[med-svn] [kineticstools] 04/05: Imported Upstream version 0.6.1+dfsg
Afif Elghraoui
afif at moszumanska.debian.org
Sun Dec 18 08:04:18 UTC 2016
This is an automated email from the git hooks/post-receive script.
afif pushed a commit to branch master
in repository kineticstools.
commit 737e59669f40fa6b38ad86de5f5416419fc463ee
Author: Afif Elghraoui <afif at debian.org>
Date: Wed Nov 30 23:22:35 2016 -0800
Imported Upstream version 0.6.1+dfsg
---
doc/manual.rst | 116 +++++++++++++++---------------
kineticsTools/ReferenceUtils.py | 3 +-
kineticsTools/ResultWriter.py | 63 ++++++++--------
kineticsTools/ipdSummary.py | 23 ++++--
kineticsTools/summarizeModifications.py | 4 +-
kineticsTools/tasks/gather_kinetics_h5.py | 4 +-
setup.py | 2 +-
test/cram/version.t | 2 +-
test/test_gather_h5.py | 48 ++++++++++---
test/test_outputs.py | 13 ++--
test/test_tool_contract.py | 10 +--
11 files changed, 162 insertions(+), 126 deletions(-)
diff --git a/doc/manual.rst b/doc/manual.rst
index c9b2c21..5c4105b 100644
--- a/doc/manual.rst
+++ b/doc/manual.rst
@@ -41,7 +41,7 @@ Studies of the relationship between IPD and sequence context reveal that most of
Filtering and Trimming
----------------------
-kineticsTools uses the Mapping QV generated by BLASR and stored in the cmp.h5 file to ignore reads that aren't confidently mapped. The default minimum Mapping QV required is 10, implying that BLASR has :math:`90\%` confidence that the read is correctly mapped. Because of the range of readlengths inherent in PacBio dataThis can be changed in using the --mapQvThreshold command line argument, or via the SMRTPortal configuration dialog for Modification Detection.
+kineticsTools uses the Mapping QV generated by BLASR and stored in the cmp.h5 or BAM file (or AlignmentSet) to ignore reads that aren't confidently mapped. The default minimum Mapping QV required is 10, implying that BLASR has :math:`90\%` confidence that the read is correctly mapped. Because of the range of readlengths inherent in PacBio dataThis can be changed in using the --mapQvThreshold command line argument, or via the SMRTPortal configuration dialog for Modification Detection.
There are a few features of PacBio data that require special attention in order to acheive good modification detection performance.
kineticsTools inspects the alignment between the observed bases and the reference sequence -- in order for an IPD measurement to be included in the analysis, the PacBio read sequence must match the reference sequence for :math:`k` around the cognate base. In the current module :math:`k=1`
@@ -55,19 +55,35 @@ Statistical Testing
-------------------
We test the hypothesis that IPDs observed at a particular locus in the sample have a longer means than IPDs observed at the same locus in unmodified DNA. If we have generated a Whole Genome Amplified dataset, which removes DNA modifications, we use a case-control, two-sample t-test. This tool also provides a pre-calibrated 'synthetic control' model which predicts the unmodified IPD, given a 12 base sequence context. In the synthetic control case we use a one-sample t-test, with an adju [...]
+
+=============
+Example Usage
+=============
+
+Basic use with BAM input, GFF+HDF5 output::
+
+ ipdSummary aligned.bam --reference ref.fasta --identify m6A,m4C --gff basemods.gff --csv_h5 kinetics.h5
+
+With cmp.h5 input, methyl fraction calculation and GFF+CSV output::
+
+ ipdSummary aligned.cmp.h5 --reference ref.fasta --identify m6A,m4C --methylFraction --gff basemods.gff --csv kinetics.csv
+
+
======
Inputs
======
-aligned_reads.cmp.h5
---------------------
+Aligned Reads
+-------------
-A standard cmp.h5 file contain alignments and IPD information supplies the kinetic data used to perform modification detection. The standard cmp.h5 file of a SMRTportal jobs is data/aligned_read.cmp.h5.
+A standard PacBio alignment file - either AlignmentSet XML, BAM, or cmp.h5 -
+containing alignments and IPD information supplies the kinetic data used to perform modification detection. The standard cmp.h5 file of a SMRTportal jobs is data/aligned_read.cmp.h5.
