[med-svn] [iva] 01/03: Imported Upstream version 0.10.1
Jorge Soares
jssoares-guest at moszumanska.debian.org
Mon Dec 8 11:20:28 UTC 2014
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jssoares-guest pushed a commit to branch master
in repository iva.
commit b7cc516243cc092d34ecb440a5eec1779eec6d8b
Author: Jorge Soares <j.s.soares at gmail.com>
Date: Mon Dec 8 08:43:27 2014 +0000
Imported Upstream version 0.10.1
---
iva/assembly.py | 6 +++---
iva/common.py | 10 +++++++++-
iva/external_progs.py | 2 +-
iva/kcount.py | 2 +-
iva/kraken.py | 2 +-
iva/mapping.py | 6 +++---
iva/qc.py | 1 +
setup.py | 3 ++-
8 files changed, 21 insertions(+), 11 deletions(-)
diff --git a/iva/assembly.py b/iva/assembly.py
index 3a92bb6..5c4d4ed 100644
--- a/iva/assembly.py
+++ b/iva/assembly.py
@@ -2,7 +2,7 @@ import os
import pysam
import tempfile
import shutil
-from iva import contig, mapping, seed, mummer, graph, edge
+from iva import contig, mapping, seed, mummer, graph, edge, common
import fastaq
class Assembly:
@@ -158,10 +158,10 @@ class Assembly:
if sam_type == mapping.CAN_EXTEND_LEFT:
name = mapping.get_ref_name(sam, sam_reader)
clipped = mapping.soft_clipped(sam)[0]
- self.contigs[name].add_left_kmer(sam.seq[:clipped].decode())
+ self.contigs[name].add_left_kmer(common.decode(sam.seq[:clipped]))
elif sam_type == mapping.CAN_EXTEND_RIGHT:
name = mapping.get_ref_name(sam, sam_reader)
- self.contigs[name].add_right_kmer(sam.seq[sam.qend:].decode())
+ self.contigs[name].add_right_kmer(common.decode(sam.seq[sam.qend:]))
if out_prefix is not None and sam_type in keep_read_types:
if sam.is_read1:
diff --git a/iva/common.py b/iva/common.py
index ba73bc5..e8deeed 100644
--- a/iva/common.py
+++ b/iva/common.py
@@ -2,7 +2,7 @@ import argparse
import os
import sys
import subprocess
-version = '0.10.0'
+version = '0.10.1'
class abspathAction(argparse.Action):
def __call__(self, parser, namespace, value, option_string):
@@ -30,3 +30,11 @@ def syscall(cmd, allow_fail=False, verbose=False):
sys.exit(1)
return True
+
+
+def decode(x):
+ try:
+ s = x.decode()
+ except:
+ return x
+ return s
diff --git a/iva/external_progs.py b/iva/external_progs.py
index 221f7c6..475b784 100644
--- a/iva/external_progs.py
+++ b/iva/external_progs.py
@@ -68,7 +68,7 @@ def get_version(prog, must_be_in_path=True):
cmd, regex = prog_to_version_cmd[prog]
cmd_output = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE).communicate()
- cmd_output = cmd_output[0].decode().split('\n')[:-1] + cmd_output[1].decode().split('\n')[:-1]
+ cmd_output = common.decode(cmd_output[0]).split('\n')[:-1] + common.decode(cmd_output[1]).split('\n')[:-1]
for line in cmd_output:
hits = regex.search(line)
if hits:
diff --git a/iva/kcount.py b/iva/kcount.py
index 48a67ab..d79c540 100644
--- a/iva/kcount.py
+++ b/iva/kcount.py
@@ -149,7 +149,7 @@ def _kmc_to_kmer_counts(infile, number, kmers_to_ignore=None, contigs_to_check=N
except:
raise Error('Error getting count from sequence name in bam:\n' + sam.qname)
- counts[sam.seq.decode()] = count
+ counts[common.decode(sam.seq)] = count
sam_reader.close()
shutil.rmtree(tmpdir)
