[med-svn] [Git][med-team/htseq][master] 6 commits: New upstream version 2.0.2
Andreas Tille (@tille)
gitlab at salsa.debian.org
Fri Jan 20 21:24:57 GMT 2023
Andreas Tille pushed to branch master at Debian Med / htseq
Commits:
3eaeb299 by Andreas Tille at 2023-01-20T21:59:16+01:00
New upstream version 2.0.2
- - - - -
4435a4e8 by Andreas Tille at 2023-01-20T21:59:16+01:00
routine-update: New upstream version
- - - - -
281589ff by Andreas Tille at 2023-01-20T21:59:18+01:00
Update upstream source from tag 'upstream/2.0.2'
Update to upstream version '2.0.2'
with Debian dir 55967416496e01be18d3e863cd4be39a496a9f02
- - - - -
328267e0 by Andreas Tille at 2023-01-20T21:59:18+01:00
routine-update: Standards-Version: 4.6.2
- - - - -
1e528bf1 by Andreas Tille at 2023-01-20T21:59:21+01:00
Remove duplicate line from changelog.
Changes-By: lintian-brush
- - - - -
a256fbb3 by Andreas Tille at 2023-01-20T22:03:32+01:00
Upload to experimental
- - - - -
9 changed files:
- HTSeq/_version.py
- HTSeq/scripts/count_features/count_features_per_file.py
- + HTSeq/scripts/count_old.py
- PKG-INFO
- VERSION
- debian/changelog
- debian/control
- setup.py
- src/HTSeq/_HTSeq.pyx
Changes:
=====================================
HTSeq/_version.py
=====================================
@@ -1 +1 @@
-__version__ = "2.0.1"
\ No newline at end of file
+__version__ = "2.0.2"
\ No newline at end of file
=====================================
HTSeq/scripts/count_features/count_features_per_file.py
=====================================
@@ -124,8 +124,7 @@ def count_reads_single_file(
read_stats.print_progress()
read_stats.add_num_reads_processed()
- # todo can move this into a function, but not necessary.
- # this basically try to get the interval/read sequence.
+ # get the interval/read sequence.
if not read_io_obj.pe_mode:
skip_read = _assess_non_pe_read(
read_sequence=r,
@@ -141,10 +140,11 @@ def count_reads_single_file(
iv_seq = _get_iv_seq_non_pe_read(com, r, stranded)
else:
- # todo these assessor used to be at the bottom, after creating
- # the iv_seq and checking whether the first element of the
- # paired end is aligned. Kind of nuts really as it wastes time?
- # need more testing though
+ # NOTE: the logic here is a little arbitrary and might benefit
+ # from an optional arg. If the reads are paired-end but one of
+ # the two is missing, ATM we rely on the other one for info,
+ # however the data is technically inconsistent and we might
+ # want to let the user choose.
skip_read = _assess_pe_read(
minaqual,
multimapped_mode,
@@ -341,7 +341,12 @@ def _assess_pe_read(
-------
"""
- if (read_sequence[0] is None) or not (read_sequence[0].aligned):
+ # NOTE: Sometimes read1 is None or not aligned but read2 is fine, in that
+ # case we should not exclude the entire pair but rather use the interval
+ # of the second read
+ read1_miss = (read_sequence[0] is None) or (not read_sequence[0].aligned)
+ read2_miss = (read_sequence[1] is None) or (not read_sequence[1].aligned)
+ if read1_miss and read2_miss:
read_stats.add_not_aligned_read(read_sequence=read_sequence)
return True
=====================================
HTSeq/scripts/count_old.py
=====================================
@@ -0,0 +1,688 @@
+# DEPRECATE AND REMOVE ME IN THE FUTURE
+import sys
+import argparse
+import operator
+import itertools
+import warnings
+import traceback
+import os.path
+import multiprocessing
