New upstream version 0.10.0 (cb923c31) · Commits · Debian Med / htseq

PKG-INFO

+7 −4

Original line number	Diff line number	Diff line
		Metadata-Version: 1.1
		Metadata-Version: 2.1
		Name: HTSeq
		Version: 0.9.1
		Version: 0.10.0
		Summary: A framework to process and analyze data from high-throughput sequencing (HTS) assays
		Home-page: https://github.com/simon-anders/htseq
		Author: Fabio Zanini
		Author-email: fabio.zanini@stanford.edu
		Author: Simon Anders
		Author-email: sanders@fs.tum.de
		Maintainer: Fabio Zanini
		Maintainer-email: fabio.zanini@stanford.edu
		License: GPL3
		Description:
		A framework to process and analyze data from high-throughput sequencing
		@@ -21,3 +23,4 @@ Classifier: Intended Audience :: Science/Research
		Classifier: License :: OSI Approved :: GNU General Public License (GPL)
		Classifier: Operating System :: POSIX
		Classifier: Programming Language :: Python
		Provides-Extra: htseq-qa

VERSION

+1 −1

Original line number	Diff line number	Diff line
		0.9.1
		0.10.0

python2/HTSeq/init.py

+746 −730

Original line number	Diff line number	Diff line
		@@ -3,7 +3,10 @@
		See htseq.readthedocs.io/en/master/index.html for documentation.
		"""

		import itertools, warnings, os, shlex
		import itertools
		import warnings
		import os
		import shlex

		try:
		from _HTSeq import *
		@@ -44,7 +47,7 @@ class FileOrSequence( object ):

		def __iter__(self):
		self.line_no = 1
		if isinstance( self.fos, str ):
		if isinstance(self.fos, basestring):
		if self.fos.lower().endswith((".gz", ".gzip")):
		lines = gzip.open(self.fos, 'rt')
		else:
		@@ -83,7 +86,6 @@ class FileOrSequence( object ):
		#########################

		class GenomicFeature(object):

		"""A genomic feature, i.e., an interval on a genome with metadata.

		At minimum, the following information should be provided by slots:
		@@ -144,6 +146,7 @@ class GenomicFeature( object ):
		_re_attr_main = re.compile("\s([^\s\=]+)[\s=]+(.)")
		_re_attr_empty = re.compile("^\s*$")


		def parse_GFF_attribute_string(attrStr, extra_return_first_value=False):
		"""Parses a GFF attribute string and returns it as a dictionary.

		@@ -158,10 +161,10 @@ def parse_GFF_attribute_string( attrStr, extra_return_first_value=False ):
		if _re_attr_empty.match(attr):
		continue
		if attr.count('"') not in (0, 2):
		raise ValueError, "The attribute string seems to contain mismatched quotes."
		raise ValueError("The attribute string seems to contain mismatched quotes.")
		mo = _re_attr_main.match(attr)
		if not mo:
		raise ValueError, "Failure parsing GFF attribute line"
		raise ValueError("Failure parsing GFF attribute line")
		val = mo.group(2)
		if val.startswith('"') and val.endswith('"'):
		val = val[1:-1]
		@@ -174,10 +177,11 @@ def parse_GFF_attribute_string( attrStr, extra_return_first_value=False ):
		else:
		return d


		_re_gff_meta_comment = re.compile("##\s(\S+)\s+(\S)")

		class GFF_Reader( FileOrSequence ):

		class GFF_Reader(FileOrSequence):
		"""Parse a GFF file

		Pass the constructor either a file name or an iterator of lines of a
		@@ -192,7 +196,6 @@ class GFF_Reader( FileOrSequence ):
		self.end_included = end_included
		self.metadata = {}


		def __iter__(self):
		for line in FileOrSequence.__iter__(self):
		if line == "\n":
		@@ -256,7 +259,6 @@ def make_feature_dict( feature_sequence ):
		return res



		#########################
		## GenomicArray
		#########################
		@@ -272,6 +274,7 @@ def read_chrom_lens( filename, delimiter="\t" ):