Reference Sequence
------------------
-The tool requires the reference sequence used to perform alignments. Currently this must be supplied via the path to a SMRTportal reference repository entry.
+The tool requires the reference sequence used to perform alignments. This can
+be either a FASTA file or a ReferenceSet XML.
=======
Outputs
@@ -77,10 +93,45 @@ The modification detection tool provides results in a variety of formats suitabl
quick reference, and comsumption by visualization tools such as PacBio SMRTView.
Results are generally indexed by reference position and reference strand. In all cases the strand value refers to the strand carrying the modification in DNA sample. Remember that the kinetic effect of the modification is observed in read sequences aligning to the opposite strand. So reads aligning to the positive strand carry information about modification on the negative strand and vice versa, but in this toolkit we alway report the strand containing the putative modification.
+The following output options are available:
+
+ - ``--gff FILENAME``: GFF format
+ - ``--csv FILENAME``: comma-separated value format
+ - ``--csv_h5 FILENAME``: compact binary equivalent of CSV in HDF5 format
+ - ``--bigwig FILENAME``: BigWig file (mostly only useful for SMRTView)
+
+
+modifications.gff
+-----------------
+The modifications.gff is compliant with the GFF Version 3 specification (http://www.sequenceontology.org/gff3.shtml). Each template position / strand pair whose p-value exceeds the pvalue threshold appears as a row. The template position is 1-based, per the GFF spec. The strand column refers to the strand carrying the detected modification, which is the opposite strand from those used to detect the modification. The GFF confidence column is a Phred-transformed pvalue of detection.
+
+**Note on genome browser compatibility**
+
+The modifications.gff file will not work directly with most genome browsers. You will likely need to make a copy of the GFF file and convert the _seqid_ columns from the generic 'ref0000x' names generated by PacBio, to the FASTA headers present in the original reference FASTA file. The mapping table is written in the header of the modifications.gff file in ``#sequence-header`` tags. This issue will be resolved in the 1.4 release of kineticsTools.
+
+The auxiliary data column of the GFF file contains other statistics which may be useful downstream analysis or filtering. In particular the coverage level of the reads used to make the call, and +/- 20bp sequence context surrounding the site.
+
+================ ===========
+Column Description
+================ ===========
+seqid Fasta contig name
+source Name of tool -- 'kinModCall'
+type Modification type -- in identification mode this will be m6A, m4C, or m5C for identified bases, or the generic tag 'modified_base' if a kinetic event was detected that does not match a known modification signature
+start Modification position on contig
+end Modification position on contig
+score Phred transformed p-value of detection - this is the single-site detection p-value
+strand Sample strand containing modification
+phase Not applicable
+attributes Extra fields relevant to base mods. IPDRatio is traditional IPDRatio, context is the reference sequence -20bp to +20bp around the modification, and coverage level is the number of IPD observations used after Mapping QV filtering and accuracy filtering. If the row results from an identified modification we also include an identificationQv tag with the from the modification identification procedure. identificationQv is the phred-transformed probability of an incorre [...]
+================ ===========
+
+
modifications.csv
-----------------
The modifications.csv file contains one row for each (reference position, strand) pair that appeared in the dataset with coverage at least x.
-x defaults to 3, but is configurable with '--minCoverage' flag to ipdSummary.py. The reference position index is 1-based for compatibility with the gff file the R environment.
+x defaults to 3, but is configurable with '--minCoverage' flag to ipdSummary.py. The reference position index is 1-based for compatibility with the gff file the R environment. Note that this output type scales poorly and is not
+recommended for large genomes; the HDF5 output should perform much better in
+these cases.
Output columns
--------------
@@ -125,56 +176,3 @@ coverage mean of case and control coverage
controlCoverage count of valid control IPDs at this position (see Filtering section for details)
caseCoverage count of valid case IPDs at this position (see Filtering section for details)
================ ===========
-
-
-
-modifications.gff
------------------
-The modifications.gff is compliant with the GFF Version 3 specification (http://www.sequenceontology.org/gff3.shtml). Each template position / strand pair whose p-value exceeds the pvalue threshold appears as a row. The template position is 1-based, per the GFF spec. The strand column refers to the strand carrying the detected modification, which is the opposite strand from those used to detect the modification. The GFF confidence column is a Phred-transformed pvalue of detection.