+import numpy as np
+import pysam
+import random
+
+import HTSeq
+from HTSeq.scripts.utils import (
+ UnknownChrom,
+ my_showwarning,
+ invert_strand,
+ _write_output,
+)
+
+
+def count_reads_single_file(
+ isam,
+ sam_filename,
+ features,
+ feature_attr,
+ order,
+ max_buffer_size,
+ stranded,
+ overlap_mode,
+ multimapped_mode,
+ secondary_alignment_mode,
+ supplementary_alignment_mode,
+ feature_type,
+ id_attribute,
+ additional_attributes,
+ quiet,
+ minaqual,
+ samout_format,
+ samout_filename,
+ ):
+
+ def write_to_samout(r, assignment, samoutfile, template=None):
+ if samoutfile is None:
+ return
+ if not pe_mode:
+ r = (r,)
+ for read in r:
+ if read is not None:
+ read.optional_fields.append(('XF', assignment))
+ if template is not None:
+ samoutfile.write(read.to_pysam_AlignedSegment(template))
+ elif samout_format in ('SAM', 'sam'):
+ samoutfile.write(read.get_sam_line() + "\n")
+ else:
+ raise ValueError(
+ 'BAM/SAM output: no template and not a test SAM file',
+ )
+
+ try:
+ if sam_filename == "-":
+ read_seq_file = HTSeq.BAM_Reader(sys.stdin)
+ else:
+ read_seq_file = HTSeq.BAM_Reader(sam_filename)
+
+ # Get template for output BAM/SAM if possible
+ if samout_filename is None:
+ template = None
+ samoutfile = None
+ elif samout_format in ('bam', 'BAM'):
+ template = read_seq_file.get_template()
+ samoutfile = pysam.AlignmentFile(
+ samout_filename, 'wb',
+ template=template,
+ )
+ elif (samout_format in ('sam', 'SAM')) and \
+ hasattr(read_seq_file, 'get_template'):
+ template = read_seq_file.get_template()
+ samoutfile = pysam.AlignmentFile(
+ samout_filename, 'w',
+ template=template,
+ )
+ else:
+ template = None
+ samoutfile = open(samout_filename, 'w')
+
+ read_seq_iter = iter(read_seq_file)
+ # Catch empty BAM files
+ try:
+ first_read = next(read_seq_iter)
+ pe_mode = first_read.paired_end
+ # FIXME: catchall can hide subtle bugs
+ except:
+ first_read = None
+ pe_mode = False
+ if first_read is not None:
+ read_seq = itertools.chain([first_read], read_seq_iter)
+ else:
+ read_seq = []
+ except:
+ sys.stderr.write(
+ "Error occured when reading beginning of SAM/BAM file.\n")
+ raise
+
+ # CIGAR match characters (including alignment match, sequence match, and
+ # sequence mismatch
+ com = ('M', '=', 'X')
+ counts = {key: 0 for key in feature_attr}
+
+ try:
+ if pe_mode:
+ if ((supplementary_alignment_mode == 'ignore') and
+ (secondary_alignment_mode == 'ignore')):
+ primary_only = True
+ else:
+ primary_only = False
+ if order == "name":
+ read_seq = HTSeq.pair_SAM_alignments(
+ read_seq,
+ primary_only=primary_only)
+ elif order == "pos":
+ read_seq = HTSeq.pair_SAM_alignments_with_buffer(
+ read_seq,
+ max_buffer_size=max_buffer_size,
+ primary_only=primary_only)
+ else:
+ raise ValueError("Illegal order specified.")
+ empty = 0
+ ambiguous = 0
+ notaligned = 0
+ lowqual = 0
+ nonunique = 0
+ i = 0
+ for r in read_seq:
+ if i > 0 and i % 100000 == 0 and not quiet:
+ sys.stderr.write(
+ "%d alignment record%s processed.\n" %
+ (i, "s" if not pe_mode else " pairs"))
+ sys.stderr.flush()
+
+ i += 1
+ if not pe_mode:
+ if not r.aligned:
+ notaligned += 1
+ write_to_samout(
+ r, "__not_aligned", samoutfile,
+ template)
+ continue
+ if ((secondary_alignment_mode == 'ignore') and
+ r.not_primary_alignment):
+ continue
+ if ((supplementary_alignment_mode == 'ignore') and
+ r.supplementary):
+ continue
+ try:
