New upstream version 0.5.7 (739f7379) · Commits · Debian Med / python-pyfaidx

.travis.yml

+0 −2

Original line number	Diff line number	Diff line
		@@ -7,9 +7,7 @@ python:
		- '3.6'
		- '3.5'
		- '3.4'
		- '3.3'
		- '2.7'
		- '2.6'
		- 'pypy'
		- 'pypy3'
		install:

README.rst

+4 −3

Original line number	Diff line number	Diff line
		\|Travis\| \|PyPI\| \|Landscape\| \|Coverage\| \|Depsy\| \|Appveyor\|
		\|Travis\| \|PyPI\| \|Coverage\| \|Depsy\|

		Description
		-----------
		@@ -54,7 +54,8 @@ Acts like a dictionary.

		.. code:: python

		>>> genes.keys() ('AB821309.1', 'KF435150.1', 'KF435149.1', 'NR_104216.1', 'NR_104215.1', 'NR_104212.1', 'NM_001282545.1', 'NM_001282543.1', 'NM_000465.3', 'NM_001282549.1', 'NM_001282548.1', 'XM_005249645.1', 'XM_005249644.1', 'XM_005249643.1', 'XM_005249642.1', 'XM_005265508.1', 'XM_005265507.1', 'XR_241081.1', 'XR_241080.1', 'XR_241079.1')
		>>> genes.keys()
		('AB821309.1', 'KF435150.1', 'KF435149.1', 'NR_104216.1', 'NR_104215.1', 'NR_104212.1', 'NM_001282545.1', 'NM_001282543.1', 'NM_000465.3', 'NM_001282549.1', 'NM_001282548.1', 'XM_005249645.1', 'XM_005249644.1', 'XM_005249643.1', 'XM_005249642.1', 'XM_005265508.1', 'XM_005265507.1', 'XR_241081.1', 'XR_241080.1', 'XR_241079.1')

		>>> genes['NM_001282543.1'][200:230]
		>NM_001282543.1:201-230
		@@ -544,7 +545,7 @@ Support for compressed FASTA
		----------------------------

		``pyfaidx`` can create and read ``.fai`` indices for FASTA files that have
		been compressed using the `bgzip <http://www.htslib.org/doc/tabix.html>`_
		been compressed using the `bgzip <https://www.htslib.org/doc/bgzip.html>`_
		tool from `samtools <http://www.htslib.org/>`_. ``bgzip`` writes compressed
		data in a ``BGZF`` format. ``BGZF`` is ``gzip`` compatible, consisting of
		multiple concatenated ``gzip`` blocks, each with an additional ``gzip``

pyfaidx/init.py

+41 −18

Original line number	Diff line number	Diff line
		@@ -25,7 +25,7 @@ if sys.version_info > (3, ):

		dna_bases = re.compile(r'([ACTGNactgnYRWSKMDVHBXyrwskmdvhbx]+)')

		__version__ = '0.5.5.2'
		__version__ = '0.5.7'


		class KeyFunctionError(ValueError):
		@@ -123,7 +123,7 @@ class Sequence(object):
		>chr1
		AC
		"""
		if self.start is None or self.end is None:
		if self.start is None or self.end is None or len(self.seq) == 0:
		correction_factor = 0
		elif len(
		self.seq
		@@ -461,7 +461,7 @@ class Faidx(object):
		rname, rlen, offset, lenc, lenb = line.split('\t')
		rlen, offset, lenc, lenb = map(int,
		(rlen, offset, lenc, lenb))
		newlines = int(ceil(rlen / lenc) * (lenb - lenc))
		newlines = int(ceil(rlen / lenc) * (lenb - lenc)) if lenc else 0
		bend = offset + newlines + rlen
		rec = IndexRecord(rlen, offset, lenc, lenb, bend,
		prev_bend)
		@@ -508,8 +508,8 @@ class Faidx(object):
		rname = None # reference sequence name
		offset = 0 # binary offset of end of current line
		rlen = 0 # reference character length
		blen = None # binary line length (includes newline)
		clen = None # character line length
		blen = 0 # binary line length (includes newline)
		clen = 0 # character line length
		bad_lines = [] # lines > \|\| < than blen
		thisoffset = offset
		valid_entry = False
		@@ -535,9 +535,9 @@ class Faidx(object):
		"Inconsistent line found in >{0} at "
		"line {1:n}.".format(
		rname, bad_lines[0][0] + 1))
		blen = None
		blen = 0
		rlen = 0
		clen = None
		clen = 0
		bad_lines = []
		try: # must catch empty deflines (actually these might be okay: https://github.com/samtools/htslib/pull/258)
		rname = line.rstrip('\n\r')[1:].split()[
		@@ -648,8 +648,8 @@ class Faidx(object):

