit in GENES.items():
# Start writing output string (to HTML tab file)
gene_name = gene.split("_")[0] # Not perfeft can differ from specific mutation
- regex = r"promoter-size-(\d+)(?:bp)"
- promtr_gene_objt = re.search(regex, gene_name)
-
- if promtr_gene_objt:
- gene_name = gene.split("_")[0]
-
+ gene_name = PhenoDB.if_promoter_gene_rename(gene_name)
output_strings[1] += "\n%s\n" % (gene_name)
# Ignore excluded genes
@@ -421,7 +432,11 @@ class PointFinder(CGEFinder):
f"_{mis_match[3].lower()}")
mis_match_key_aa = (f"{gene_db_id}_{mis_match[1]}"
f"_{mis_match[-1].lower()}")
- elif mis_match[4].startswith('r.'):#RNA substitution
+ elif mis_match[4].startswith('r.'): # RNA substitution
+ mis_match_key_aa = ""
+ mis_match_key_nuc = (f"{gene_db_id}_{mis_match[2]}"
+ f"_{mis_match[3].lower()}")
+ elif mis_match[4].startswith('n.'): # non-coding DNA substitution
mis_match_key_aa = ""
mis_match_key_nuc = (f"{gene_db_id}_{mis_match[2]}"
f"_{mis_match[3].lower()}")
@@ -621,6 +636,7 @@ class PointFinder(CGEFinder):
gene_name = str(mutation[0].split("_")[0])
# Only consider mutations in genes found in the gene list
if gene_name in gene_list:
+ gene_name = PhenoDB.if_promoter_gene_rename(gene_name)
mut_pos = int(mutation[3])
ref_codon = mutation[4] # Ref_nuc (1 or 3?)
ref_aa = mutation[5] # Ref_codon
@@ -849,10 +865,6 @@ class PointFinder(CGEFinder):
# If alternative query overlap excist save it
if pre_qry_overlap != next_qry_overlap:
- eprint("OVERLAP WARNING:")
- eprint("{}\n{}"
- .format(pre_qry_overlap, next_qry_overlap))
-
# Save alternative overlaps
alternative_overlaps += [(next_block_start,
overlap_end_pos,
@@ -934,13 +946,8 @@ class PointFinder(CGEFinder):
qry_seq)
else:
# Check if the gene sequence is with a promoter
- regex = r"promoter-size-(\d+)(?:bp)"
- promtr_gene_objt = re.search(regex, gene)
-
- # Check for promoter sequences
- if promtr_gene_objt:
- # Get promoter length
- promtr_len = int(promtr_gene_objt.group(1))
+ promtr_len = self.promoters.get(gene_name, None)
+ if promtr_len is not None:
# Extract promoter sequence, while considering gaps
# --------agt-->----
=====================================
src/resfinder/cge/resfinder.py
=====================================
@@ -73,6 +73,7 @@ class ResFinder(CGEFinder):
min_cov=min_cov, threshold=threshold, blast=blast,
allowed_overlap=allowed_overlap)
self.blast_results = blast_run.results
+
return blast_run
def load_phenos(self, pheno_file):
=====================================
src/resfinder/run_resfinder.py
=====================================
@@ -282,37 +282,25 @@ def main():
conf)
else:
- if (conf.nanopore):
- kma_run = acquired_finder.kma(
- inputfile_1=conf.inputfastq_1,
- inputfile_2=conf.inputfastq_2,
- out_path=conf.outPath_res_kma,
- db_path_kma=conf.db_path_res_kma,
- min_cov=conf.rf_gene_cov,
- threshold=conf.rf_gene_id,
- kma_path=conf.kma,
- databases=acquired_finder.databases,
- sample_name="",
- kma_cge=True,
- kma_apm="p",
- kma_1t1=True,
- kma_add_args='-ont -md 5'
- )
- else:
- kma_run = acquired_finder.kma(
- inputfile_1=conf.inputfastq_1,
- inputfile_2=conf.inputfastq_2,
- out_path=conf.outPath_res_kma,
- db_path_kma=conf.db_path_res_kma,
- min_cov=conf.rf_gene_cov,
- threshold=conf.rf_gene_id,
- kma_path=conf.kma,
- databases=acquired_finder.databases,
- sample_name="",
- kma_cge=True,
- kma_apm="p",
- kma_1t1=True
- )
+ kma_nano_args = None
+ if conf.nanopore:
+ kma_nano_args = '-ont -md 5'
+
+ kma_run = acquired_finder.kma(
+ inputfile_1=conf.inputfastq_1,
+ inputfile_2=conf.inputfastq_2,
+ out_path=conf.outPath_res_kma,
+ db_path_kma=conf.db_path_res_kma,
+ min_cov=conf.rf_gene_cov,
+ threshold=conf.rf_gene_id,
+ kma_path=conf.kma,
+ databases=acquired_finder.databases,
+ sample_name="",
+ kma_cge=True,
+ kma_apm="p",
+ kma_1t1=True,
+ kma_add_args=kma_nano_args
+ )
# DEPRECATED
# TODO: make a write method that depends on the json output
@@ -363,37 +351,25 @@ def main():
conf)
else:
- if (conf.nanopore):
- kma_run = disinf_finder.kma(
- inputfile_1=conf.inputfastq_1,
- inputfile_2=conf.inputfastq_2,
- out_path=conf.outPath_disinf_kma,
- db_path_kma=conf.db_path_disinf_kma,
- min_cov=conf.dis_gene_cov,
- threshold=conf.dis_gene_id,
- kma_path=conf.kma,
- databases=disinf_finder.databases,
- sample_name="",
- kma_cge=True,
- kma_apm="p",
- kma_1t1=True,
- kma_add_args='-ont -md 5'
- )
- else:
- kma_run = disinf_finder.kma(
- inputfile_1=conf.inputfastq_1,
- inputfile_2=conf.inputfastq_2,
- out_path=conf.outPath_disinf_kma,
- db_path_kma=conf.db_path_disinf_kma,
- min_cov=conf.dis_gene_cov,
- threshold=conf.dis_gene_id,
- kma_path=conf.kma,
- databases=disinf_finder.databases,
- sample_name="",
- kma_cge=True,
- kma_apm="p",
- kma_1t1=True
- )
+ kma_nano_args = None
+ if conf.nanopore:
+ kma_nano_args = '-ont -md 5'
+
+ kma_run = disinf_finder.kma(
+ inputfile_1=conf.inputfastq_1,
+ inputfile_2=conf.inputfastq_2,
+ out_path=conf.outPath_disinf_kma,
+ db_path_kma=conf.db_path_disinf_kma,
+ min_cov=conf.dis_gene_cov,
+ threshold=conf.dis_gene_id,
+ kma_path=conf.kma,
+ databases=disinf_finder.databases,
+ sample_name="",
+ kma_cge=True,
+ kma_apm="p",
+ kma_1t1=True,
+ kma_add_args=kma_nano_args
+ )
# DEPRECATED
# TODO: make a write method that depends on the json output
@@ -434,38 +410,30 @@ def main():
results = blast_run.results
else:
-
+ kma_nano_args = None
+ if conf.nanopore:
+ kma_nano_args = '-ont -md 5'
+
method = PointFinder.TYPE_KMA
- if (conf.nanopore):
- kma_run = finder.kma(inputfile_1=conf.inputfastq_1,
- inputfile_2=conf.inputfastq_2,
- out_path=conf.outPath_point_kma,
- db_path_kma=conf.db_path_point,
- databases=[conf.species_dir],
- min_cov=0.01, # Sorts on coverage later
- threshold=conf.pf_gene_id,
- kma_path=conf.kma,
- sample_name=conf.sample_name,
- kma_cge=True,
- kma_apm="p",
- kma_1t1=True,
- kma_add_args='-ont -md 5')
- else:
- kma_run = finder.kma(inputfile_1=conf.inputfastq_1,
- inputfile_2=conf.inputfastq_2,
- out_path=conf.outPath_point_kma,
- db_path_kma=conf.db_path_point,
- databases=[conf.species_dir],
- min_cov=0.01, # Sorts on coverage later
- threshold=conf.pf_gene_id,
- kma_path=conf.kma,
- sample_name=conf.sample_name,
- kma_cge=True,
- kma_apm="p",
- kma_1t1=True)
+
+ kma_run = finder.kma(inputfile_1=conf.inputfastq_1,
+ inputfile_2=conf.inputfastq_2,
+ out_path=conf.outPath_point_kma,
+ db_path_kma=conf.db_path_point,
+ databases=[conf.species_dir],
+ min_cov=0.01, # Sorts on coverage later
+ threshold=conf.pf_gene_id,
+ kma_path=conf.kma,