+ if r.optional_field("NH") > 1:
+ nonunique += 1
+ write_to_samout(
+ r,
+ "__alignment_not_unique",
+ samoutfile,
+ template)
+ if multimapped_mode == 'none':
+ continue
+ except KeyError:
+ pass
+ if r.aQual < minaqual:
+ lowqual += 1
+ write_to_samout(
+ r, "__too_low_aQual", samoutfile,
+ template)
+ continue
+ if stranded != "reverse":
+ iv_seq = (co.ref_iv for co in r.cigar if co.type in com
+ and co.size > 0)
+ else:
+ iv_seq = (invert_strand(co.ref_iv)
+ for co in r.cigar if (co.type in com and
+ co.size > 0))
+ else:
+ if r[0] is not None and r[0].aligned:
+ if stranded != "reverse":
+ iv_seq = (co.ref_iv for co in r[0].cigar
+ if co.type in com and co.size > 0)
+ else:
+ iv_seq = (invert_strand(co.ref_iv) for co in r[0].cigar
+ if co.type in com and co.size > 0)
+ else:
+ iv_seq = tuple()
+ if r[1] is not None and r[1].aligned:
+ if stranded != "reverse":
+ iv_seq = itertools.chain(
+ iv_seq,
+ (invert_strand(co.ref_iv) for co in r[1].cigar
+ if co.type in com and co.size > 0))
+ else:
+ iv_seq = itertools.chain(
+ iv_seq,
+ (co.ref_iv for co in r[1].cigar
+ if co.type in com and co.size > 0))
+ else:
+ if (r[0] is None) or not (r[0].aligned):
+ write_to_samout(
+ r, "__not_aligned", samoutfile,
+ template)
+ notaligned += 1
+ continue
+ if secondary_alignment_mode == 'ignore':
+ if (r[0] is not None) and r[0].not_primary_alignment:
+ continue
+ elif (r[1] is not None) and r[1].not_primary_alignment:
+ continue
+ if supplementary_alignment_mode == 'ignore':
+ if (r[0] is not None) and r[0].supplementary:
+ continue
+ elif (r[1] is not None) and r[1].supplementary:
+ continue
+ try:
+ if ((r[0] is not None and r[0].optional_field("NH") > 1) or
+ (r[1] is not None and r[1].optional_field("NH") > 1)):
+ nonunique += 1
+ write_to_samout(
+ r, "__alignment_not_unique", samoutfile,
+ template)
+ if multimapped_mode == 'none':
+ continue
+ except KeyError:
+ pass
+ if ((r[0] and r[0].aQual < minaqual) or
+ (r[1] and r[1].aQual < minaqual)):
+ lowqual += 1
+ write_to_samout(
+ r, "__too_low_aQual", samoutfile,
+ template)
+ continue
+
+ try:
+ if overlap_mode == "union":
+ fs = set()
+ for iv in iv_seq:
+ if iv.chrom not in features.chrom_vectors:
+ raise UnknownChrom
+ for iv2, fs2 in features[iv].steps():
+ fs = fs.union(fs2)
+ elif overlap_mode in ("intersection-strict",
+ "intersection-nonempty"):
+ fs = None
+ for iv in iv_seq:
+ if iv.chrom not in features.chrom_vectors:
+ raise UnknownChrom
+ for iv2, fs2 in features[iv].steps():
+ if ((len(fs2) > 0) or
+ (overlap_mode == "intersection-strict")):
+ if fs is None:
+ fs = fs2.copy()
+ else:
+ fs = fs.intersection(fs2)
+ else:
+ sys.exit("Illegal overlap mode.")
+
+ if fs is None or len(fs) == 0:
+ write_to_samout(
+ r, "__no_feature", samoutfile,
+ template)
+ empty += 1
+ elif len(fs) > 1:
+ write_to_samout(
+ r, "__ambiguous[" + '+'.join(sorted(fs)) + "]",
+ samoutfile,
+ template)
+ ambiguous += 1
+ else:
+ write_to_samout(
+ r, list(fs)[0], samoutfile,
+ template)
+
+ if fs is not None and len(fs) > 0:
+ if multimapped_mode == 'none':
+ if len(fs) == 1:
+ counts[list(fs)[0]] += 1
+ elif multimapped_mode == 'all':
+ for fsi in list(fs):
+ counts[fsi] += 1
+ elif multimapped_mode == 'fraction':
+ for fsi in list(fs):
+ counts[fsi] += 1.0 / len(fs)
+ elif multimapped_mode == 'random':
+ fsi = random.choice(list(fs))
+ counts[fsi] += 1
+ else:
+ sys.exit("Illegal multimap mode.")