-
-**Note on genome browser compatibility**
-
-The modifications.gff file will not work directly with most genome browsers. You will likely need to make a copy of the GFF file and convert the _seqid_ columns from the generic 'ref0000x' names generated by PacBio, to the FASTA headers present in the original reference FASTA file. The mapping table is written in the header of the modifications.gff file in ``#sequence-header`` tags. This issue will be resolved in the 1.4 release of kineticsTools.
-
-The auxiliary data column of the GFF file contains other statistics which may be useful downstream analysis or filtering. In particular the coverage level of the reads used to make the call, and +/- 20bp sequence context surrounding the site.
-
-
-================ ===========
-Column Description
-================ ===========
-seqid Fasta contig name
-source Name of tool -- 'kinModCall'
-type Modification type -- in identification mode this will be m6A, m4C, or m5C for identified bases, or the generic tag 'modified_base' if a kinetic event was detected that does not match a known modification signature
-start Modification position on contig
-end Modification position on contig
-score Phred transformed p-value of detection - this is the single-site detection p-value
-strand Sample strand containing modification
-phase Not applicable
-attributes Extra fields relevant to base mods. IPDRatio is traditional IPDRatio, context is the reference sequence -20bp to +20bp around the modification, and coverage level is the number of IPD observations used after Mapping QV filtering and accuracy filtering. If the row results from an identified modification we also include an identificationQv tag with the from the modification identification procedure. identificationQv is the phred-transformed probability of an incorre [...]
-================ ===========
-
-motifs.gff
-----------
-If the Motif Finder tool is run, it will generate motifs.gff, which a reprocessed version of modifications.gff with the following changes. If a detected modification occurs on a motif detected by the motif finder, the modification is annotated with motif data. An attribute 'motif' is added containing the motif string, and an attribute 'id' is added containing the motif id, which is the motif string for unpaired motifs or 'motifString1/motifString2' for paired motifs. If a motif instance [...]
-
-
-motif_summary.csv
------------------
-
-If the Motif Finder tool is run, motif_summary.csv is generated, summarizing the modified motifs discovered by the tool. The CSV contains one row per detected motif, with the following columns
-
-================== ===========
-Column Description
-================== ===========
-motifString Detected motif sequence
-centerPos Position in motif of modification (0-based)
-fraction Fraction of instances of this motif with modification QV above the QV threshold
-nDetected Number of instances of this motif with above threshold
-nGenome Number of instances of this motif in reference sequence
-groupTag A string idetifying the motif grouping. For paired motifs this is "<motifString1>/<motifString2>", For unpaired motifs this equals motifString
-partnerMotifString motifString of paired motif (motif with reverse-complementary motifString)
-meanScore Mean Modification Qv of detected instances
-meanIpdRatio Mean IPD ratio of detected instances
-meanCoverage Mean coverage of detected instances
-objectiveScore Objective score of this motif in the motif finder algorithm
-================== ===========
diff --git a/kineticsTools/ReferenceUtils.py b/kineticsTools/ReferenceUtils.py
index e63758c..ae8a5ab 100755
--- a/kineticsTools/ReferenceUtils.py