+ sample_name=conf.sample_name,
+ kma_cge=True,
+ kma_apm="p",
+ kma_1t1=True,
+ kma_add_args=kma_nano_args)
results = kma_run.results
-
+
+ PointFinderResultHandler.rename_promoter_results(results, method)
+
if (conf.specific_gene):
results = PointFinder.discard_from_dict(
in_dict=results, wanted_list=conf.specific_gene)
=====================================
tests/data/test_isolate_12.fa
=====================================
@@ -0,0 +1,25 @@
+>erm(38)_first1-321
+GTGTCCACACCACATCACGGCCGGCACGAGCTCGGCCAGAACTTCCTGTCCGATCGGCGC
+GTCATCGCCGATATCGTCGAAATCGTCTCGCGCACAAACGGTCCGATCATCGAGATCGGG
+GCGGGCGACGGCGCGCTGACCATACCCTTGCAACGACTCGCCCGCCCGCTCACCGCCGTC
+GAGGTCGACGCGCGGCGCGCGCGGCGGTTGGCGCAGCGCACCGCGAGATCCGCCCCGGGG
+CCTGCCTCGCGGCCCACCGAGGTCGTCGCCGCCGACTTCCTGCGCTACCCACTGCCCCGC
+TCACCCCACGTGGTCGTGGGC
+>erm(38)_middel201-578
+CGGCGGTTGGCGCAGCGCACCGCGAGATCCGCCCCGGGG
+CCTGCCTCGCGGCCCACCGAGGTCGTCGCCGCCGACTTCCTGCGCTACCCACTGCCCCGC
+TCACCCCACGTGGTCGTGGGCAACCTGCCGTTCCACCTCACCACCGCGATCCTGCGGCGA
+CTGCTGCACGGTCCGGGCTGGACCACGGCCGTGCTGCTCATGCAGTGGGAGGTGGCCCGC
+CGACGCGCCGCGGTGGGCGGCGCCACCATGATGACCGCCCAGTGGTGGCCGTGGTTCGAA
+TTCGGCCTTGCCCGAAAGGTTTCCGCGGCGAGCTTCACGCCGCGGCCCGCGGTCGACGCC
+GGACTGCTCACCATCACGCGCCGCAGCCGGCCGCTGGTCGACGTCGCGGACCGGGCGCGT
+>erm(38)_last630-1161
+GGACGCGGACACGGCATGGCGCAGATCCTG
+CAACGGTTGCCCACGCCGGTGCCCCGCACTTGGTTGCGGGCCAACGGGATAGCACCGAAC
+TCCCTGCCCCGCCAGTTGTCCGCGGCGCAGTGGGCGGCGCTGTTCGAGCAGACGCGTCTA
+ACTGGTGCCCAACGGGTCGATCGTCCACGCGATGTACAGCACGGCCGCGCTCACCGTCGC
+CGTGGTGGCGAAGTCGATCGCCCGGCTACGCACCACAAGCAGACCGGCCCGGTCGTCGGT
+CAGCGCCAACCGCAGCGCGGCCGCGACGCCGACGCCGATCCCGATGACCAGCGCACCGCG
+CCGCCAGTAACCCGCCACCACCAGGGCGAACGCCGCGATGAAGATCAGGCCGACCACCAG
+GATCGGCCATTGACCGGCGAACACCTTGCGGGCGAATTCCTTTGGCGTCACGCCAGTTTC
+GACTCTTCGGCTTCGACGACGTTGGTCAGCAGGAAGGCGCGGGTCAACGGGCCCACGCCA
=====================================
tests/data/test_isolate_14.fa
=====================================
@@ -0,0 +1,60 @@
+>test_isolate_14_contig_01
+GGTGGTAACTATAACCATCCTAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGC
+ACGAATGGCGTAACGACTTCTCAACTGTCTCAACCATAGACTCGGCGAAATTGCACTACG
+AGTAAAGATGCTCGTTACGCGCGGCAGGACGAAAAGACCCCGGGACCTTCACTACAACTT
+GGTATTGATGTTCGGTACGGTTTGTGTAGGATAGGTGGGAGACTGTGAAACCTCGACGCC
+AGTTGGGGCGGAGTCGTTGTTGAAATACCACTCTGATCGTATTGGGCATCTAACCTCGAA
+CCCTGAATCGGGTTTAGGGACAGTGCCTGGCGGGTAGTTTAACTGGGGCGGTTGCCTCCT
+AAAATGTAACGGAGGCGCCCA
+>test_isolate_14_contig_02
+GCTTCCTGCTCTGGCATGTCATCGGCGCGAATTCGTCGGACGACGGCTACATCCTGGGCA
+TGGCCCGAGTCGCCGACCACGCCGGCTACATGTCCAACTATTTCCGCTGGTTCGGCAGCC
+CGGAGGATCCCTTCGGCTGGTATTACAACCTGCTGGCGCTGATGACCCATGTCAGCGACG
+CCAGTCTGTGGATGCGCCTGCCAGACCTGGCCGCCGGGCTAGTGTGCTGGCTGCTGCTGT
+CGCGTGAGGTGCTGCCCCGCCTCGGGCCGGCGGTGGCGGCCAGCAAACCCGCCTACTGGG
+CGGCGGCCATGGTCTTGCTGACCGCGTGGATGCCGTTCAACAACGGCCTGCGGCCGGAGG
+GCATCATCGCGCTCGGCTCGCTGGTCACCTATGTGCTGATCGAGCGGTCCATGCGGTACA
+GCCGGCTCACACCGGCGGCGCTGGCCGTCGTTACCGCCGCATTCACACTGGGTGTGCAGC
+CCACCGGCCTGATCGCGGTGGCCGCGCTGGTGGCCGGCGGCCGCCCGATGCTGCGGATCT
+TGGTGCGCCGTCATCGCCTGGTCGGCACGTTGCCGTTGGTGTCGCCGATGCTGGCCGCCG
+GCACCGTCATCCTGACCGTGGTGTTCGCCGACCAGACCCTGTCAACGGTGTTGGAAGCCA
+CCAGGGTTCGCGCCAAAATCGGGCCGAGCCAGGCGTGGTATACCGAGAACCTGCGTTACT
+ACTACCTCATCCTGCCCACCGTCGACGGTTCGCTGTCGCGGCGCTTCGGCTTTTTGATCA
+CCGCGCTATGCCTGTTCACCGCGGTGTTCATCATGTTGCGGCG
+>test_isolate_14_contig_03
+GCACGCCGCGGCGGCGCGAGCGCAGCCACAGCGCTTTTGCACGCAATTGCGCGGTCAGTT
+CCACACCCTGCGGCACGTACACGTCTTTATGTAGCGCGACATACCTGCTGCGCAATTCGT
+AGGGCGTCAATACACCCGCAGCCAGGGCCTCGCTGCCCAGAAAGGGATCCGTCATGGTCG
+AAGTGTGCTGAGTCACACCGACAAACGTCACGAGCGTAACCCCAGTGCGAAAGTTCCCGC
+CGGAAATCGCAGCCACGTTACGCTCGTGGACATACCGATTTCGGCCCGGCCGCGGCGAGA
+CGATAGGTTGTCGGGGTGACTGCCACAGCCACTGAAGGGGCCAAACCCCCATTCGTATCC
+CGTTCAGTCCTGGTTACCGGAGGAAACCGGGGGATCGGGCTGGCGATCGCACAGCGGCTG
+GCTGCCGACGGCCACAAGGTGGCCGTCACCCACCGTGGATCCGGAGCGCCAAAGGGG
+>test_isolate_14_contig_04
+CGGCGCTGATCGTCGGCGGTCACACTTTCGGTAAGACCCATGGCGCCGGCCCGGCCGATC
+TGGTCGGCCCCGAACCCGAGGCTGCTCCGCTGGAGCAGATGGGCTTGGGCTGGAAGAGCT
+CGTATGGCACCGGAACCGGTAAGGACGCGATCACCAGCGGCATCGAGGTCGTATGGACGA
+ACACCCCGACGAAATGGGACAACAGTTTCCTCGAGATCCTGTACGGCTACGAGTGGGAGC
+TGACGAAGAGCCCTGCTGGCGCTTGGCAATACACCGCCAAGGACGGCGCCGGTGCCGGCA
+CCATCCCGGACCCGTTCGGCGGGCCAGGGCGCTCCCCGACGATGCTGGCCACTGACCTCT
+CGCTGCGGGTGGATCCGATCTATGAGCGGATCACGCGTCGCTGGCTGGAACACCCCGAGG
+AATTGGCCGACGAGTTCGCCAAGGCCTGGTACAAGCTGATCCACCGAGACATGGGTCCCG
+TTGCGAGATACCTTGGGCCGCTGGTCCCCAAGCAGACCCTGCTGTGGCAGGATCCGGTCC
+CTGCGGTCAGCCACGACCTCGTCGGCGAAGCCGAGATTGCCAGCCTTAAGAGCCAGATCC
+TGGCATCGGGATTGACTGTCTCACAGCTAGTTTCGACCGCATGGGCG
+>test_isolate_14_contig_05
+GACGTATGCGGGCGTTGATCATCGTCGACGTGCAGAACGACTTCTGCGAGGGTGGCTCGC
+TGGCGGTAACCGGTGGCGCCGCGCTGGCCCGCGCCATCAGCGACTACCTGGCCGAAGCGG
+CGGACTACCATCACGTCGTGGCAACCAAGGACTTCCACATCGACCCGGGTGACGACTTCT
+CCGGCACACCGGACTATTCCTCGTCGTGGCCACCGCATTGCGTCAGCGGTACTCCCGGCG
+CGGACTTCCATCCCAGTCTGGACACGTCGGCAATCGAGGCGGTGTTCTACAAGGGTGCCT
+ACACCGGAGCGTACAGCGGCTTCGAAGGAGTCGACGAGAACGGCACGCCACTGCTGAATT
+GGCTGCGGCAACGCGGCGTCGATGAGGTCGATGTGGTCGGTATTGCCACCGATCATTGTG
+TGCGCCAGACGGCCGAGGACGCGGTACGCAATGGCTTGGCCACCAGGGTGCTGGTGGACC
+TGACAGCGGGTGTGTCGGCCGATACCACCGTCGCCGCGCTGGAGGAGATGCGCACCGCCA
+GCGTCGAGTTGGTTTGCAGCTCCTGATGGCACCGCC
+>test_isolate_14_contig_06
+ACGTTGATCAACATCCGGCCGGTGGTCGCCGCGATCAAGGAGTTCTTCGGCACCAGCCAG
+CTGAGCCAATTCATGGACCAGAACAACCCGCTGTCGGGGTTGACCCACAAGCGCCGACTG
+TCGGCGCTGGGGCCCGGCGGTCTGTCACGTGAGCGTGCCGGGCTGGAGGTCCGCGACGTG
+CACCCGTCGCACTACGGCCGGATGTGCCCGATCGAAACCCCTGAGGGGC
=====================================
tests/data/test_isolate_14_1.fq
=====================================
@@ -0,0 +1,360 @@
+ at test_isolate_14_contig_01-20
+GGTATTGATGTTCGGTACGGTTTGTGTAGGATAGGTGGGAGACTGTGAAACCTCGACGCCAGTTGGGGCGGAGTCGTTGTTGAAATACCACTCTGATCGTATTGGGCATCTAACCTCGAACCCTGAATCGGGTTTAGGGACAGTGCCTGG
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_01-18
+TAACTATAACCATCCTAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAACGACTTCTCAACTGTCTCAACCATAGACTCGGCGAAATTGCACTACGAGTAAAGATGCTCGTTACGCGCGGCAGGACGAAAA
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_01-16
+AAAGACCCCGGGACCTTCACTACAACTTGGTATTGATGTTCGGTACGGTTTGTGTAGGATAGGTGGGAGACTGTGAAACCTCGACGCCAGTTGGGGCGGAGTCGTTGTTGAAATACCACTCTGATCGTATTGGGCATCTAACCTCGAACC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_01-14
+GGACCTTCACTACAACTTGGTATTGATGTTCGGTACGGTTTGTGTAGGATAGGTGGGAGACTGTGAAACCTCGACGCCAGTTGGGGCGGAGTCGTTGTTGAAATACCACTCTGATCGTATTGGGCATCTAACCTCGAACCCTGAATCGGG
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_01-12
+ACTTGGTATTGATGTTCGGTACGGTTTGTGTAGGATAGGTGGGAGACTGTGAAACCTCGACGCCAGTTGGGGCGGAGTCGTTGTTGAAATACCACTCTGATCGTATTGGGCATCTAACCTCGAACCCTGAATCGGGTTTAGGGACAGTGC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_01-10