+
+ except UnknownChrom:
+ write_to_samout(
+ r, "__no_feature", samoutfile,
+ template)
+ empty += 1
+
+ except:
+ sys.stderr.write(
+ "Error occured when processing input (%s):\n" %
+ (read_seq_file.get_line_number_string()))
+ raise
+
+ if not quiet:
+ sys.stderr.write(
+ "%d %s processed.\n" %
+ (i, "alignments " if not pe_mode else "alignment pairs"))
+ sys.stderr.flush()
+
+ if samoutfile is not None:
+ samoutfile.close()
+
+ return {
+ 'isam': isam,
+ 'counts': counts,
+ 'empty': empty,
+ 'ambiguous': ambiguous,
+ 'lowqual': lowqual,
+ 'notaligned': notaligned,
+ 'nonunique': nonunique,
+ }
+
+
+def count_reads_in_features(
+ sam_filenames,
+ gff_filename,
+ order,
+ max_buffer_size,
+ stranded,
+ overlap_mode,
+ multimapped_mode,
+ secondary_alignment_mode,
+ supplementary_alignment_mode,
+ feature_type,
+ id_attribute,
+ additional_attributes,
+ add_chromosome_info,
+ quiet,
+ minaqual,
+ samouts,
+ samout_format,
+ output_delimiter,
+ output_filename,
+ output_append,
+ nprocesses,
+ feature_query,
+ counts_output_sparse,
+ ):
+ '''Count reads in features, parallelizing by file'''
+
+ # Never use more CPUs than files
+ nprocesses = min(nprocesses, len(sam_filenames))
+
+ if samouts != []:
+ if len(samouts) != len(sam_filenames):
+ raise ValueError(
+ 'Select the same number of input and output files')
+ # Try to open samout files early in case any of them has issues
+ if samout_format in ('SAM', 'sam'):
+ for samout in samouts:
+ with open(samout, 'w'):
+ pass
+ else:
+ # We don't have a template if the input is stdin
+ if (len(sam_filenames) != 1) or (sam_filenames[0] != '-'):
+ for sam_filename, samout in zip(sam_filenames, samouts):
+ with pysam.AlignmentFile(sam_filename, 'r') as sf:
+ with pysam.AlignmentFile(samout, 'w', template=sf):
+ pass
+ else:
+ samouts = [None for x in sam_filenames]
+
+ # Try to open samfiles to fail early in case any of them is not there
+ if (len(sam_filenames) != 1) or (sam_filenames[0] != '-'):
+ for sam_filename in sam_filenames:
+ with pysam.AlignmentFile(sam_filename, 'r') as sf:
+ pass
+
+ # Deal with custom id_attribute lists. This is never shorter than 1 because
+ # gene_id is the default. However, if the option was called at least once,
+ # that should _override_ the default, which means skipping the first
+ # element (i.e., gene_id).
+ if len(id_attribute) > 1:
+ del id_attribute[0]
+
+ # Prepare features
+ gff = HTSeq.GFF_Reader(gff_filename)
+ feature_scan = HTSeq.make_feature_genomicarrayofsets(
+ gff,
+ id_attribute,
+ feature_type=feature_type,
+ feature_query=feature_query,
+ additional_attributes=additional_attributes,
+ stranded=stranded != 'no',
+ verbose=not quiet,
+ add_chromosome_info=add_chromosome_info,
+ )
+ features = feature_scan['features']
+ attributes = feature_scan['attributes']
+ feature_attr = sorted(attributes.keys())
+
+ if len(feature_attr) == 0:
+ sys.stderr.write(
+ "Warning: No features of type '%s' found.\n" % feature_type)
+
+ # Prepare arguments for counting function
+ args = []
+ for isam, (sam_filename, samout_filename) in enumerate(zip(sam_filenames, samouts)):
+ args.append((
+ isam,
+ sam_filename,
+ features,
+ feature_attr,
+ order,
+ max_buffer_size,
+ stranded,
+ overlap_mode,
+ multimapped_mode,
+ secondary_alignment_mode,
+ supplementary_alignment_mode,
+ feature_type,
+ id_attribute,
+ additional_attributes,
+ quiet,
+ minaqual,
+ samout_format,
+ samout_filename,
+ ))
+
+ # Count reads in parallel
+ if nprocesses > 1:
+ with multiprocessing.Pool(nprocesses) as pool:
+ results = pool.starmap(count_reads_single_file, args)
+ results.sort(key=operator.itemgetter('isam'))
+ else:
+ results = list(itertools.starmap(count_reads_single_file, args))
+
+ # Merge and write output
+ _write_output(
+ results,
+ sam_filenames,
+ attributes,
+ additional_attributes,
+ output_filename,
+ output_delimiter,
+ output_append,
+ sparse=counts_output_sparse,
+ dtype=np.float32,
+ )
+
+
+def main():
+
+ pa = argparse.ArgumentParser(
+ usage="%(prog)s [options] alignment_file gff_file",