+++ b/kineticsTools/ReferenceUtils.py
@@ -75,7 +75,8 @@ class ReferenceUtils():
# Mark each contig with it's ID from the cmp.h5 - match them up using MD5s
for x in alignmentSet.referenceInfoTable:
- contigDict[x.FullName].cmph5ID = x.ID
+ if x.FullName in contigDict:
+ contigDict[x.FullName].cmph5ID = x.ID
return contigs
diff --git a/kineticsTools/ResultWriter.py b/kineticsTools/ResultWriter.py
index 0671fcd..dbcdedd 100755
--- a/kineticsTools/ResultWriter.py
+++ b/kineticsTools/ResultWriter.py
@@ -42,7 +42,7 @@ import sys
from kineticsTools.pipelineTools import consumer
import math
-
+DEFAULT_NCHUNKS = 256
# Labels for modified fraction:
FRAC = 'frac'
FRAClow = 'fracLow'
@@ -359,24 +359,23 @@ class KineticsWriter(ResultCollectorProcess):
y = [int(ref.Length) for ref in self.refInfo]
dataLength = 2 * sum(y)
y.append(8192)
- chunkSize = min(dataLength, 8192 * 2)
- # print "dataLength = ", dataLength, " chunkSize = ", chunkSize, " y = ", y
-
- refIdDataset = grp.create_dataset('refId', (dataLength,), dtype="u4", compression="gzip", chunks=(chunkSize,), compression_opts=2)
- tplDataset = grp.create_dataset('tpl', (dataLength,), dtype="u4", compression="gzip", chunks=(chunkSize,), compression_opts=2)
- strandDataset = grp.create_dataset('strand', (dataLength,), dtype="u1", compression="gzip", chunks=(chunkSize,), compression_opts=2)
- baseDataset = grp.create_dataset('base', (dataLength,), dtype="a1", compression="gzip", chunks=(chunkSize,), compression_opts=2)
- scoreDataset = grp.create_dataset('score', (dataLength,), dtype="u4", compression="gzip", chunks=(chunkSize,), compression_opts=2)
- tMeanDataset = grp.create_dataset('tMean', (dataLength,), dtype="f4", compression="gzip", chunks=(chunkSize,), compression_opts=2)
- tErrDataset = grp.create_dataset('tErr', (dataLength,), dtype="f4", compression="gzip", chunks=(chunkSize,), compression_opts=2)
- modelPredictionDataset = grp.create_dataset('modelPrediction', (dataLength,), dtype="f4", compression="gzip", chunks=(chunkSize,), compression_opts=2)
- ipdRatioDataset = grp.create_dataset('ipdRatio', (dataLength,), dtype="f4", compression="gzip", chunks=(chunkSize,), compression_opts=2)
- coverageDataset = grp.create_dataset('coverage', (dataLength,), dtype="u4", compression="gzip", chunks=(chunkSize,), compression_opts=2)
+ nChunks = min(dataLength, DEFAULT_NCHUNKS)
+
+ refIdDataset = grp.create_dataset('refId', (dataLength,), dtype="u4", compression="gzip", chunks=(nChunks,), compression_opts=2)
+ tplDataset = grp.create_dataset('tpl', (dataLength,), dtype="u4", compression="gzip", chunks=(nChunks,), compression_opts=2)
+ strandDataset = grp.create_dataset('strand', (dataLength,), dtype="u1", compression="gzip", chunks=(nChunks,), compression_opts=2)
+ baseDataset = grp.create_dataset('base', (dataLength,), dtype="a1", compression="gzip", chunks=(nChunks,), compression_opts=2)
+ scoreDataset = grp.create_dataset('score', (dataLength,), dtype="u4", compression="gzip", chunks=(nChunks,), compression_opts=2)
+ tMeanDataset = grp.create_dataset('tMean', (dataLength,), dtype="f4", compression="gzip", chunks=(nChunks,), compression_opts=2)
+ tErrDataset = grp.create_dataset('tErr', (dataLength,), dtype="f4", compression="gzip", chunks=(nChunks,), compression_opts=2)
+ modelPredictionDataset = grp.create_dataset('modelPrediction', (dataLength,), dtype="f4", compression="gzip", chunks=(nChunks,), compression_opts=2)
+ ipdRatioDataset = grp.create_dataset('ipdRatio', (dataLength,), dtype="f4", compression="gzip", chunks=(nChunks,), compression_opts=2)
+ coverageDataset = grp.create_dataset('coverage', (dataLength,), dtype="u4", compression="gzip", chunks=(nChunks,), compression_opts=2)