+ACCCCGGGACCTTCACTACAACTTGGTATTGATGTTCGGTACGGTTTGTGTAGGATAGGTGGGAGACTGTGAAACCTCGACGCCAGTTGGGGCGGAGTCGTTGTTGAAATACCACTCTGATCGTATTGGGCATCTAACCTCGAACCCTGA
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_01-8
+ACGAGTAAAGATGCTCGTTACGCGCGGCAGGACGAAAAGACCCCGGGACCTTCACTACAACTTGGTATTGATGTTCGGTACGGTTTGTGTAGGATAGGTGGGAGACTGTGAAACCTCGACGCCAGTTGGGGCGGAGTCGTTGTTGAAATA
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_01-6
+ACAACTTGGTATTGATGTTCGGTACGGTTTGTGTAGGATAGGTGGGAGACTGTGAAACCTCGACGCCAGTTGGGGCGGAGTCGTTGTTGAAATACCACTCTGATCGTATTGGGCATCTAACCTCGAACCCTGAATCGGGTTTAGGGACAG
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_01-4
+CCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAACGACTTCTCAACTGTCTCAACCATAGACTCGGCGAAATTGCACTACGAGTAAAGATGCTCGTTACGCGCGGCAGGACGAAAAGACCCCGGGACCTTCACTACAACTTGGTAT
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_01-2
+GGGACCTTCACTACAACTTGGTATTGATGTTCGGTACGGTTTGTGTAGGATAGGTGGGAGACTGTGAAACCTCGACGCCAGTTGGGGCGGAGTCGTTGTTGAAATACCACTCTGATCGTATTGGGCATCTAACCTCGAACCCTGAATCGG
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_02-50
+GCTGATGACCCATGTCAGCGACGCCAGTCTGTGGATGCGCCTGCCAGACCTGGCCGCCGGGCTAGTGTGCTGGCTGCTGCTGTCGCGTGAGGTGCTGCCCCGCCTCGGGCCGGCGGTGGCGGCCAGCAAACCCGCCTACTGGGCGGCGGC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_02-48
+GCCCGGAGGATCCCTTCGGCTGGTATTACAACCTGCTGGCGCTGATGACCCATGTCAGCGACGCCAGTCTGTGGATGCGCCTGCCAGACCTGGCCGCCGGGCTAGTGTGCTGGCTGCTGCTGTCGCGTGAGGTGCTGCCCCGCCTCGGGC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_02-46
+GTCATCGCCTGGTCGGCACGTTGCCGTTGGTGTCGCCGATGCTGGCCGCCGGCACCGTCATCCTGACCGTGGTGTTCGCCGACCAGACCCTGTCAACGGTGTTGGAAGCCACCAGGGTTCGCGCCAAAATCGGGCCGAGCCAGGCGTGGT
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_02-44
+GCTGATCGAGCGGTCCATGCGGTACAGCCGGCTCACACCGGCGGCGCTGGCCGTCGTTACCGCCGCATTCACACTGGGTGTGCAGCCCACCGGCCTGATCGCGGTGGCCGCGCTGGTGGCCGGCGGCCGCCCGATGCTGCGGATCTTGGT
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_02-42
+GTCCATGCGGTACAGCCGGCTCACACCGGCGGCGCTGGCCGTCGTTACCGCCGCATTCACACTGGGTGTGCAGCCCACCGGCCTGATCGCGGTGGCCGCGCTGGTGGCCGGCGGCCGCCCGATGCTGCGGATCTTGGTGCGCCGTCATCG
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_02-40
+TGTCGCGTGAGGTGCTGCCCCGCCTCGGGCCGGCGGTGGCGGCCAGCAAACCCGCCTACTGGGCGGCGGCCATGGTCTTGCTGACCGCGTGGATGCCGTTCAACAACGGCCTGCGGCCGGAGGGCATCATCGCGCTCGGCTCGCTGGTCA
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_02-38
+CTGATGACCCATGTCAGCGACGCCAGTCTGTGGATGCGCCTGCCAGACCTGGCCGCCGGGCTAGTGTGCTGGCTGCTGCTGTCGCGTGAGGTGCTGCCCCGCCTCGGGCCGGCGGTGGCGGCCAGCAAACCCGCCTACTGGGCGGCGGCC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_02-36
+CTCGGGCCGGCGGTGGCGGCCAGCAAACCCGCCTACTGGGCGGCGGCCATGGTCTTGCTGACCGCGTGGATGCCGTTCAACAACGGCCTGCGGCCGGAGGGCATCATCGCGCTCGGCTCGCTGGTCACCTATGTGCTGATCGAGCGGTCC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_02-34
+CATCCTGACCGTGGTGTTCGCCGACCAGACCCTGTCAACGGTGTTGGAAGCCACCAGGGTTCGCGCCAAAATCGGGCCGAGCCAGGCGTGGTATACCGAGAACCTGCGTTACTACTACCTCATCCTGCCCACCGTCGACGGTTCGCTGTC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_02-32
+CGTTCAACAACGGCCTGCGGCCGGAGGGCATCATCGCGCTCGGCTCGCTGGTCACCTATGTGCTGATCGAGCGGTCCATGCGGTACAGCCGGCTCACACCGGCGGCGCTGGCCGTCGTTACCGCCGCATTCACACTGGGTGTGCAGCCCA
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_02-30
+GACCGTGGTGTTCGCCGACCAGACCCTGTCAACGGTGTTGGAAGCCACCAGGGTTCGCGCCAAAATCGGGCCGAGCCAGGCGTGGTATACCGAGAACCTGCGTTACTACTACCTCATCCTGCCCACCGTCGACGGTTCGCTGTCGCGGCG
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_02-28
+ATGACCCATGTCAGCGACGCCAGTCTGTGGATGCGCCTGCCAGACCTGGCCGCCGGGCTAGTGTGCTGGCTGCTGCTGTCGCGTGAGGTGCTGCCCCGCCTCGGGCCGGCGGTGGCGGCCAGCAAACCCGCCTACTGGGCGGCGGCCATG
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_02-26
+CTACATGTCCAACTATTTCCGCTGGTTCGGCAGCCCGGAGGATCCCTTCGGCTGGTATTACAACCTGCTGGCGCTGATGACCCATGTCAGCGACGCCAGTCTGTGGATGCGCCTGCCAGACCTGGCCGCCGGGCTAGTGTGCTGGCTGCT
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_02-24
+CGTCGTTACCGCCGCATTCACACTGGGTGTGCAGCCCACCGGCCTGATCGCGGTGGCCGCGCTGGTGGCCGGCGGCCGCCCGATGCTGCGGATCTTGGTGCGCCGTCATCGCCTGGTCGGCACGTTGCCGTTGGTGTCGCCGATGCTGGC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_02-22
+GCCGGGCTAGTGTGCTGGCTGCTGCTGTCGCGTGAGGTGCTGCCCCGCCTCGGGCCGGCGGTGGCGGCCAGCAAACCCGCCTACTGGGCGGCGGCCATGGTCTTGCTGACCGCGTGGATGCCGTTCAACAACGGCCTGCGGCCGGAGGGC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_02-20
+GGTATTACAACCTGCTGGCGCTGATGACCCATGTCAGCGACGCCAGTCTGTGGATGCGCCTGCCAGACCTGGCCGCCGGGCTAGTGTGCTGGCTGCTGCTGTCGCGTGAGGTGCTGCCCCGCCTCGGGCCGGCGGTGGCGGCCAGCAAAC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_02-18
+TGCAGCCCACCGGCCTGATCGCGGTGGCCGCGCTGGTGGCCGGCGGCCGCCCGATGCTGCGGATCTTGGTGCGCCGTCATCGCCTGGTCGGCACGTTGCCGTTGGTGTCGCCGATGCTGGCCGCCGGCACCGTCATCCTGACCGTGGTGT
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_02-16
+GAAGCCACCAGGGTTCGCGCCAAAATCGGGCCGAGCCAGGCGTGGTATACCGAGAACCTGCGTTACTACTACCTCATCCTGCCCACCGTCGACGGTTCGCTGTCGCGGCGCTTCGGCTTTTTGATCACCGCGCTATGCCTGTTCACCGCG
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_02-14
+TCGGCGCGAATTCGTCGGACGACGGCTACATCCTGGGCATGGCCCGAGTCGCCGACCACGCCGGCTACATGTCCAACTATTTCCGCTGGTTCGGCAGCCCGGAGGATCCCTTCGGCTGGTATTACAACCTGCTGGCGCTGATGACCCATG
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_02-12
+TGATCGAGCGGTCCATGCGGTACAGCCGGCTCACACCGGCGGCGCTGGCCGTCGTTACCGCCGCATTCACACTGGGTGTGCAGCCCACCGGCCTGATCGCGGTGGCCGCGCTGGTGGCCGGCGGCCGCCCGATGCTGCGGATCTTGGTGC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_02-10
+CGGCTGGTATTACAACCTGCTGGCGCTGATGACCCATGTCAGCGACGCCAGTCTGTGGATGCGCCTGCCAGACCTGGCCGCCGGGCTAGTGTGCTGGCTGCTGCTGTCGCGTGAGGTGCTGCCCCGCCTCGGGCCGGCGGTGGCGGCCAG
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_02-8
+AGCCCGGAGGATCCCTTCGGCTGGTATTACAACCTGCTGGCGCTGATGACCCATGTCAGCGACGCCAGTCTGTGGATGCGCCTGCCAGACCTGGCCGCCGGGCTAGTGTGCTGGCTGCTGCTGTCGCGTGAGGTGCTGCCCCGCCTCGGG
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_02-6
+GGTTCGGCAGCCCGGAGGATCCCTTCGGCTGGTATTACAACCTGCTGGCGCTGATGACCCATGTCAGCGACGCCAGTCTGTGGATGCGCCTGCCAGACCTGGCCGCCGGGCTAGTGTGCTGGCTGCTGCTGTCGCGTGAGGTGCTGCCCC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_02-4
+CACCTATGTGCTGATCGAGCGGTCCATGCGGTACAGCCGGCTCACACCGGCGGCGCTGGCCGTCGTTACCGCCGCATTCACACTGGGTGTGCAGCCCACCGGCCTGATCGCGGTGGCCGCGCTGGTGGCCGGCGGCCGCCCGATGCTGCG
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_02-2
+TGGATGCCGTTCAACAACGGCCTGCGGCCGGAGGGCATCATCGCGCTCGGCTCGCTGGTCACCTATGTGCTGATCGAGCGGTCCATGCGGTACAGCCGGCTCACACCGGCGGCGCTGGCCGTCGTTACCGCCGCATTCACACTGGGTGTG
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_03-30