+ description="This script takes one or more alignment files in SAM/BAM " +
+ "format and a feature file in GFF format and calculates for each feature " +
+ "the number of reads mapping to it. See " +
+ "http://htseq.readthedocs.io/en/master/count.html for details.",
+ epilog="Written by Simon Anders (sanders at fs.tum.de), " +
+ "European Molecular Biology Laboratory (EMBL) and Fabio Zanini " +
+ "(fabio.zanini at unsw.edu.au), UNSW Sydney. (c) 2010-2020. " +
+ "Released under the terms of the GNU General Public License v3. " +
+ "Part of the 'HTSeq' framework, version %s." % HTSeq.__version__)
+
+ pa.add_argument(
+ "--version", action="store_true",
+ help='Show software version and exit')
+ args, argv = pa.parse_known_args()
+ # Version is the only case where the BAM and GTF files are optional
+ if args.version:
+ print(HTSeq.__version__)
+ sys.exit()
+
+ pa.add_argument(
+ "samfilenames", nargs='+', type=str,
+ help="Path to the SAM/BAM files containing the mapped reads. " +
+ "If '-' is selected, read from standard input")
+
+ pa.add_argument(
+ "featuresfilename", type=str,
+ help="Path to the GTF file containing the features")
+
+ pa.add_argument(
+ "-f", "--format", dest="samtype",
+ choices=("sam", "bam", "auto"), default="auto",
+ help="Type of <alignment_file> data. DEPRECATED: " +
+ "file format is detected automatically. This option is ignored.")
+
+ pa.add_argument(
+ "-r", "--order", dest="order",
+ choices=("pos", "name"), default="name",
+ help="'pos' or 'name'. Sorting order of <alignment_file> (default: name). Paired-end sequencing " +
+ "data must be sorted either by position or by read name, and the sorting order " +
+ "must be specified. Ignored for single-end data.")
+
+ pa.add_argument(
+ "--max-reads-in-buffer", dest="max_buffer_size", type=int,
+ default=30000000,
+ help="When <alignment_file> is paired end sorted by position, " +
+ "allow only so many reads to stay in memory until the mates are " +
+ "found (raising this number will use more memory). Has no effect " +
+ "for single end or paired end sorted by name")
+
+ pa.add_argument(
+ "-s", "--stranded", dest="stranded",
+ choices=("yes", "no", "reverse"), default="yes",
+ help="Whether the data is from a strand-specific assay. Specify 'yes', " +
+ "'no', or 'reverse' (default: yes). " +
+ "'reverse' means 'yes' with reversed strand interpretation")
+
+ pa.add_argument(
+ "-a", "--minaqual", type=int, dest="minaqual",
+ default=10,
+ help="Skip all reads with MAPQ alignment quality lower than the given " +
+ "minimum value (default: 10). MAPQ is the 5th column of a SAM/BAM " +
+ "file and its usage depends on the software used to map the reads.")
+
+ pa.add_argument(
+ "-t", "--type", type=str, dest="featuretype",
+ default="exon",
+ help="Feature type (3rd column in GTF file) to be used, " +
+ "all features of other type are ignored (default, suitable for Ensembl " +
+ "GTF files: exon)")
+
+ pa.add_argument(
+ "-i", "--idattr", type=str, dest="idattr",
+ action='append',
+ default=["gene_id"],
+ help="GTF attribute to be used as feature ID (default, " +
+ "suitable for Ensembl GTF files: gene_id). All feature of the " +
+ "right type (see -t option) within the same GTF attribute will " +
+ "be added together. The typical way of using this option is to " +
+ "count all exonic reads from each gene and add the exons " +
+ "but other uses are possible as well. You can call this option " +
+ "multiple times: in that case, the combination of all attributes " +
+ "separated by colons (:) will be used as a unique identifier, " +
+ "e.g. for exons you might use -i gene_id -i exon_number.")
+
+ pa.add_argument(
+ "--additional-attr", type=str,
+ action='append',
+ default=[],
+ help="Additional feature attributes (default: none, " +
+ "suitable for Ensembl GTF files: gene_name). Use multiple times " +
+ "for more than one additional attribute. These attributes are " +
+ "only used as annotations in the output, while the determination " +
+ "of how the counts are added together is done based on option -i.")