		_re_fasta_header_line = re.compile(r'>\s(\S+)\s(.*)')


		class FastaReader(FileOrSequence):
		"""A Fasta_Reader is associated with a FASTA file or an open connection
		to a file-like object with content in FASTA format.
		@@ -365,6 +368,7 @@ class FastaReader( FileOrSequence ):
		else:
		return ans[0].get_reverse_complement()


		class FastqReader(FileOrSequence):
		"""A Fastq object is associated with a FASTQ self.file. When an iterator
		is requested from the object, the FASTQ file is read.
		@@ -376,7 +380,7 @@ class FastqReader( FileOrSequence ):
		FileOrSequence.__init__(self, file_)
		self.qual_scale = qual_scale
		if qual_scale not in ("phred", "solexa", "solexa-old"):
		raise ValueError, "Illegal quality scale."
		raise ValueError("Illegal quality scale.")
		self.raw_iterator = raw_iterator

		def __iter__(self):
		@@ -388,7 +392,8 @@ class FastqReader( FileOrSequence ):
		qual = fin.next()
		if qual == "":
		if id1 != "":
		warnings.warn( "Number of lines in FASTQ file is not "
		warnings.warn(
		"Number of lines in FASTQ file is not "
		"a multiple of 4. Discarding the last, "
		"incomplete record")
		break
		@@ -412,6 +417,7 @@ class FastqReader( FileOrSequence ):
		self.qual_scale)
		yield s


		class BowtieReader(FileOrSequence):
		"""A BowtieFile object is associated with a Bowtie output file that
		contains short read alignments. It can generate an iterator of Alignment
		@@ -428,6 +434,7 @@ class BowtieReader( FileOrSequence ):
		RuntimeWarning)
		yield algnt


		def bundle_multiple_alignments(sequence_of_alignments):
		"""Some alignment programs, e.g., Bowtie, can output multiple alignments,
		i.e., the same read is reported consecutively with different alignments.
		@@ -537,6 +544,7 @@ class SolexaExportReader( FileOrSequence ):
		start + len(fields['read_seq']), strand)
		yield record


		class SAM_Reader(FileOrSequence):
		"""A SAM_Reader object is associated with a SAM file that
		contains short read alignments. It can generate an iterator of Alignment
		@@ -554,8 +562,8 @@ class SAM_Reader( FileOrSequence ):
		raise
		yield algnt

		class GenomicArrayOfSets( GenomicArray ):

		class GenomicArrayOfSets(GenomicArray):
		"""A GenomicArrayOfSets is a specialization of GenomicArray that allows to store
		sets of objects. On construction, the step vectors are initialized with empty sets.
		By using the 'add_value' method, objects can be added to intervals. If an object
		@@ -871,7 +879,7 @@ class VCF_Reader( FileOrSequence ):

		def meta_info(self, header_filename=None):
		ret = []
		if header_filename == None:
		if header_filename is None:
		the_iter = FileOrSequence.__iter__(self)
		else:
		the_iter = open(header_filename, "r")
		@@ -941,13 +949,15 @@ class WiggleReader( FileOrSequence ):
		pos = int(tmp[0])
		yield (GenomicInterval(chrom, pos, pos + span, '.'), float(tmp[1]))


		class BAM_Reader(object):

		def __init__( self, filename ):
		def __init__(self, filename, check_sq=True):
		global pysam
		self.filename = filename
		self.sf = None # This one is only used by __getitem__
		self.record_no = -1
		self.check_sq = check_sq
		try:
		import pysam
		except ImportError:
		@@ -955,7 +965,7 @@ class BAM_Reader( object ):
		raise

		def __iter__(self):
		sf = pysam.Samfile(self.filename, "rb")
		sf = pysam.Samfile(self.filename, "rb", check_sq=self.check_sq)
		self.record_no = 0
		for pa in sf:
		#yield SAM_Alignment.from_pysam_AlignedRead(pa, sf)
		@@ -963,7 +973,7 @@ class BAM_Reader( object ):
		self.record_no += 1

		def fetch(self, reference=None, start=None, end=None, region=None):
		sf = pysam.Samfile(self.filename, "rb")
		sf = pysam.Samfile(self.filename, "rb", check_sq=self.check_sq)
		self.record_no = 0
		try:
		for pa in sf.fetch(reference, start, end, region):
		@@ -986,17 +996,17 @@ class BAM_Reader( object ):