+CACCCTGCGGCACGTACACGTCTTTATGTAGCGCGACATACCTGCTGCGCAATTCGTAGGGCGTCAATACACCCGCAGCCAGGGCCTCGCTGCCCAGAAAGGGATCCGTCATGGTCGAAGTGTGCTGAGTCACACCGACAAACGTCACGA
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_03-28
+TAGCGCGACATACCTGCTGCGCAATTCGTAGGGCGTCAATACACCCGCAGCCAGGGCCTCGCTGCCCAGAAAGGGATCCGTCATGGTCGAAGTGTGCTGAGTCACACCGACAAACGTCACGAGCGTAACCCCAGTGCGAAAGTTCCCGCC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_03-26
+GGGATCCGTCATGGTCGAAGTGTGCTGAGTCACACCGACAAACGTCACGAGCGTAACCCCAGTGCGAAAGTTCCCGCCGGAAATCGCAGCCACGTTACGCTCGTGGACATACCGATTTCGGCCCGGCCGCGGCGAGACGATAGGTTGTCG
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_03-24
+CACCGACAAACGTCACGAGCGTAACCCCAGTGCGAAAGTTCCCGCCGGAAATCGCAGCCACGTTACGCTCGTGGACATACCGATTTCGGCCCGGCCGCGGCGAGACGATAGGTTGTCGGGGTGACTGCCACAGCCACTGAAGGGGCCAAA
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_03-22
+ATGTAGCGCGACATACCTGCTGCGCAATTCGTAGGGCGTCAATACACCCGCAGCCAGGGCCTCGCTGCCCAGAAAGGGATCCGTCATGGTCGAAGTGTGCTGAGTCACACCGACAAACGTCACGAGCGTAACCCCAGTGCGAAAGTTCCC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_03-20
+CCGCGGCGGCGCGAGCGCAGCCACAGCGCTTTTGCACGCAATTGCGCGGTCAGTTCCACACCCTGCGGCACGTACACGTCTTTATGTAGCGCGACATACCTGCTGCGCAATTCGTAGGGCGTCAATACACCCGCAGCCAGGGCCTCGCTG
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_03-18
+GCCCGGCCGCGGCGAGACGATAGGTTGTCGGGGTGACTGCCACAGCCACTGAAGGGGCCAAACCCCCATTCGTATCCCGTTCAGTCCTGGTTACCGGAGGAAACCGGGGGATCGGGCTGGCGATCGCACAGCGGCTGGCTGCCGACGGCC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_03-16
+TAGGGCGTCAATACACCCGCAGCCAGGGCCTCGCTGCCCAGAAAGGGATCCGTCATGGTCGAAGTGTGCTGAGTCACACCGACAAACGTCACGAGCGTAACCCCAGTGCGAAAGTTCCCGCCGGAAATCGCAGCCACGTTACGCTCGTGG
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_03-14
+TTTATGTAGCGCGACATACCTGCTGCGCAATTCGTAGGGCGTCAATACACCCGCAGCCAGGGCCTCGCTGCCCAGAAAGGGATCCGTCATGGTCGAAGTGTGCTGAGTCACACCGACAAACGTCACGAGCGTAACCCCAGTGCGAAAGTT
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_03-12
+AGGGCGTCAATACACCCGCAGCCAGGGCCTCGCTGCCCAGAAAGGGATCCGTCATGGTCGAAGTGTGCTGAGTCACACCGACAAACGTCACGAGCGTAACCCCAGTGCGAAAGTTCCCGCCGGAAATCGCAGCCACGTTACGCTCGTGGA
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_03-10
+CACACCCTGCGGCACGTACACGTCTTTATGTAGCGCGACATACCTGCTGCGCAATTCGTAGGGCGTCAATACACCCGCAGCCAGGGCCTCGCTGCCCAGAAAGGGATCCGTCATGGTCGAAGTGTGCTGAGTCACACCGACAAACGTCAC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_03-8
+CTGAGTCACACCGACAAACGTCACGAGCGTAACCCCAGTGCGAAAGTTCCCGCCGGAAATCGCAGCCACGTTACGCTCGTGGACATACCGATTTCGGCCCGGCCGCGGCGAGACGATAGGTTGTCGGGGTGACTGCCACAGCCACTGAAG
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_03-6
+TGCCCAGAAAGGGATCCGTCATGGTCGAAGTGTGCTGAGTCACACCGACAAACGTCACGAGCGTAACCCCAGTGCGAAAGTTCCCGCCGGAAATCGCAGCCACGTTACGCTCGTGGACATACCGATTTCGGCCCGGCCGCGGCGAGACGA
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_03-4
+GGCCTCGCTGCCCAGAAAGGGATCCGTCATGGTCGAAGTGTGCTGAGTCACACCGACAAACGTCACGAGCGTAACCCCAGTGCGAAAGTTCCCGCCGGAAATCGCAGCCACGTTACGCTCGTGGACATACCGATTTCGGCCCGGCCGCGG
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_03-2
+AATACACCCGCAGCCAGGGCCTCGCTGCCCAGAAAGGGATCCGTCATGGTCGAAGTGTGCTGAGTCACACCGACAAACGTCACGAGCGTAACCCCAGTGCGAAAGTTCCCGCCGGAAATCGCAGCCACGTTACGCTCGTGGACATACCGA
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_04-40
+GTGGATCCGATCTATGAGCGGATCACGCGTCGCTGGCTGGAACACCCCGAGGAATTGGCCGACGAGTTCGCCAAGGCCTGGTACAAGCTGATCCACCGAGACATGGGTCCCGTTGCGAGATACCTTGGGCCGCTGGTCCCCAAGCAGACC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_04-38
+GATCTGGTCGGCCCCGAACCCGAGGCTGCTCCGCTGGAGCAGATGGGCTTGGGCTGGAAGAGCTCGTATGGCACCGGAACCGGTAAGGACGCGATCACCAGCGGCATCGAGGTCGTATGGACGAACACCCCGACGAAATGGGACAACAGT
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_04-36
+GGAGCTGACGAAGAGCCCTGCTGGCGCTTGGCAATACACCGCCAAGGACGGCGCCGGTGCCGGCACCATCCCGGACCCGTTCGGCGGGCCAGGGCGCTCCCCGACGATGCTGGCCACTGACCTCTCGCTGCGGGTGGATCCGATCTATGA
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_04-34
+CGACGATGCTGGCCACTGACCTCTCGCTGCGGGTGGATCCGATCTATGAGCGGATCACGCGTCGCTGGCTGGAACACCCCGAGGAATTGGCCGACGAGTTCGCCAAGGCCTGGTACAAGCTGATCCACCGAGACATGGGTCCCGTTGCGA
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_04-32
+CTCGTATGGCACCGGAACCGGTAAGGACGCGATCACCAGCGGCATCGAGGTCGTATGGACGAACACCCCGACGAAATGGGACAACAGTTTCCTCGAGATCCTGTACGGCTACGAGTGGGAGCTGACGAAGAGCCCTGCTGGCGCTTGGCA
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_04-30
+ACGAGTGGGAGCTGACGAAGAGCCCTGCTGGCGCTTGGCAATACACCGCCAAGGACGGCGCCGGTGCCGGCACCATCCCGGACCCGTTCGGCGGGCCAGGGCGCTCCCCGACGATGCTGGCCACTGACCTCTCGCTGCGGGTGGATCCGA
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_04-28
+CCTTGGGCCGCTGGTCCCCAAGCAGACCCTGCTGTGGCAGGATCCGGTCCCTGCGGTCAGCCACGACCTCGTCGGCGAAGCCGAGATTGCCAGCCTTAAGAGCCAGATCCTGGCATCGGGATTGACTGTCTCACAGCTAGTTTCGACCGC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_04-26
+CAAGGACGGCGCCGGTGCCGGCACCATCCCGGACCCGTTCGGCGGGCCAGGGCGCTCCCCGACGATGCTGGCCACTGACCTCTCGCTGCGGGTGGATCCGATCTATGAGCGGATCACGCGTCGCTGGCTGGAACACCCCGAGGAATTGGC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_04-24
+TGGAACACCCCGAGGAATTGGCCGACGAGTTCGCCAAGGCCTGGTACAAGCTGATCCACCGAGACATGGGTCCCGTTGCGAGATACCTTGGGCCGCTGGTCCCCAAGCAGACCCTGCTGTGGCAGGATCCGGTCCCTGCGGTCAGCCACG
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_04-22
+GCTACGAGTGGGAGCTGACGAAGAGCCCTGCTGGCGCTTGGCAATACACCGCCAAGGACGGCGCCGGTGCCGGCACCATCCCGGACCCGTTCGGCGGGCCAGGGCGCTCCCCGACGATGCTGGCCACTGACCTCTCGCTGCGGGTGGATC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_04-20
+ACACCCCGAGGAATTGGCCGACGAGTTCGCCAAGGCCTGGTACAAGCTGATCCACCGAGACATGGGTCCCGTTGCGAGATACCTTGGGCCGCTGGTCCCCAAGCAGACCCTGCTGTGGCAGGATCCGGTCCCTGCGGTCAGCCACGACCT
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_04-18
+CGGGTGGATCCGATCTATGAGCGGATCACGCGTCGCTGGCTGGAACACCCCGAGGAATTGGCCGACGAGTTCGCCAAGGCCTGGTACAAGCTGATCCACCGAGACATGGGTCCCGTTGCGAGATACCTTGGGCCGCTGGTCCCCAAGCAG
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_04-16
+GACGCGATCACCAGCGGCATCGAGGTCGTATGGACGAACACCCCGACGAAATGGGACAACAGTTTCCTCGAGATCCTGTACGGCTACGAGTGGGAGCTGACGAAGAGCCCTGCTGGCGCTTGGCAATACACCGCCAAGGACGGCGCCGGT
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_04-14
+TTGGGCCGCTGGTCCCCAAGCAGACCCTGCTGTGGCAGGATCCGGTCCCTGCGGTCAGCCACGACCTCGTCGGCGAAGCCGAGATTGCCAGCCTTAAGAGCCAGATCCTGGCATCGGGATTGACTGTCTCACAGCTAGTTTCGACCGCAT
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_04-12
+CAGGGCGCTCCCCGACGATGCTGGCCACTGACCTCTCGCTGCGGGTGGATCCGATCTATGAGCGGATCACGCGTCGCTGGCTGGAACACCCCGAGGAATTGGCCGACGAGTTCGCCAAGGCCTGGTACAAGCTGATCCACCGAGACATGG
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_04-10
+CACCCCGAGGAATTGGCCGACGAGTTCGCCAAGGCCTGGTACAAGCTGATCCACCGAGACATGGGTCCCGTTGCGAGATACCTTGGGCCGCTGGTCCCCAAGCAGACCCTGCTGTGGCAGGATCCGGTCCCTGCGGTCAGCCACGACCTC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_04-8