if self.options.methylFraction:
- fracDataset = grp.create_dataset(FRAC, (dataLength,), dtype="f4", compression="gzip", chunks=(chunkSize,), compression_opts=2)
- fracLowDataset = grp.create_dataset(FRAClow, (dataLength,), dtype="f4", compression="gzip", chunks=(chunkSize,), compression_opts=2)
- fracUpDataset = grp.create_dataset(FRACup, (dataLength,), dtype="f4", compression="gzip", chunks=(chunkSize,), compression_opts=2)
+ fracDataset = grp.create_dataset(FRAC, (dataLength,), dtype="f4", compression="gzip", chunks=(nChunks,), compression_opts=2)
+ fracLowDataset = grp.create_dataset(FRAClow, (dataLength,), dtype="f4", compression="gzip", chunks=(nChunks,), compression_opts=2)
+ fracUpDataset = grp.create_dataset(FRACup, (dataLength,), dtype="f4", compression="gzip", chunks=(nChunks,), compression_opts=2)
try:
while True:
@@ -495,25 +494,25 @@ class KineticsWriter(ResultCollectorProcess):
for ref in self.refInfo:
# Each reference group will house a collection of datasets:
dataLength = ref.Length * 2
- chunkSize = min(dataLength, 8192)
+ nChunks = min(dataLength, DEFAULT_NCHUNKS)
# Create a group for each reference:
grp = f.create_group(str(ref.Name))
- ds = grp.create_dataset('tpl', (dataLength,), dtype="u4", compression="gzip", chunks=(chunkSize,))
- ds = grp.create_dataset('strand', (dataLength,), dtype="u1", compression="gzip", chunks=(chunkSize,))
- ds = grp.create_dataset('base', (dataLength,), dtype="a1", compression="gzip", chunks=(chunkSize,))
- ds = grp.create_dataset('score', (dataLength,), dtype="u4", compression="gzip", chunks=(chunkSize,))
- ds = grp.create_dataset('tMean', (dataLength,), dtype="f4", compression="gzip", chunks=(chunkSize,))
- ds = grp.create_dataset('tErr', (dataLength,), dtype="f4", compression="gzip", chunks=(chunkSize,))
- ds = grp.create_dataset('modelPrediction', (dataLength,), dtype="f4", compression="gzip", chunks=(chunkSize,))
- ds = grp.create_dataset('ipdRatio', (dataLength,), dtype="f4", compression="gzip", chunks=(chunkSize,))
- ds = grp.create_dataset('coverage', (dataLength,), dtype="u4", compression="gzip", chunks=(chunkSize,))
+ ds = grp.create_dataset('tpl', (dataLength,), dtype="u4", compression="gzip", chunks=(nChunks,))
+ ds = grp.create_dataset('strand', (dataLength,), dtype="u1", compression="gzip", chunks=(nChunks,))
+ ds = grp.create_dataset('base', (dataLength,), dtype="a1", compression="gzip", chunks=(nChunks,))
+ ds = grp.create_dataset('score', (dataLength,), dtype="u4", compression="gzip", chunks=(nChunks,))
+ ds = grp.create_dataset('tMean', (dataLength,), dtype="f4", compression="gzip", chunks=(nChunks,))
+ ds = grp.create_dataset('tErr', (dataLength,), dtype="f4", compression="gzip", chunks=(nChunks,))
+ ds = grp.create_dataset('modelPrediction', (dataLength,), dtype="f4", compression="gzip", chunks=(nChunks,))
+ ds = grp.create_dataset('ipdRatio', (dataLength,), dtype="f4", compression="gzip", chunks=(nChunks,))
+ ds = grp.create_dataset('coverage', (dataLength,), dtype="u4", compression="gzip", chunks=(nChunks,))
if self.options.methylFraction:
- ds = grp.create_dataset(FRAC, (dataLength,), dtype="f4", compression="gzip", chunks=(chunkSize,))
- ds = grp.create_dataset(FRAClow, (dataLength,), dtype="f4", compression="gzip", chunks=(chunkSize,))
- ds = grp.create_dataset(FRACup, (dataLength,), dtype="f4", compression="gzip", chunks=(chunkSize,))
+ ds = grp.create_dataset(FRAC, (dataLength,), dtype="f4", compression="gzip", chunks=(nChunks,))
+ ds = grp.create_dataset(FRAClow, (dataLength,), dtype="f4", compression="gzip", chunks=(nChunks,))
+ ds = grp.create_dataset(FRACup, (dataLength,), dtype="f4", compression="gzip", chunks=(nChunks,))