		# Calculate offset (https://github.com/samtools/htslib/blob/20238f354894775ed22156cdd077bc0d544fa933/faidx.c#L398)
		newlines_before = int(
		(start0 - 1) / i.lenc * (i.lenb - i.lenc)) if start0 > 0 else 0
		newlines_to_end = int(end / i.lenc * (i.lenb - i.lenc))
		(start0 - 1) / i.lenc * (i.lenb - i.lenc)) if start0 > 0 and i.lenc else 0
		newlines_to_end = int(end / i.lenc * (i.lenb - i.lenc)) if i.lenc else 0
		newlines_inside = newlines_to_end - newlines_before
		seq_blen = newlines_inside + seq_len
		bstart = i.offset + newlines_before + start0
		@@ -669,12 +669,15 @@ class Faidx(object):
		else:
		self.file.seek(bstart)

		# If the requested sequence exceeds len(FastaRecord), return as much as possible
		if bstart + seq_blen > i.bend and not self.strict_bounds:
		seq_blen = i.bend - bstart

		# Otherwise it should be safe to read the sequence
		if seq_blen > 0:
		seq = self.file.read(seq_blen).decode()
		elif seq_blen <= 0 and not self.strict_bounds:
		# If the requested sequence is negative, we will pad the empty string with default_seq.
		# This was changed to support #155 with strict_bounds=True.
		elif seq_blen <= 0:
		seq = ''

		if not internals:
		@@ -994,13 +997,9 @@ class Fasta(object):
		sequence_always_upper=sequence_always_upper,
		rebuild=rebuild,
		build_index=build_index)
		self.keys = self.faidx.index.keys
		if not self.mutable:
		self.records = dict(
		[(rname, FastaRecord(rname, self)) for rname in self.keys()])
		elif self.mutable:
		self.records = dict([(rname, MutableFastaRecord(rname, self))
		for rname in self.keys()])

		_record_constructor = MutableFastaRecord if self.mutable else FastaRecord
		self.records = OrderedDict([(rname, _record_constructor(rname, self)) for rname in self.faidx.index.keys()])

		def __contains__(self, rname):
		"""Return True if genome contains record."""
		@@ -1057,6 +1056,15 @@ class Fasta(object):
		# len(Sequence.seq) != end - start
		return Sequence(name=name, seq=seq, start=None, end=None)

		def keys(self):
		return self.records.keys()

		def values(self):
		return self.records.values()

		def items(self):
		return self.records.items()

		def close(self):
		self.__exit__()

		@@ -1259,6 +1267,21 @@ def check_bad_lines(rname, bad_lines, i):
		"Please report this issue at https://github.com/mdshw5/pyfaidx/issues " + \
		str(bad_lines))

		def get_valid_filename(s):
		"""
		From https://github.com/django/django/blob/efc3e32d6d7fb9bb41be73b80c8607b653c1fbd6/django/utils/text.py#L222-L232
		Return the given string converted to a string that can be used for a clean
		filename. Remove leading and trailing spaces; convert other spaces to
		underscores; and remove anything that is not an alphanumeric, dash,
		underscore, or dot.
		>>> get_valid_filename("HPV16_144-1.fa")
		'HPV16_144-1.fa'
		>>> get_valid_filename("chromosome 6.fa")
		'chromosome_6.fa'
		"""
		s = str(s).strip().replace(' ', '_')
		return re.sub(r'(?u)[^-\w.]', '', s)


		if __name__ == "__main__":
		import doctest

pyfaidx/cli.py

+2 −4

Original line number	Diff line number	Diff line
		@@ -3,11 +3,9 @@ import argparse
		import sys
		import os.path
		import re
		from pyfaidx import Fasta, wrap_sequence, FetchError, ucsc_split, bed_split
		from pyfaidx import Fasta, wrap_sequence, FetchError, ucsc_split, bed_split, get_valid_filename
		from collections import defaultdict

		keepcharacters = (' ', '.', '_')

		def write_sequence(args):
		_, ext = os.path.splitext(args.fasta)
		if ext:
		@@ -36,7 +34,7 @@ def write_sequence(args):
		continue
		if args.split_files: # open output file based on sequence name
		filename = '.'.join(str(e) for e in (name, start, end, ext) if e)
		filename = ''.join(c for c in filename if c.isalnum() or c in keepcharacters)
		filename = get_valid_filename(filename)
		outfile = open(filename, 'w')
		elif args.out:
		outfile = args.out

setup.py

+2 −3

Original line number	Diff line number	Diff line
		@@ -36,12 +36,11 @@ setup(
		"Intended Audience :: Science/Research",
		"Natural Language :: English",
		"Operating System :: Unix",
		"Programming Language :: Python :: 3.7",
		"Programming Language :: Python :: 3.6",
		"Programming Language :: Python :: 3.5",
		"Programming Language :: Python :: 3.4",
		"Programming Language :: Python :: 3.3",
		"Programming Language :: Python :: 3.2",
		"Programming Language :: Python :: 2.7",
		"Programming Language :: Python :: 2.6",
		"Programming Language :: Python :: Implementation :: PyPy",
		"Topic :: Scientific/Engineering :: Bio-Informatics"
		]