+AGGACGCGATCACCAGCGGCATCGAGGTCGTATGGACGAACACCCCGACGAAATGGGACAACAGTTTCCTCGAGATCCTGTACGGCTACGAGTGGGAGCTGACGAAGAGCCCTGCTGGCGCTTGGCAATACACCGCCAAGGACGGCGCCG
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_04-6
+CGATCTATGAGCGGATCACGCGTCGCTGGCTGGAACACCCCGAGGAATTGGCCGACGAGTTCGCCAAGGCCTGGTACAAGCTGATCCACCGAGACATGGGTCCCGTTGCGAGATACCTTGGGCCGCTGGTCCCCAAGCAGACCCTGCTGT
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_04-4
+GCGGCATCGAGGTCGTATGGACGAACACCCCGACGAAATGGGACAACAGTTTCCTCGAGATCCTGTACGGCTACGAGTGGGAGCTGACGAAGAGCCCTGCTGGCGCTTGGCAATACACCGCCAAGGACGGCGCCGGTGCCGGCACCATCC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_04-2
+GGAACCGGTAAGGACGCGATCACCAGCGGCATCGAGGTCGTATGGACGAACACCCCGACGAAATGGGACAACAGTTTCCTCGAGATCCTGTACGGCTACGAGTGGGAGCTGACGAAGAGCCCTGCTGGCGCTTGGCAATACACCGCCAAG
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_05-30
+GGCACGCCACTGCTGAATTGGCTGCGGCAACGCGGCGTCGATGAGGTCGATGTGGTCGGTATTGCCACCGATCATTGTGTGCGCCAGACGGCCGAGGACGCGGTACGCAATGGCTTGGCCACCAGGGTGCTGGTGGACCTGACAGCGGGT
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_05-28
+AGCGTACAGCGGCTTCGAAGGAGTCGACGAGAACGGCACGCCACTGCTGAATTGGCTGCGGCAACGCGGCGTCGATGAGGTCGATGTGGTCGGTATTGCCACCGATCATTGTGTGCGCCAGACGGCCGAGGACGCGGTACGCAATGGCTT
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_05-26
+TGCCACCGATCATTGTGTGCGCCAGACGGCCGAGGACGCGGTACGCAATGGCTTGGCCACCAGGGTGCTGGTGGACCTGACAGCGGGTGTGTCGGCCGATACCACCGTCGCCGCGCTGGAGGAGATGCGCACCGCCAGCGTCGAGTTGGT
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_05-24
+AACGCGGCGTCGATGAGGTCGATGTGGTCGGTATTGCCACCGATCATTGTGTGCGCCAGACGGCCGAGGACGCGGTACGCAATGGCTTGGCCACCAGGGTGCTGGTGGACCTGACAGCGGGTGTGTCGGCCGATACCACCGTCGCCGCGC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_05-22
+CAACGCGGCGTCGATGAGGTCGATGTGGTCGGTATTGCCACCGATCATTGTGTGCGCCAGACGGCCGAGGACGCGGTACGCAATGGCTTGGCCACCAGGGTGCTGGTGGACCTGACAGCGGGTGTGTCGGCCGATACCACCGTCGCCGCG
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_05-20
+CGCGCCATCAGCGACTACCTGGCCGAAGCGGCGGACTACCATCACGTCGTGGCAACCAAGGACTTCCACATCGACCCGGGTGACGACTTCTCCGGCACACCGGACTATTCCTCGTCGTGGCCACCGCATTGCGTCAGCGGTACTCCCGGC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_05-18
+TGGCTGCGGCAACGCGGCGTCGATGAGGTCGATGTGGTCGGTATTGCCACCGATCATTGTGTGCGCCAGACGGCCGAGGACGCGGTACGCAATGGCTTGGCCACCAGGGTGCTGGTGGACCTGACAGCGGGTGTGTCGGCCGATACCACC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_05-16
+GGCACACCGGACTATTCCTCGTCGTGGCCACCGCATTGCGTCAGCGGTACTCCCGGCGCGGACTTCCATCCCAGTCTGGACACGTCGGCAATCGAGGCGGTGTTCTACAAGGGTGCCTACACCGGAGCGTACAGCGGCTTCGAAGGAGTC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_05-14
+CGAGAACGGCACGCCACTGCTGAATTGGCTGCGGCAACGCGGCGTCGATGAGGTCGATGTGGTCGGTATTGCCACCGATCATTGTGTGCGCCAGACGGCCGAGGACGCGGTACGCAATGGCTTGGCCACCAGGGTGCTGGTGGACCTGAC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_05-12
+GTGCGCCAGACGGCCGAGGACGCGGTACGCAATGGCTTGGCCACCAGGGTGCTGGTGGACCTGACAGCGGGTGTGTCGGCCGATACCACCGTCGCCGCGCTGGAGGAGATGCGCACCGCCAGCGTCGAGTTGGTTTGCAGCTCCTGATGG
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_05-10
+GTGTTCTACAAGGGTGCCTACACCGGAGCGTACAGCGGCTTCGAAGGAGTCGACGAGAACGGCACGCCACTGCTGAATTGGCTGCGGCAACGCGGCGTCGATGAGGTCGATGTGGTCGGTATTGCCACCGATCATTGTGTGCGCCAGACG
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_05-8
+CTGCTGAATTGGCTGCGGCAACGCGGCGTCGATGAGGTCGATGTGGTCGGTATTGCCACCGATCATTGTGTGCGCCAGACGGCCGAGGACGCGGTACGCAATGGCTTGGCCACCAGGGTGCTGGTGGACCTGACAGCGGGTGTGTCGGCC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_05-6
+CGAAGGAGTCGACGAGAACGGCACGCCACTGCTGAATTGGCTGCGGCAACGCGGCGTCGATGAGGTCGATGTGGTCGGTATTGCCACCGATCATTGTGTGCGCCAGACGGCCGAGGACGCGGTACGCAATGGCTTGGCCACCAGGGTGCT
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_05-4
+CCGCGCCATCAGCGACTACCTGGCCGAAGCGGCGGACTACCATCACGTCGTGGCAACCAAGGACTTCCACATCGACCCGGGTGACGACTTCTCCGGCACACCGGACTATTCCTCGTCGTGGCCACCGCATTGCGTCAGCGGTACTCCCGG
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_05-2
+CATCGACCCGGGTGACGACTTCTCCGGCACACCGGACTATTCCTCGTCGTGGCCACCGCATTGCGTCAGCGGTACTCCCGGCGCGGACTTCCATCCCAGTCTGGACACGTCGGCAATCGAGGCGGTGTTCTACAAGGGTGCCTACACCGG
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_06-10
+ACGTTGATCAACATCCGGCCGGTGGTCGCCGCGATCAAGGAGTTCTTCGGCACCAGCCAGCTGAGCCAATTCATGGACCAGAACAACCCGCTGTCGGGGTTGACCCACAAGCGCCGACTGTCGGCGCTGGGGCCCGGCGGTCTGTCACGT
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_06-8
+AGCCAATTCATGGACCAGAACAACCCGCTGTCGGGGTTGACCCACAAGCGCCGACTGTCGGCGCTGGGGCCCGGCGGTCTGTCACGTGAGCGTGCCGGGCTGGAGGTCCGCGACGTGCACCCGTCGCACTACGGCCGGATGTGCCCGATC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_06-6
+AGCCAATTCATGGACCAGAACAACCCGCTGTCGGGGTTGACCCACAAGCGCCGACTGTCGGCGCTGGGGCCCGGCGGTCTGTCACGTGAGCGTGCCGGGCTGGAGGTCCGCGACGTGCACCCGTCGCACTACGGCCGGATGTGCCCGATC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_06-4
+GCACCAGCCAGCTGAGCCAATTCATGGACCAGAACAACCCGCTGTCGGGGTTGACCCACAAGCGCCGACTGTCGGCGCTGGGGCCCGGCGGTCTGTCACGTGAGCGTGCCGGGCTGGAGGTCCGCGACGTGCACCCGTCGCACTACGGCC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_06-2
+CAGCTGAGCCAATTCATGGACCAGAACAACCCGCTGTCGGGGTTGACCCACAAGCGCCGACTGTCGGCGCTGGGGCCCGGCGGTCTGTCACGTGAGCGTGCCGGGCTGGAGGTCCGCGACGTGCACCCGTCGCACTACGGCCGGATGTGC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
=====================================
tests/data/test_isolate_14_2.fq
=====================================
@@ -0,0 +1,360 @@
+ at test_isolate_14_contig_01-20
+GCTCGTTACGCGCGGCAGGACGAAAAGACCCCGGGACCTTCACTACAACTTGGTATTGATGTTCGGTACGGTTTGTGTAGGATAGGTGGGAGACTGTGAAACCTCGACGCCAGTTGGGGCGGAGTCGTTGTTGAAATACCACTCTGATCG
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_01-18
+ACCTGCACGAATGGCGTAACGACTTCTCAACTGTCTCAACCATAGACTCGGCGAAATTGCACTACGAGTAAAGATGCTCGTTACGCGCGGCAGGACGAAAAGACCCCGGGACCTTCACTACAACTTGGTATTGATGTTCGGTACGGTTTG
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_01-16
+GTCTCAACCATAGACTCGGCGAAATTGCACTACGAGTAAAGATGCTCGTTACGCGCGGCAGGACGAAAAGACCCCGGGACCTTCACTACAACTTGGTATTGATGTTCGGTACGGTTTGTGTAGGATAGGTGGGAGACTGTGAAACCTCGA
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_01-14
+AGACTGTGAAACCTCGACGCCAGTTGGGGCGGAGTCGTTGTTGAAATACCACTCTGATCGTATTGGGCATCTAACCTCGAACCCTGAATCGGGTTTAGGGACAGTGCCTGGCGGGTAGTTTAACTGGGGCGGTTGCCTCCTAAAATGTAA
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_01-12
+ACGAGTAAAGATGCTCGTTACGCGCGGCAGGACGAAAAGACCCCGGGACCTTCACTACAACTTGGTATTGATGTTCGGTACGGTTTGTGTAGGATAGGTGGGAGACTGTGAAACCTCGACGCCAGTTGGGGCGGAGTCGTTGTTGAAATA
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_01-10
+GGTACGGTTTGTGTAGGATAGGTGGGAGACTGTGAAACCTCGACGCCAGTTGGGGCGGAGTCGTTGTTGAAATACCACTCTGATCGTATTGGGCATCTAACCTCGAACCCTGAATCGGGTTTAGGGACAGTGCCTGGCGGGTAGTTTAAC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_01-8