# Maintain a dictionary of group paths?
dsDict[ref.ID] = grp
@@ -633,12 +632,12 @@ class KineticsWriter(ResultCollectorProcess):
# FIXME -- create with good chunk parameters, activate compression
log.info("Creating IpdRatio dataset w/ name: %s, Size: %d" % (str(ref.Name), ref.Length))
- chunkSize = min(ref.Length, 8192)
+ nChunks = min(ref.Length, DEFAULT_NCHUNKS)
ds = f.create_dataset(str(ref.Name), (ref.Length,),
dtype="u4",
compression='gzip',
- chunks=(chunkSize,))
+ chunks=(nChunks,))
dsDict[ref.ID] = ds
diff --git a/kineticsTools/ipdSummary.py b/kineticsTools/ipdSummary.py
index 6bfd088..c93e369 100755
--- a/kineticsTools/ipdSummary.py
+++ b/kineticsTools/ipdSummary.py
@@ -126,16 +126,16 @@ def get_parser():
type=validateFile, help="Fasta or Reference DataSet")
# XXX GFF and CSV are "option" for arg parser, not tool contract
tcp.add_output_file_type(FileTypes.GFF, "gff",
- name="Modified bases GFF",
- description="GFF file of modified bases",
+ name="Modifications",
+ description="Summary of analysis results for each kinModCall",
default_name="basemods")
tcp.add_output_file_type(FileTypes.BIGWIG, "bigwig",
- name="BigWig file encoding base IpdRatios",
- description="Compressed binary format containing the IpdRatios for every base (both strands)",
+ name="IPD Ratios",
+ description="BigWig file encoding base IpdRatios",
default_name="basemods")
tcp.add_output_file_type(FileTypes.H5, "csv_h5",
- name="HDF5 file containing per-base information",
- description="HDF5 equivalent of CSV output",
+ name="Full Kinetics Summary",
+ description="HDF5 file containing per-base information",
default_name="basemods")
argp.add_argument("--gff", action="store", default=None,
help="Output GFF file of modified bases")
@@ -567,6 +567,17 @@ class KineticsToolsRunner(object):
sys.exit(1)
majorityChem = ReferenceUtils.loadAlignmentChemistry(self.alignments)
+
+ # Temporary solution for Sequel chemistries: we do not
+ # have trained kinetics models in hand yet for Sequel
+ # chemistries. However we have observed that the P5-C3
+ # training seems to yield fairly good results on Sequel
+ # chemistries to date. So for the moment, we will use
+ # that model for Sequel data.
+ if majorityChem.startswith("S/"):
+ logging.info("No trained model available yet for Sequel chemistries; modeling as P5-C3")
+ majorityChem = "P5-C3"
+
ipdModel = os.path.join(self.args.paramsPath, majorityChem + ".h5")
if majorityChem == 'unknown':
logging.error("Chemistry cannot be identified---cannot perform kinetic analysis")
diff --git a/kineticsTools/summarizeModifications.py b/kineticsTools/summarizeModifications.py
index 2f2c669..5581314 100755
--- a/kineticsTools/summarizeModifications.py
+++ b/kineticsTools/summarizeModifications.py
@@ -178,8 +178,8 @@ def get_parser():
name="GFF file",
description="Alignment summary GFF")
p.add_output_file_type(FileTypes.GFF, "gff_out",
- name="Alignment summary with basemods",
- description="Modified alignment summary file",
+ name="Coverage and Base Modifications Summary",
+ description="Coverage summary for regions (bins) spanning the reference with basemod results for each region",
default_name="alignment_summary_with_basemods")
return p
diff --git a/kineticsTools/tasks/gather_kinetics_h5.py b/kineticsTools/tasks/gather_kinetics_h5.py
index 76703f5..2115846 100644
--- a/kineticsTools/tasks/gather_kinetics_h5.py
+++ b/kineticsTools/tasks/gather_kinetics_h5.py
@@ -15,6 +15,8 @@ from pbcommand.cli import pbparser_runner
from pbcommand.models import get_gather_pbparser, FileTypes