+
+ pa.add_argument(
+ "--add-chromosome-info", action='store_true',
+ help="Store information about the chromosome of each feature as " +
+ "an additional attribute (e.g. colunm in the TSV output file).",
+ )
+
+ pa.add_argument(
+ "-m", "--mode", dest="mode",
+ choices=("union", "intersection-strict", "intersection-nonempty"),
+ default="union",
+ help="Mode to handle reads overlapping more than one feature " +
+ "(choices: union, intersection-strict, intersection-nonempty; default: union)")
+
+ pa.add_argument(
+ "--nonunique", dest="nonunique", type=str,
+ choices=("none", "all", "fraction", "random"), default="none",
+ help="Whether and how to score reads that are not uniquely aligned " +
+ "or ambiguously assigned to features " +
+ "(choices: none, all, fraction, random; default: none)")
+
+ pa.add_argument(
+ "--secondary-alignments", dest="secondary_alignments", type=str,
+ choices=("score", "ignore"), default="ignore",
+ help="Whether to score secondary alignments (0x100 flag)")
+
+ pa.add_argument(
+ "--supplementary-alignments", dest="supplementary_alignments", type=str,
+ choices=("score", "ignore"), default="ignore",
+ help="Whether to score supplementary alignments (0x800 flag)")
+
+ pa.add_argument(
+ "-o", "--samout", type=str, dest="samouts",
+ action='append',
+ default=[],
+ help="Write out all SAM alignment records into " +
+ "SAM/BAM files (one per input file needed), annotating each line " +
+ "with its feature assignment (as an optional field with tag 'XF')" +
+ ". See the -p option to use BAM instead of SAM.")
+
+ pa.add_argument(
+ "-p", '--samout-format', type=str, dest='samout_format',
+ choices=('SAM', 'BAM', 'sam', 'bam'), default='SAM',
+ help="Format to use with the --samout option."
+ )
+
+ pa.add_argument(
+ "-d", '--delimiter', type=str, dest='output_delimiter',
+ default='\t',
+ help="Column delimiter in output (default: TAB)."
+ )
+ pa.add_argument(
+ "-c", '--counts_output', type=str, dest='output_filename',
+ default='',
+ help="Filename to output the counts to instead of stdout."
+ )
+
+ pa.add_argument(
+ "--counts-output-sparse", action='store_true',
+ help="Store the counts as a sparse matrix (mtx, h5ad, loom)."
+ )
+
+ pa.add_argument(
+ '--append-output', action='store_true', dest='output_append',
+ help='Append counts output to an existing file instead of ' +
+ 'creating a new one. This option is useful if you have ' +
+ 'already creates a TSV/CSV/similar file with a header for your ' +
+ 'samples (with additional columns for the feature name and any ' +
+ 'additionl attributes) and want to fill in the rest of the file.'
+ )
+
+ pa.add_argument(
+ "-n", '--nprocesses', type=int, dest='nprocesses',
+ default=1,
+ help="Number of parallel CPU processes to use (default: 1). " +
+ "This option is useful to process several input files at once. " +
+ "Each file will use only 1 CPU. It is possible, of course, to " +
+ "split a very large input SAM/BAM files into smaller chunks " +
+ "upstream to make use of this option."