diff --git a/iva/kraken.py b/iva/kraken.py
index d12f17c..63f69f1 100644
--- a/iva/kraken.py
+++ b/iva/kraken.py
@@ -100,7 +100,7 @@ class Database:
for i in range(max_tries):
try:
url = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&rettype=' + filetype + '&retmode=text&id=' + gi
- file_contents = urllib.request.urlopen(url).read().decode().rstrip()
+ file_contents = iva.common.decode(urllib.request.urlopen(url).read()).rstrip()
except:
time.sleep(delay)
continue
diff --git a/iva/mapping.py b/iva/mapping.py
index bc345b5..f291531 100644
--- a/iva/mapping.py
+++ b/iva/mapping.py
@@ -107,7 +107,7 @@ def get_bam_region_coverage(bam, seqname, seq_length, rev=False, verbose=0, both
mpileup_cmd = 'samtools mpileup -r ' + seqname + ' ' + flags + ' ' + bam + ' | cut -f 2,4'
if verbose >= 2:
print(' get_bam_region_coverage:', mpileup_cmd)
- mpileup_out = subprocess.Popen(mpileup_cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.DEVNULL).communicate()[0].decode().split('\n')[:-1]
+ mpileup_out = common.decode(subprocess.Popen(mpileup_cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.DEVNULL).communicate()[0]).split('\n')[:-1]
for line in mpileup_out:
pos, depth = [int(killer_rabbit) for killer_rabbit in line.rstrip().split()]
@@ -174,7 +174,7 @@ def find_incorrect_ref_bases(bam, ref_fasta):
bad_bases = {}
fastaq.tasks.file_to_dict(ref_fasta, ref_seqs)
mpileup_cmd = 'samtools mpileup ' + bam + ' | cut -f 1,2,5'
- mpileup_out = subprocess.Popen(mpileup_cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.DEVNULL).communicate()[0].decode().split('\n')[:-1]
+ mpileup_out = common.decode(subprocess.Popen(mpileup_cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.DEVNULL).communicate()[0]).split('\n')[:-1]
for line in mpileup_out:
# somteimes mpileup has an empty bases column, so skip those
@@ -214,7 +214,7 @@ def sam_to_fasta(s):
else:
raise Error('Read', name, 'must be first of second of pair according to flag. Cannot continue')
- seq = fastaq.sequences.Fasta(name, s.seq.decode())
+ seq = fastaq.sequences.Fasta(name, common.decode(s.seq))
if s.is_reverse:
seq.revcomp()
diff --git a/iva/qc.py b/iva/qc.py
index 845eade..301b5e9 100644
--- a/iva/qc.py
+++ b/iva/qc.py
@@ -651,6 +651,7 @@ class Qc:
self._calculate_incorrect_assembly_bases()
self._calculate_contig_placement()
self._write_fasta_contigs_hit_ref()
+ self._write_fasta_contigs_not_hit_ref()
self._calculate_ref_read_coverage()
self._calculate_ref_read_region_coverage()
self._calculate_ref_positions_covered_by_contigs()
diff --git a/setup.py b/setup.py
index a0220ea..0a53ca1 100644
--- a/setup.py
+++ b/setup.py
@@ -7,7 +7,7 @@ def read(fname):
setup(
name='iva',
- version='0.10.0',
+ version='0.10.1',
description='Iterative Virus Assembler',
long_description=read('README.md'),
packages = find_packages(),
@@ -18,5 +18,6 @@ setup(
scripts=glob.glob('scripts/*'),
test_suite='nose.collector',
install_requires=['nose >= 1.3', 'fastaq >= 1.6.0', 'networkx'],
+ dependency_links=['http://github.com/sanger-pathogens/fastaq/tarball/master#egg=fastaq-1.7.0'],
license='GPLv3',
)
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