from pbcommand.utils import setup_log
+from kineticsTools.ResultWriter import DEFAULT_NCHUNKS
+
log = logging.getLogger(__name__)
@@ -122,7 +124,7 @@ def gather_kinetics_h5_byref(chunked_files, output_file):
s=ref_sizes[ref_name]))
grp = out.create_group(ref_name)
dataLength = ref_sizes[ref_name]
- chunkSize = min(dataLength, 8192)
+ chunkSize = min(dataLength, DEFAULT_NCHUNKS)
for ds_id, ds_type in ds_types.iteritems():
log.debug(" dataset {i} ({t})".format(i=ds_id, t=ds_type))
ds = grp.create_dataset(ds_id, (dataLength,), dtype=ds_type,
diff --git a/setup.py b/setup.py
index e1eb4bf..cf697c8 100755
--- a/setup.py
+++ b/setup.py
@@ -4,7 +4,7 @@ import sys
setup(
name='kineticsTools',
- version='0.6.0',
+ version='0.6.1',
author='Pacific Biosciences',
author_email='devnet at pacificbiosciences.com',
license=open('LICENSES.txt').read(),
diff --git a/test/cram/version.t b/test/cram/version.t
index 91ce3dd..bb10400 100644
--- a/test/cram/version.t
+++ b/test/cram/version.t
@@ -1,7 +1,7 @@
A simple test of the version and help options:
$ ipdSummary --version
- 2.2
+ 2.3
$ ipdSummary
usage: ipdSummary [-h] [--version] [--emit-tool-contract]
diff --git a/test/test_gather_h5.py b/test/test_gather_h5.py
index 954fa26..1a4310f 100644
--- a/test/test_gather_h5.py
+++ b/test/test_gather_h5.py
@@ -1,4 +1,6 @@
+# TODO test with more than one simulated reference contig
+
import unittest
import tempfile
@@ -9,7 +11,8 @@ import pbcommand.testkit.core
from pbcommand.models import PipelineChunk
from pbcommand.pb_io.common import write_pipeline_chunks
-from kineticsTools.tasks.gather_kinetics_h5 import gather_kinetics_h5
+from kineticsTools.tasks.gather_kinetics_h5 import (gather_kinetics_h5,
+ gather_kinetics_h5_byref)
class SetUpHDF5(object):
DATALENGTH = 10000
@@ -20,16 +23,24 @@ class SetUpHDF5(object):
]
@classmethod
+ def get_base_group_input(cls, f):
+ return f.create_group("chr1")
+
+ def get_base_group_output(self, f):
+ return f[f.keys()[0]]
+
+ @classmethod
def makeInputs(cls):
for k, ifn in enumerate(cls.CHUNKED_FILES):
f = h5py.File(cls.CHUNKED_FILES[k], "w")
- a = f.create_dataset("base", (cls.DATALENGTH,),
+ g = cls.get_base_group_input(f)
+ a = g.create_dataset("base", (cls.DATALENGTH,),
dtype="a1", compression="gzip",
chunks=(cls.CHUNKSIZE,), compression_opts=2)
- b = f.create_dataset("score", (cls.DATALENGTH,),
+ b = g.create_dataset("score", (cls.DATALENGTH,),
dtype="u4", compression="gzip",
chunks=(cls.CHUNKSIZE,), compression_opts=2)
- c = f.create_dataset("tMean", (cls.DATALENGTH,),
+ c = g.create_dataset("tMean", (cls.DATALENGTH,),
dtype="f4", compression="gzip",
chunks=(cls.CHUNKSIZE,), compression_opts=2)
start = k * (cls.DATALENGTH / 2)
@@ -46,18 +57,35 @@ class TestGatherHDF5(unittest.TestCase, SetUpHDF5):
def setUpClass(cls):
cls.makeInputs()
+ def _gather(self, ofn):
+ gather_kinetics_h5_byref(self.CHUNKED_FILES, ofn)
+
def test_gather_kinetics_h5(self):
ofn = tempfile.NamedTemporaryFile(suffix=".h5").name
- gather_kinetics_h5(self.CHUNKED_FILES, ofn)
+ self._gather(ofn)
f = h5py.File(ofn)
- self.assertTrue(all(f['base'].__array__() == 'A'))
- self.assertTrue(all(f['score'].__array__() > 0))
- self.assertEqual(f['score'].__array__().mean(), 3)
- self.assertTrue(all(f['tMean'].__array__() > 0))
- d = np.round(f['tMean'].__array__() ** 2).astype("u4")
+ g = self.get_base_group_output(f)
+ self.assertTrue(all(g['base'].__array__() == 'A'))
+ self.assertTrue(all(g['score'].__array__() > 0))
+ self.assertEqual(g['score'].__array__().mean(), 3)
+ self.assertTrue(all(g['tMean'].__array__() > 0))