+AACCATAGACTCGGCGAAATTGCACTACGAGTAAAGATGCTCGTTACGCGCGGCAGGACGAAAAGACCCCGGGACCTTCACTACAACTTGGTATTGATGTTCGGTACGGTTTGTGTAGGATAGGTGGGAGACTGTGAAACCTCGACGCCA
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_01-6
+GGGAGACTGTGAAACCTCGACGCCAGTTGGGGCGGAGTCGTTGTTGAAATACCACTCTGATCGTATTGGGCATCTAACCTCGAACCCTGAATCGGGTTTAGGGACAGTGCCTGGCGGGTAGTTTAACTGGGGCGGTTGCCTCCTAAAATG
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_01-4
+CTGTCTCAACCATAGACTCGGCGAAATTGCACTACGAGTAAAGATGCTCGTTACGCGCGGCAGGACGAAAAGACCCCGGGACCTTCACTACAACTTGGTATTGATGTTCGGTACGGTTTGTGTAGGATAGGTGGGAGACTGTGAAACCTC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_01-2
+GGCGAAATTGCACTACGAGTAAAGATGCTCGTTACGCGCGGCAGGACGAAAAGACCCCGGGACCTTCACTACAACTTGGTATTGATGTTCGGTACGGTTTGTGTAGGATAGGTGGGAGACTGTGAAACCTCGACGCCAGTTGGGGCGGAG
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_02-50
+GGTTCGGCAGCCCGGAGGATCCCTTCGGCTGGTATTACAACCTGCTGGCGCTGATGACCCATGTCAGCGACGCCAGTCTGTGGATGCGCCTGCCAGACCTGGCCGCCGGGCTAGTGTGCTGGCTGCTGCTGTCGCGTGAGGTGCTGCCCC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_02-48
+GCCGGCTACATGTCCAACTATTTCCGCTGGTTCGGCAGCCCGGAGGATCCCTTCGGCTGGTATTACAACCTGCTGGCGCTGATGACCCATGTCAGCGACGCCAGTCTGTGGATGCGCCTGCCAGACCTGGCCGCCGGGCTAGTGTGCTGG
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_02-46
+CTGGTGGCCGGCGGCCGCCCGATGCTGCGGATCTTGGTGCGCCGTCATCGCCTGGTCGGCACGTTGCCGTTGGTGTCGCCGATGCTGGCCGCCGGCACCGTCATCCTGACCGTGGTGTTCGCCGACCAGACCCTGTCAACGGTGTTGGAA
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_02-44
+CGTCGTTACCGCCGCATTCACACTGGGTGTGCAGCCCACCGGCCTGATCGCGGTGGCCGCGCTGGTGGCCGGCGGCCGCCCGATGCTGCGGATCTTGGTGCGCCGTCATCGCCTGGTCGGCACGTTGCCGTTGGTGTCGCCGATGCTGGC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_02-42
+TGCGGCCGGAGGGCATCATCGCGCTCGGCTCGCTGGTCACCTATGTGCTGATCGAGCGGTCCATGCGGTACAGCCGGCTCACACCGGCGGCGCTGGCCGTCGTTACCGCCGCATTCACACTGGGTGTGCAGCCCACCGGCCTGATCGCGG
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_02-40
+GCGCCTGCCAGACCTGGCCGCCGGGCTAGTGTGCTGGCTGCTGCTGTCGCGTGAGGTGCTGCCCCGCCTCGGGCCGGCGGTGGCGGCCAGCAAACCCGCCTACTGGGCGGCGGCCATGGTCTTGCTGACCGCGTGGATGCCGTTCAACAA
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_02-38
+CAGCCCGGAGGATCCCTTCGGCTGGTATTACAACCTGCTGGCGCTGATGACCCATGTCAGCGACGCCAGTCTGTGGATGCGCCTGCCAGACCTGGCCGCCGGGCTAGTGTGCTGGCTGCTGCTGTCGCGTGAGGTGCTGCCCCGCCTCGG
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_02-36
+GGTCTTGCTGACCGCGTGGATGCCGTTCAACAACGGCCTGCGGCCGGAGGGCATCATCGCGCTCGGCTCGCTGGTCACCTATGTGCTGATCGAGCGGTCCATGCGGTACAGCCGGCTCACACCGGCGGCGCTGGCCGTCGTTACCGCCGC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_02-34
+GCACGTTGCCGTTGGTGTCGCCGATGCTGGCCGCCGGCACCGTCATCCTGACCGTGGTGTTCGCCGACCAGACCCTGTCAACGGTGTTGGAAGCCACCAGGGTTCGCGCCAAAATCGGGCCGAGCCAGGCGTGGTATACCGAGAACCTGC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_02-32
+GGCTCGCTGGTCACCTATGTGCTGATCGAGCGGTCCATGCGGTACAGCCGGCTCACACCGGCGGCGCTGGCCGTCGTTACCGCCGCATTCACACTGGGTGTGCAGCCCACCGGCCTGATCGCGGTGGCCGCGCTGGTGGCCGGCGGCCGC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_02-30
+CTGGTCGGCACGTTGCCGTTGGTGTCGCCGATGCTGGCCGCCGGCACCGTCATCCTGACCGTGGTGTTCGCCGACCAGACCCTGTCAACGGTGTTGGAAGCCACCAGGGTTCGCGCCAAAATCGGGCCGAGCCAGGCGTGGTATACCGAG
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_02-28
+CAGCCCGGAGGATCCCTTCGGCTGGTATTACAACCTGCTGGCGCTGATGACCCATGTCAGCGACGCCAGTCTGTGGATGCGCCTGCCAGACCTGGCCGCCGGGCTAGTGTGCTGGCTGCTGCTGTCGCGTGAGGTGCTGCCCCGCCTCGG
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_02-26
+GACGACGGCTACATCCTGGGCATGGCCCGAGTCGCCGACCACGCCGGCTACATGTCCAACTATTTCCGCTGGTTCGGCAGCCCGGAGGATCCCTTCGGCTGGTATTACAACCTGCTGGCGCTGATGACCCATGTCAGCGACGCCAGTCTG
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_02-24
+GGTCCATGCGGTACAGCCGGCTCACACCGGCGGCGCTGGCCGTCGTTACCGCCGCATTCACACTGGGTGTGCAGCCCACCGGCCTGATCGCGGTGGCCGCGCTGGTGGCCGGCGGCCGCCCGATGCTGCGGATCTTGGTGCGCCGTCATC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_02-22
+ATGTCAGCGACGCCAGTCTGTGGATGCGCCTGCCAGACCTGGCCGCCGGGCTAGTGTGCTGGCTGCTGCTGTCGCGTGAGGTGCTGCCCCGCCTCGGGCCGGCGGTGGCGGCCAGCAAACCCGCCTACTGGGCGGCGGCCATGGTCTTGC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_02-20
+TGGATGCGCCTGCCAGACCTGGCCGCCGGGCTAGTGTGCTGGCTGCTGCTGTCGCGTGAGGTGCTGCCCCGCCTCGGGCCGGCGGTGGCGGCCAGCAAACCCGCCTACTGGGCGGCGGCCATGGTCTTGCTGACCGCGTGGATGCCGTTC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_02-18
+CCGATGCTGCGGATCTTGGTGCGCCGTCATCGCCTGGTCGGCACGTTGCCGTTGGTGTCGCCGATGCTGGCCGCCGGCACCGTCATCCTGACCGTGGTGTTCGCCGACCAGACCCTGTCAACGGTGTTGGAAGCCACCAGGGTTCGCGCC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_02-16
+CTGACCGTGGTGTTCGCCGACCAGACCCTGTCAACGGTGTTGGAAGCCACCAGGGTTCGCGCCAAAATCGGGCCGAGCCAGGCGTGGTATACCGAGAACCTGCGTTACTACTACCTCATCCTGCCCACCGTCGACGGTTCGCTGTCGCGG
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_02-14
+TCGCCGACCACGCCGGCTACATGTCCAACTATTTCCGCTGGTTCGGCAGCCCGGAGGATCCCTTCGGCTGGTATTACAACCTGCTGGCGCTGATGACCCATGTCAGCGACGCCAGTCTGTGGATGCGCCTGCCAGACCTGGCCGCCGGGC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_02-12
+ATTCACACTGGGTGTGCAGCCCACCGGCCTGATCGCGGTGGCCGCGCTGGTGGCCGGCGGCCGCCCGATGCTGCGGATCTTGGTGCGCCGTCATCGCCTGGTCGGCACGTTGCCGTTGGTGTCGCCGATGCTGGCCGCCGGCACCGTCAT
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_02-10
+CCAGTCTGTGGATGCGCCTGCCAGACCTGGCCGCCGGGCTAGTGTGCTGGCTGCTGCTGTCGCGTGAGGTGCTGCCCCGCCTCGGGCCGGCGGTGGCGGCCAGCAAACCCGCCTACTGGGCGGCGGCCATGGTCTTGCTGACCGCGTGGA
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_02-8
+GACCCATGTCAGCGACGCCAGTCTGTGGATGCGCCTGCCAGACCTGGCCGCCGGGCTAGTGTGCTGGCTGCTGCTGTCGCGTGAGGTGCTGCCCCGCCTCGGGCCGGCGGTGGCGGCCAGCAAACCCGCCTACTGGGCGGCGGCCATGGT
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_02-6
+TGGCCCGAGTCGCCGACCACGCCGGCTACATGTCCAACTATTTCCGCTGGTTCGGCAGCCCGGAGGATCCCTTCGGCTGGTATTACAACCTGCTGGCGCTGATGACCCATGTCAGCGACGCCAGTCTGTGGATGCGCCTGCCAGACCTGG
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_02-4
+CATCATCGCGCTCGGCTCGCTGGTCACCTATGTGCTGATCGAGCGGTCCATGCGGTACAGCCGGCTCACACCGGCGGCGCTGGCCGTCGTTACCGCCGCATTCACACTGGGTGTGCAGCCCACCGGCCTGATCGCGGTGGCCGCGCTGGT
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_02-2
+TGGTCACCTATGTGCTGATCGAGCGGTCCATGCGGTACAGCCGGCTCACACCGGCGGCGCTGGCCGTCGTTACCGCCGCATTCACACTGGGTGTGCAGCCCACCGGCCTGATCGCGGTGGCCGCGCTGGTGGCCGGCGGCCGCCCGATGC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_03-30
+CAATTCGTAGGGCGTCAATACACCCGCAGCCAGGGCCTCGCTGCCCAGAAAGGGATCCGTCATGGTCGAAGTGTGCTGAGTCACACCGACAAACGTCACGAGCGTAACCCCAGTGCGAAAGTTCCCGCCGGAAATCGCAGCCACGTTACG
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_03-28
+AATTGCGCGGTCAGTTCCACACCCTGCGGCACGTACACGTCTTTATGTAGCGCGACATACCTGCTGCGCAATTCGTAGGGCGTCAATACACCCGCAGCCAGGGCCTCGCTGCCCAGAAAGGGATCCGTCATGGTCGAAGTGTGCTGAGTC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_03-26