+ )
+
+ pa.add_argument(
+ '--feature-query', type=str, dest='feature_query',
+ default=None,
+ help='Restrict to features descibed in this expression. Currently ' +
+ 'supports a single kind of expression: attribute == "one attr" to ' +
+ 'restrict the GFF to a single gene or transcript, e.g. ' +
+ '--feature-query \'gene_name == "ACTB"\' - notice the single ' +
+ 'quotes around the argument of this option and the double ' +
+ 'quotes around the gene name. Broader queries might become ' +
+ 'available in the future.',
+ )
+
+ pa.add_argument(
+ "-q", "--quiet", action="store_true", dest="quiet",
+ help="Suppress progress report") # and warnings" )
+
+ args = pa.parse_args()
+
+ warnings.showwarning = my_showwarning
+ try:
+ count_reads_in_features(
+ args.samfilenames,
+ args.featuresfilename,
+ args.order,
+ args.max_buffer_size,
+ args.stranded,
+ args.mode,
+ args.nonunique,
+ args.secondary_alignments,
+ args.supplementary_alignments,
+ args.featuretype,
+ args.idattr,
+ args.additional_attr,
+ args.add_chromosome_info,
+ args.quiet,
+ args.minaqual,
+ args.samouts,
+ args.samout_format,
+ args.output_delimiter,
+ args.output_filename,
+ args.output_append,
+ args.nprocesses,
+ args.feature_query,
+ args.counts_output_sparse,
+ )
+ except:
+ sys.stderr.write(" %s\n" % str(sys.exc_info()[1]))
+ sys.stderr.write(" [Exception type: %s, raised in %s:%d]\n" %
+ (sys.exc_info()[1].__class__.__name__,
+ os.path.basename(traceback.extract_tb(
+ sys.exc_info()[2])[-1][0]),
+ traceback.extract_tb(sys.exc_info()[2])[-1][1]))
+ sys.exit(1)
+
+
+if __name__ == "__main__":
+ main()
=====================================
PKG-INFO
=====================================
@@ -1,6 +1,6 @@
Metadata-Version: 2.1
Name: HTSeq
-Version: 2.0.1
+Version: 2.0.2
Summary: A framework to process and analyze data from high-throughput sequencing (HTS) assays
Home-page: https://github.com/htseq
Author: Simon Anders, Fabio Zanini
@@ -8,7 +8,6 @@ Author-email: fabio.zanini at unsw.edu.au
Maintainer: Fabio Zanini
Maintainer-email: fabio.zanini at unsw.edu.au
License: GPL3
-Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Intended Audience :: Developers
@@ -122,5 +121,3 @@ A virtual environment is created in the `.venv` folder and `HTSeq` is installed
- 2021-: Givanna Putri ([ghar1821](https://github.com/ghar1821))
- 2016-: Fabio Zanini ([iosonofabio](https://github.com/iosonofabio))@ https://fabilab.org
- 2010-2015: Simon Anders ([simon-anders](https://github.com/simon-anders)), Wolfgang Huber
-
-
=====================================
VERSION
=====================================
@@ -1 +1 @@
-2.0.1
+2.0.2
=====================================
debian/changelog
=====================================
@@ -1,10 +1,9 @@
-htseq (2.0.1-1) UNRELEASED; urgency=medium
+htseq (2.0.2-1) experimental; urgency=medium
* New upstream version
- * Standards-Version: 4.6.1 (routine-update)
- TODO: Build time test error in connection with checking pysam version
+ * Standards-Version: 4.6.2 (routine-update)
- -- Andreas Tille <tille at debian.org> Wed, 29 Jun 2022 17:33:38 +0200
+ -- Andreas Tille <tille at debian.org> Fri, 20 Jan 2023 21:59:16 +0100
htseq (1.99.2-1) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -16,7 +16,7 @@ Build-Depends: 2to3,
python3-pysam,
swig,
cython3
-Standards-Version: 4.6.1
+Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/htseq
Vcs-Git: https://salsa.debian.org/med-team/htseq.git
Homepage: https://www-huber.embl.de/users/anders/HTSeq/doc/overview.html
=====================================
setup.py
=====================================
@@ -21,6 +21,7 @@ def update_version():
output = output.decode().strip('\n')
if output.startswith('release_'):
version = output.split('_')[1]
+ print('VERSION updated: '+version)
except:
pass
=====================================
src/HTSeq/_HTSeq.pyx
=====================================
@@ -790,6 +790,13 @@ cdef class GenomicArray(object):
def __reduce__(self):
return (_GenomicArray_unpickle, (self.stranded, self.typecode, self.chrom_vectors))
+ def __contains__(self, iv):
+ '''Check if the GenomicArray contains a certain interval
+
+ TODO: this is not implemented yet and will throw NotImplementedError.
+ '''
+ raise NotImplementedError
+
def write_bedgraph_file(
self,
file_or_filename,
View it on GitLab: https://salsa.debian.org/med-team/htseq/-/compare/02d6278c4469ef16c7c78b6a9f4b2510d12539bd...a256fbb3df6c5f34a1bab40fc22ddb59d6f4b06b
--
View it on GitLab: https://salsa.debian.org/med-team/htseq/-/compare/02d6278c4469ef16c7c78b6a9f4b2510d12539bd...a256fbb3df6c5f34a1bab40fc22ddb59d6f4b06b
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20230120/5a9bad46/attachment-0001.htm>
More information about the debian-med-commit
mailing list