+ d = np.round(g['tMean'].__array__() ** 2).astype("u4")
self.assertTrue(all(d == np.array(range(1, self.DATALENGTH+1))))
+class TestGatherHDF5Flat(TestGatherHDF5):
+
+ @classmethod
+ def get_base_group_input(cls, f):
+ return f
+
+ def get_base_group_output(self, f):
+ return f
+
+ def _gather(self, ofn):
+ gather_kinetics_h5(self.CHUNKED_FILES, ofn)
+
+
class TestGatherH5ToolContract(pbcommand.testkit.core.PbTestGatherApp, SetUpHDF5):
DRIVER_BASE = "python -m kineticsTools.tasks.gather_kinetics_h5 "
INPUT_FILES = [tempfile.NamedTemporaryFile(suffix=".json").name]
diff --git a/test/test_outputs.py b/test/test_outputs.py
index 03430de..59565c2 100644
--- a/test/test_outputs.py
+++ b/test/test_outputs.py
@@ -63,22 +63,23 @@ class TestOutputs(unittest.TestCase):
def test_h5_output(self):
f = h5py.File(self.h5_file)
- bases = f['base'].__array__()
+ g = f[f.keys()[0]] # just one group in this file
+ bases = g['base'].__array__()
self.assertEqual(bases[0], "A")
self.assertEqual(bases[100], "T")
self.assertEqual(list(bases[0:400] != "").count(True), 400)
- seqh_fwd = ''.join([f['base'][x*2] for x in range(200)])
+ seqh_fwd = ''.join([g['base'][x*2] for x in range(200)])
seqc_fwd = ''.join([self.csv_records[x*2][3] for x in range(200)])
self.assertEqual(seqh_fwd, seqc_fwd)
- seqh_rev = ''.join([f['base'][(x*2)+1] for x in range(200)])
+ seqh_rev = ''.join([g['base'][(x*2)+1] for x in range(200)])
seqc_rev = ''.join([self.csv_records[(x*2)+1][3] for x in range(200)])
self.assertEqual(seqh_rev, seqc_rev)
- tpl_fwd = [f['tpl'][x*2] for x in range(200)]
+ tpl_fwd = [g['tpl'][x*2] for x in range(200)]
self.assertEqual(tpl_fwd, range(1, 201))
f = h5py.File(self.h5_file)
for i_rec, rec in enumerate(self.csv_records):
- self.assertEqual(str(f['tpl'][i_rec]), self.csv_records[i_rec][1])
- self.assertEqual("%.3f"%f['ipdRatio'][i_rec],
+ self.assertEqual(str(g['tpl'][i_rec]), self.csv_records[i_rec][1])
+ self.assertEqual("%.3f"%g['ipdRatio'][i_rec],
self.csv_records[i_rec][8])
def test_csv_output(self):
diff --git a/test/test_tool_contract.py b/test/test_tool_contract.py
index 023d585..0f06e51 100755
--- a/test/test_tool_contract.py
+++ b/test/test_tool_contract.py
@@ -21,11 +21,6 @@ REF_DIR = "/pbi/dept/secondary/siv/references/Helicobacter_pylori_J99"
class Constants(object):
N_LINES_GFF = 338
- N_LINES_CSV = 13357
- INITIAL_LINES_CSV = """\
-refName,tpl,strand,base,score,tMean,tErr,modelPrediction,ipdRatio,coverage
-"gi|12057207|gb|AE001439.1|",1,0,A,10,2.387,0.464,1.710,1.396,29
-"gi|12057207|gb|AE001439.1|",1,1,T,1,0.492,0.075,0.602,0.817,57"""
INITIAL_LINES_GFF = """\
gi|12057207|gb|AE001439.1|\tkinModCall\tm6A\t35\t35\t187\t-\t.\tcoverage=118;context=TTTAAGGGCGTTTTATGCCTAAATTTAAAAAATGATGCTGT;IPDRatio=5.68;identificationQv=196
gi|12057207|gb|AE001439.1|\tkinModCall\tm4C\t60\t60\t49\t-\t.\tcoverage=112;context=AAAAAGCTCGCTCAAAAACCCTTGATTTAAGGGCGTTTTAT;IPDRatio=2.58;identificationQv=33
@@ -64,8 +59,9 @@ class TestIpdSummary(pbcommand.testkit.PbTestApp):
return "\n".join(out)
self.assertEqual(head2(gff_file, 3), Constants.INITIAL_LINES_GFF)
f = h5py.File(rtc.task.output_files[2])
- seqh_fwd = ''.join([f['base'][x*2] for x in range(5000)])
- seqh_rev = ''.join([f['base'][(x*2)+1] for x in range(5000)])
+ g = f[f.keys()[0]]
+ seqh_fwd = ''.join([g['base'][x*2] for x in range(5000)])
+ seqh_rev = ''.join([g['base'][(x*2)+1] for x in range(5000)])
self.assertEqual(len(seqh_fwd), 5000)
self.assertEqual(len(seqh_rev), 5000)
--
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