+GCTGCGCAATTCGTAGGGCGTCAATACACCCGCAGCCAGGGCCTCGCTGCCCAGAAAGGGATCCGTCATGGTCGAAGTGTGCTGAGTCACACCGACAAACGTCACGAGCGTAACCCCAGTGCGAAAGTTCCCGCCGGAAATCGCAGCCAC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_03-24
+TACACCCGCAGCCAGGGCCTCGCTGCCCAGAAAGGGATCCGTCATGGTCGAAGTGTGCTGAGTCACACCGACAAACGTCACGAGCGTAACCCCAGTGCGAAAGTTCCCGCCGGAAATCGCAGCCACGTTACGCTCGTGGACATACCGATT
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_03-22
+GCAATTGCGCGGTCAGTTCCACACCCTGCGGCACGTACACGTCTTTATGTAGCGCGACATACCTGCTGCGCAATTCGTAGGGCGTCAATACACCCGCAGCCAGGGCCTCGCTGCCCAGAAAGGGATCCGTCATGGTCGAAGTGTGCTGAG
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_03-20
+CCTGCGGCACGTACACGTCTTTATGTAGCGCGACATACCTGCTGCGCAATTCGTAGGGCGTCAATACACCCGCAGCCAGGGCCTCGCTGCCCAGAAAGGGATCCGTCATGGTCGAAGTGTGCTGAGTCACACCGACAAACGTCACGAGCG
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_03-18
+TAACCCCAGTGCGAAAGTTCCCGCCGGAAATCGCAGCCACGTTACGCTCGTGGACATACCGATTTCGGCCCGGCCGCGGCGAGACGATAGGTTGTCGGGGTGACTGCCACAGCCACTGAAGGGGCCAAACCCCCATTCGTATCCCGTTCA
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_03-16
+AAGGGATCCGTCATGGTCGAAGTGTGCTGAGTCACACCGACAAACGTCACGAGCGTAACCCCAGTGCGAAAGTTCCCGCCGGAAATCGCAGCCACGTTACGCTCGTGGACATACCGATTTCGGCCCGGCCGCGGCGAGACGATAGGTTGT
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_03-14
+GCAATTGCGCGGTCAGTTCCACACCCTGCGGCACGTACACGTCTTTATGTAGCGCGACATACCTGCTGCGCAATTCGTAGGGCGTCAATACACCCGCAGCCAGGGCCTCGCTGCCCAGAAAGGGATCCGTCATGGTCGAAGTGTGCTGAG
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_03-12
+AGTCACACCGACAAACGTCACGAGCGTAACCCCAGTGCGAAAGTTCCCGCCGGAAATCGCAGCCACGTTACGCTCGTGGACATACCGATTTCGGCCCGGCCGCGGCGAGACGATAGGTTGTCGGGGTGACTGCCACAGCCACTGAAGGGG
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_03-10
+TACCTGCTGCGCAATTCGTAGGGCGTCAATACACCCGCAGCCAGGGCCTCGCTGCCCAGAAAGGGATCCGTCATGGTCGAAGTGTGCTGAGTCACACCGACAAACGTCACGAGCGTAACCCCAGTGCGAAAGTTCCCGCCGGAAATCGCA
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_03-8
+AGGGCGTCAATACACCCGCAGCCAGGGCCTCGCTGCCCAGAAAGGGATCCGTCATGGTCGAAGTGTGCTGAGTCACACCGACAAACGTCACGAGCGTAACCCCAGTGCGAAAGTTCCCGCCGGAAATCGCAGCCACGTTACGCTCGTGGA
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_03-6
+TAACCCCAGTGCGAAAGTTCCCGCCGGAAATCGCAGCCACGTTACGCTCGTGGACATACCGATTTCGGCCCGGCCGCGGCGAGACGATAGGTTGTCGGGGTGACTGCCACAGCCACTGAAGGGGCCAAACCCCCATTCGTATCCCGTTCA
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_03-4
+GTCACACCGACAAACGTCACGAGCGTAACCCCAGTGCGAAAGTTCCCGCCGGAAATCGCAGCCACGTTACGCTCGTGGACATACCGATTTCGGCCCGGCCGCGGCGAGACGATAGGTTGTCGGGGTGACTGCCACAGCCACTGAAGGGGC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_03-2
+TGGTCGAAGTGTGCTGAGTCACACCGACAAACGTCACGAGCGTAACCCCAGTGCGAAAGTTCCCGCCGGAAATCGCAGCCACGTTACGCTCGTGGACATACCGATTTCGGCCCGGCCGCGGCGAGACGATAGGTTGTCGGGGTGACTGCC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_04-40
+CGGACCCGTTCGGCGGGCCAGGGCGCTCCCCGACGATGCTGGCCACTGACCTCTCGCTGCGGGTGGATCCGATCTATGAGCGGATCACGCGTCGCTGGCTGGAACACCCCGAGGAATTGGCCGACGAGTTCGCCAAGGCCTGGTACAAGC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_04-38
+TCGTCGGCGGTCACACTTTCGGTAAGACCCATGGCGCCGGCCCGGCCGATCTGGTCGGCCCCGAACCCGAGGCTGCTCCGCTGGAGCAGATGGGCTTGGGCTGGAAGAGCTCGTATGGCACCGGAACCGGTAAGGACGCGATCACCAGCG
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_04-36
+CGACGAAATGGGACAACAGTTTCCTCGAGATCCTGTACGGCTACGAGTGGGAGCTGACGAAGAGCCCTGCTGGCGCTTGGCAATACACCGCCAAGGACGGCGCCGGTGCCGGCACCATCCCGGACCCGTTCGGCGGGCCAGGGCGCTCCC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_04-34
+CGCGTCGCTGGCTGGAACACCCCGAGGAATTGGCCGACGAGTTCGCCAAGGCCTGGTACAAGCTGATCCACCGAGACATGGGTCCCGTTGCGAGATACCTTGGGCCGCTGGTCCCCAAGCAGACCCTGCTGTGGCAGGATCCGGTCCCTG
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_04-32
+TCGGCCCCGAACCCGAGGCTGCTCCGCTGGAGCAGATGGGCTTGGGCTGGAAGAGCTCGTATGGCACCGGAACCGGTAAGGACGCGATCACCAGCGGCATCGAGGTCGTATGGACGAACACCCCGACGAAATGGGACAACAGTTTCCTCG
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_04-30
+GAACACCCCGACGAAATGGGACAACAGTTTCCTCGAGATCCTGTACGGCTACGAGTGGGAGCTGACGAAGAGCCCTGCTGGCGCTTGGCAATACACCGCCAAGGACGGCGCCGGTGCCGGCACCATCCCGGACCCGTTCGGCGGGCCAGG
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_04-28
+CGACGAGTTCGCCAAGGCCTGGTACAAGCTGATCCACCGAGACATGGGTCCCGTTGCGAGATACCTTGGGCCGCTGGTCCCCAAGCAGACCCTGCTGTGGCAGGATCCGGTCCCTGCGGTCAGCCACGACCTCGTCGGCGAAGCCGAGAT
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_04-26
+TACGAGTGGGAGCTGACGAAGAGCCCTGCTGGCGCTTGGCAATACACCGCCAAGGACGGCGCCGGTGCCGGCACCATCCCGGACCCGTTCGGCGGGCCAGGGCGCTCCCCGACGATGCTGGCCACTGACCTCTCGCTGCGGGTGGATCCG
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_04-24
+CCACTGACCTCTCGCTGCGGGTGGATCCGATCTATGAGCGGATCACGCGTCGCTGGCTGGAACACCCCGAGGAATTGGCCGACGAGTTCGCCAAGGCCTGGTACAAGCTGATCCACCGAGACATGGGTCCCGTTGCGAGATACCTTGGGC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_04-22
+AAATGGGACAACAGTTTCCTCGAGATCCTGTACGGCTACGAGTGGGAGCTGACGAAGAGCCCTGCTGGCGCTTGGCAATACACCGCCAAGGACGGCGCCGGTGCCGGCACCATCCCGGACCCGTTCGGCGGGCCAGGGCGCTCCCCGACG
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_04-20
+CTGCGGGTGGATCCGATCTATGAGCGGATCACGCGTCGCTGGCTGGAACACCCCGAGGAATTGGCCGACGAGTTCGCCAAGGCCTGGTACAAGCTGATCCACCGAGACATGGGTCCCGTTGCGAGATACCTTGGGCCGCTGGTCCCCAAG
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_04-18
+GGAATTGGCCGACGAGTTCGCCAAGGCCTGGTACAAGCTGATCCACCGAGACATGGGTCCCGTTGCGAGATACCTTGGGCCGCTGGTCCCCAAGCAGACCCTGCTGTGGCAGGATCCGGTCCCTGCGGTCAGCCACGACCTCGTCGGCGA
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_04-16
+AATGGGACAACAGTTTCCTCGAGATCCTGTACGGCTACGAGTGGGAGCTGACGAAGAGCCCTGCTGGCGCTTGGCAATACACCGCCAAGGACGGCGCCGGTGCCGGCACCATCCCGGACCCGTTCGGCGGGCCAGGGCGCTCCCCGACGA
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_04-14
+GTACAAGCTGATCCACCGAGACATGGGTCCCGTTGCGAGATACCTTGGGCCGCTGGTCCCCAAGCAGACCCTGCTGTGGCAGGATCCGGTCCCTGCGGTCAGCCACGACCTCGTCGGCGAAGCCGAGATTGCCAGCCTTAAGAGCCAGAT
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_04-12
+CGCTGCGGGTGGATCCGATCTATGAGCGGATCACGCGTCGCTGGCTGGAACACCCCGAGGAATTGGCCGACGAGTTCGCCAAGGCCTGGTACAAGCTGATCCACCGAGACATGGGTCCCGTTGCGAGATACCTTGGGCCGCTGGTCCCCA
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_04-10
+CCGTTGCGAGATACCTTGGGCCGCTGGTCCCCAAGCAGACCCTGCTGTGGCAGGATCCGGTCCCTGCGGTCAGCCACGACCTCGTCGGCGAAGCCGAGATTGCCAGCCTTAAGAGCCAGATCCTGGCATCGGGATTGACTGTCTCACAGC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_04-8
+CGCTGGAGCAGATGGGCTTGGGCTGGAAGAGCTCGTATGGCACCGGAACCGGTAAGGACGCGATCACCAGCGGCATCGAGGTCGTATGGACGAACACCCCGACGAAATGGGACAACAGTTTCCTCGAGATCCTGTACGGCTACGAGTGGG
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_04-6