		def __getitem__(self, iv):
		if not isinstance(iv, GenomicInterval):
		raise TypeError, "Use a HTSeq.GenomicInterval to access regions within .bam-file!"
		raise TypeError("Use a HTSeq.GenomicInterval to access regions within .bam-file!")
		if self.sf is None:
		self.sf = pysam.Samfile( self.filename, "rb" )
		self.sf = pysam.Samfile(self.filename, "rb", check_sq=self.check_sq)
		# NOTE: pysam 0.9 has renames _hasIndex into has_index
		if (hasattr(self.sf, '_hasIndex') and (not self.sf._hasIndex())) or (not self.sf.has_index()):
		raise ValueError, "The .bam-file has no index, random-access is disabled!"
		raise ValueError("The .bam-file has no index, random-access is disabled!")
		for pa in self.sf.fetch(iv.chrom, iv.start+1, iv.end):
		yield SAM_Alignment.from_pysam_AlignedRead(pa, self.sf)

		def get_header_dict(self):
		sf = pysam.Samfile(self.filename, "rb")
		sf = pysam.Samfile(self.filename, "rb", check_sq=self.check_sq)
		return sf.header


		@@ -1014,7 +1024,14 @@ class BAM_Writer( object ):
		self.referencelengths = referencelengths
		self.text = text
		self.header = header
		self.sf = pysam.Samfile( self.filename, mode="wb", template = self.template, referencenames = self.referencenames, referencelengths = self.referencelengths, text = self.text, header = self.header )
		self.sf = pysam.Samfile(
		self.filename,
		mode="wb",
		template=self.template,
		referencenames=self.referencenames,
		referencelengths=self.referencelengths,
		text=self.text,
		header=self.header)

		@classmethod
		def from_BAM_Reader(cls, fn, br):
		@@ -1039,13 +1056,12 @@ class BED_Reader( FileOrSequence ):
		continue
		fields = line.split()
		if len(fields) < 3:
		raise ValueError, "BED file line contains less than 3 fields"
		raise ValueError("BED file line contains less than 3 fields")
		if len(fields) > 9:
		raise ValueError, "BED file line contains more than 9 fields"
		raise ValueError("BED file line contains more than 9 fields")
		iv = GenomicInterval(fields[0], int(fields[1]), int(fields[2]), fields[5] if len(fields) > 5 else ".")
		f = GenomicFeature(fields[3] if len(fields) > 3 else "unnamed", "BED line", iv)
		f.score = float(fields[4]) if len(fields) > 4 else None
		f.thick = GenomicInterval(iv.chrom, int(fields[6]), int(fields[7]), iv.strand) if len(fields) > 7 else None
		f.itemRgb = [int(a) for a in fields[8].split(",")] if len(fields) > 8 else None
		yield(f)

python2/HTSeq/_version.py

+1 −1

Original line number	Diff line number	Diff line
		__version__ = "0.9.1"
		No newline at end of file
		__version__ = "0.10.0"
		No newline at end of file

python2/HTSeq/scripts/count.py

+4 −0

Original line number	Diff line number	Diff line
		@@ -87,6 +87,7 @@ def count_reads_in_features(sam_filenames, gff_filename,
		i += 1
		if i % 100000 == 0 and not quiet:
		sys.stderr.write("%d GFF lines processed.\n" % i)
		sys.stderr.flush()
		except:
		sys.stderr.write(
		"Error occured when processing GFF file (%s):\n" %
		@@ -95,6 +96,7 @@ def count_reads_in_features(sam_filenames, gff_filename,

		if not quiet:
		sys.stderr.write("%d GFF lines processed.\n" % i)
		sys.stderr.flush()

		if len(counts) == 0:
		sys.stderr.write(
		@@ -156,6 +158,7 @@ def count_reads_in_features(sam_filenames, gff_filename,
		sys.stderr.write(
		"%d SAM alignment record%s processed.\n" %
		(i, "s" if not pe_mode else " pairs"))
		sys.stderr.flush()

		i += 1
		if not pe_mode:
		@@ -298,6 +301,7 @@ def count_reads_in_features(sam_filenames, gff_filename,
		sys.stderr.write(
		"%d SAM %s processed.\n" %
		(i, "alignments " if not pe_mode else "alignment pairs"))
		sys.stderr.flush()

		if samoutfile is not None:
		samoutfile.close()