+CCCGTTCGGCGGGCCAGGGCGCTCCCCGACGATGCTGGCCACTGACCTCTCGCTGCGGGTGGATCCGATCTATGAGCGGATCACGCGTCGCTGGCTGGAACACCCCGAGGAATTGGCCGACGAGTTCGCCAAGGCCTGGTACAAGCTGAT
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_04-4
+GGGCTTGGGCTGGAAGAGCTCGTATGGCACCGGAACCGGTAAGGACGCGATCACCAGCGGCATCGAGGTCGTATGGACGAACACCCCGACGAAATGGGACAACAGTTTCCTCGAGATCCTGTACGGCTACGAGTGGGAGCTGACGAAGAG
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_04-2
+CGCTGGAGCAGATGGGCTTGGGCTGGAAGAGCTCGTATGGCACCGGAACCGGTAAGGACGCGATCACCAGCGGCATCGAGGTCGTATGGACGAACACCCCGACGAAATGGGACAACAGTTTCCTCGAGATCCTGTACGGCTACGAGTGGG
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_05-30
+GCCACCGATCATTGTGTGCGCCAGACGGCCGAGGACGCGGTACGCAATGGCTTGGCCACCAGGGTGCTGGTGGACCTGACAGCGGGTGTGTCGGCCGATACCACCGTCGCCGCGCTGGAGGAGATGCGCACCGCCAGCGTCGAGTTGGTT
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_05-28
+CACTGCTGAATTGGCTGCGGCAACGCGGCGTCGATGAGGTCGATGTGGTCGGTATTGCCACCGATCATTGTGTGCGCCAGACGGCCGAGGACGCGGTACGCAATGGCTTGGCCACCAGGGTGCTGGTGGACCTGACAGCGGGTGTGTCGG
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_05-26
+GCCACTGCTGAATTGGCTGCGGCAACGCGGCGTCGATGAGGTCGATGTGGTCGGTATTGCCACCGATCATTGTGTGCGCCAGACGGCCGAGGACGCGGTACGCAATGGCTTGGCCACCAGGGTGCTGGTGGACCTGACAGCGGGTGTGTC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_05-24
+AGTCGACGAGAACGGCACGCCACTGCTGAATTGGCTGCGGCAACGCGGCGTCGATGAGGTCGATGTGGTCGGTATTGCCACCGATCATTGTGTGCGCCAGACGGCCGAGGACGCGGTACGCAATGGCTTGGCCACCAGGGTGCTGGTGGA
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_05-22
+GTGTGCGCCAGACGGCCGAGGACGCGGTACGCAATGGCTTGGCCACCAGGGTGCTGGTGGACCTGACAGCGGGTGTGTCGGCCGATACCACCGTCGCCGCGCTGGAGGAGATGCGCACCGCCAGCGTCGAGTTGGTTTGCAGCTCCTGAT
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_05-20
+CGACGTGCAGAACGACTTCTGCGAGGGTGGCTCGCTGGCGGTAACCGGTGGCGCCGCGCTGGCCCGCGCCATCAGCGACTACCTGGCCGAAGCGGCGGACTACCATCACGTCGTGGCAACCAAGGACTTCCACATCGACCCGGGTGACGA
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_05-18
+GAGCGTACAGCGGCTTCGAAGGAGTCGACGAGAACGGCACGCCACTGCTGAATTGGCTGCGGCAACGCGGCGTCGATGAGGTCGATGTGGTCGGTATTGCCACCGATCATTGTGTGCGCCAGACGGCCGAGGACGCGGTACGCAATGGCT
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_05-16
+GCGACTACCTGGCCGAAGCGGCGGACTACCATCACGTCGTGGCAACCAAGGACTTCCACATCGACCCGGGTGACGACTTCTCCGGCACACCGGACTATTCCTCGTCGTGGCCACCGCATTGCGTCAGCGGTACTCCCGGCGCGGACTTCC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_05-14
+TCGGCAATCGAGGCGGTGTTCTACAAGGGTGCCTACACCGGAGCGTACAGCGGCTTCGAAGGAGTCGACGAGAACGGCACGCCACTGCTGAATTGGCTGCGGCAACGCGGCGTCGATGAGGTCGATGTGGTCGGTATTGCCACCGATCAT
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_05-12
+GCTGAATTGGCTGCGGCAACGCGGCGTCGATGAGGTCGATGTGGTCGGTATTGCCACCGATCATTGTGTGCGCCAGACGGCCGAGGACGCGGTACGCAATGGCTTGGCCACCAGGGTGCTGGTGGACCTGACAGCGGGTGTGTCGGCCGA
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_05-10
+GCGGTACTCCCGGCGCGGACTTCCATCCCAGTCTGGACACGTCGGCAATCGAGGCGGTGTTCTACAAGGGTGCCTACACCGGAGCGTACAGCGGCTTCGAAGGAGTCGACGAGAACGGCACGCCACTGCTGAATTGGCTGCGGCAACGCG
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_05-8
+TACAGCGGCTTCGAAGGAGTCGACGAGAACGGCACGCCACTGCTGAATTGGCTGCGGCAACGCGGCGTCGATGAGGTCGATGTGGTCGGTATTGCCACCGATCATTGTGTGCGCCAGACGGCCGAGGACGCGGTACGCAATGGCTTGGCC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_05-6
+GCGTCGATGAGGTCGATGTGGTCGGTATTGCCACCGATCATTGTGTGCGCCAGACGGCCGAGGACGCGGTACGCAATGGCTTGGCCACCAGGGTGCTGGTGGACCTGACAGCGGGTGTGTCGGCCGATACCACCGTCGCCGCGCTGGAGG
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_05-4
+AACCAAGGACTTCCACATCGACCCGGGTGACGACTTCTCCGGCACACCGGACTATTCCTCGTCGTGGCCACCGCATTGCGTCAGCGGTACTCCCGGCGCGGACTTCCATCCCAGTCTGGACACGTCGGCAATCGAGGCGGTGTTCTACAA
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_05-2
+GCACACCGGACTATTCCTCGTCGTGGCCACCGCATTGCGTCAGCGGTACTCCCGGCGCGGACTTCCATCCCAGTCTGGACACGTCGGCAATCGAGGCGGTGTTCTACAAGGGTGCCTACACCGGAGCGTACAGCGGCTTCGAAGGAGTCG
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_06-10
+TCTTCGGCACCAGCCAGCTGAGCCAATTCATGGACCAGAACAACCCGCTGTCGGGGTTGACCCACAAGCGCCGACTGTCGGCGCTGGGGCCCGGCGGTCTGTCACGTGAGCGTGCCGGGCTGGAGGTCCGCGACGTGCACCCGTCGCACT
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_06-8
+CAAGGAGTTCTTCGGCACCAGCCAGCTGAGCCAATTCATGGACCAGAACAACCCGCTGTCGGGGTTGACCCACAAGCGCCGACTGTCGGCGCTGGGGCCCGGCGGTCTGTCACGTGAGCGTGCCGGGCTGGAGGTCCGCGACGTGCACCC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_06-6
+GTCGCCGCGATCAAGGAGTTCTTCGGCACCAGCCAGCTGAGCCAATTCATGGACCAGAACAACCCGCTGTCGGGGTTGACCCACAAGCGCCGACTGTCGGCGCTGGGGCCCGGCGGTCTGTCACGTGAGCGTGCCGGGCTGGAGGTCCGC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_06-4
+TGATCAACATCCGGCCGGTGGTCGCCGCGATCAAGGAGTTCTTCGGCACCAGCCAGCTGAGCCAATTCATGGACCAGAACAACCCGCTGTCGGGGTTGACCCACAAGCGCCGACTGTCGGCGCTGGGGCCCGGCGGTCTGTCACGTGAGC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ at test_isolate_14_contig_06-2
+GGCCGGTGGTCGCCGCGATCAAGGAGTTCTTCGGCACCAGCCAGCTGAGCCAATTCATGGACCAGAACAACCCGCTGTCGGGGTTGACCCACAAGCGCCGACTGTCGGCGCTGGGGCCCGGCGGTCTGTCACGTGAGCGTGCCGGGCTGG
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
=====================================
tests/resfinder/cge/output/test_gene_result.md
=====================================
@@ -52,7 +52,7 @@ results from a ResFinder hit.
>>> assert(gene_result_blast["ref_acc"] == "KF986263")
>>> assert(gene_result_blast["identity"] == rf_dat_blast["perc_ident"])
>>> assert(gene_result_blast["alignment_length"] == rf_dat_blast["HSP_length"])
->>> assert(gene_result_blast["ref_seq_lenght"] == rf_dat_blast["sbjct_length"])
+>>> assert(gene_result_blast["ref_seq_length"] == rf_dat_blast["sbjct_length"])
>>> assert(gene_result_blast["ref_start_pos"] == rf_dat_blast["sbjct_start"])
>>> assert(gene_result_blast["ref_end_pos"] == rf_dat_blast["sbjct_end"])
>>> assert(gene_result_blast["query_id"] == rf_dat_blast["contig_name"])
=====================================
tests/resfinder/cge/output/test_phenotype_result.md
=====================================
@@ -64,7 +64,7 @@
... "name": "blaOXA-384",
... "identity": 98.2,
... "alignment_length": 90,
-... "ref_seq_lenght": 100,
+... "ref_seq_length": 100,
... "coverage": 90.0,
... "depth": 24.8,
... "ref_id": "blaOXA-384_1_KF986263",
@@ -84,7 +84,7 @@
... 'key': 'gyrA;;1;;CP073768.1',
... 'identity': 99.92,
... 'alignment_length': 2628,
-... 'ref_seq_lenght': 2628,
+... 'ref_seq_length': 2628,
... 'depth': 21,
... 'ref_start_pos': 1,
... 'ref_end_pos': 2628,
View it on GitLab: https://salsa.debian.org/med-team/resfinder/-/commit/014c078bf0fa59949bd35c2c651054726fed7bae
--
View it on GitLab: https://salsa.debian.org/med-team/resfinder/-/commit/014c078bf0fa59949bd35c2c651054726fed7bae
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