[med-svn] [Git][med-team/python-pyfaidx][upstream] New upstream version 0.6.2
Nilesh Patra (@nilesh)
gitlab at salsa.debian.org
Fri Sep 3 15:55:18 BST 2021
Nilesh Patra pushed to branch upstream at Debian Med / python-pyfaidx
Commits:
17438b7c by Nilesh Patra at 2021-09-03T20:15:48+05:30
New upstream version 0.6.2
- - - - -
6 changed files:
- − .gitignore
- − .travis.yml
- README.rst
- pyfaidx/__init__.py
- pyfaidx/cli.py
- setup.cfg
Changes:
=====================================
.gitignore deleted
=====================================
@@ -1,12 +0,0 @@
-/build
-venv
-__pycache__
-*.pyc
-.project
-.pydevproject
-.idea
-*.egg-info
-.tox
-.coverage
-.coverage.*
-tests/data/chr22*
=====================================
.travis.yml deleted
=====================================
@@ -1,65 +0,0 @@
-language: python
-sudo: required
-dist: bionic
-python:
- - 'nightly'
- - '3.8'
- - '3.7'
- - '3.6'
- - '3.5'
- - '2.7'
- - 'pypy'
- - 'pypy3'
-install:
- - pip install cython pysam requests coverage pyfasta pyvcf numpy
- - pip install biopython || true
- - python setup.py install
- - if [ ! -f samtools-1.2 ]; then curl -sL https://github.com/samtools/samtools/releases/download/1.2/samtools-1.2.tar.bz2 | tar -xjv; fi
- - cd samtools-1.2
- - make
- - export PATH=$PATH:$PWD
- - cd ..
- - if [ ! -f htslib-1.4 ]; then curl -sL https://github.com/samtools/htslib/releases/download/1.4/htslib-1.4.tar.bz2 | tar -xjv; fi
- - cd htslib-1.4
- - make
- - export PATH=$PATH:$PWD
- - cd ..
-before_install:
- - sudo apt-get install -y python3.6 python3-pip
- - env python3.6 -m pip install biopython requests
- - env python3.6 tests/data/download_gene_fasta.py
-script: nosetests --with-coverage --cover-package=pyfaidx
-deploy:
- provider: pypi
- user: mdshw5
- password:
- secure: MbSaeuitkVTZqxa0PJ3RcR1aMf+B/sMbcx2sWOo9xfLlRFDFpYWJZ0EfXWEhrVu2YWXpBsasgunTDWSi0jNcZMH92MzOC+UTVYr45LO5sy6hm4iSiAgm/DPgYWdjP0SFKr7eL/HWPS+gHvgkXL1upleX21O358bxaezoasuKFvs=
- on:
- all_branches: true
- python: 3.8
- tags: true
- repo: mdshw5/pyfaidx
-matrix:
- include:
- - os: windows
- language: sh
- python: "3.7"
- before_install:
- - choco install python3
- - export PATH="/c/Python37:/c/Python37/Scripts:$PATH"
- - python -m virtualenv $HOME/venv
- - source $HOME/venv/Scripts/activate
- allow_failures:
- - python: nightly
- - python: pypy3
- - python: pypy
- - os: windows
- fast_finish: true
-cache:
- directories:
- - tests/data
- - samtools-1.2
- - htslib-1.4
-after_success:
- - bash <(curl -s https://codecov.io/bash)
-
=====================================
README.rst
=====================================
@@ -356,7 +356,7 @@ cli script: faidx
optional arguments:
-h, --help show this help message and exit
- -b BED, --bed BED bed file of regions
+ -b BED, --bed BED bed file of regions (zero-based start coordinate)
-o OUT, --out OUT output file name (default: stdout)
-i {bed,chromsizes,nucleotide,transposed}, --transform {bed,chromsizes,nucleotide,transposed} transform the requested regions into another format. default: None
-c, --complement complement the sequence. default: False
@@ -593,8 +593,8 @@ Wheelan <http://sjwheelan.som.jhmi.edu>`_ and `Vasan
Yegnasubramanian <http://yegnalab.onc.jhmi.edu>`_ at the Sidney Kimmel
Comprehensive Cancer Center in the Department of Oncology.
-.. |Travis| image:: https://travis-ci.org/mdshw5/pyfaidx.svg?branch=master
- :target: https://travis-ci.org/mdshw5/pyfaidx
+.. |Travis| image:: https://travis-ci.com/mdshw5/pyfaidx.svg?branch=master
+ :target: https://travis-ci.com/mdshw5/pyfaidx
.. |PyPI| image:: https://img.shields.io/pypi/v/pyfaidx.svg?branch=master
:target: https://pypi.python.org/pypi/pyfaidx
=====================================
pyfaidx/__init__.py
=====================================
@@ -9,6 +9,7 @@ import os
import re
import string
import sys
+import shutil
import warnings
from collections import namedtuple
from itertools import islice
@@ -29,7 +30,7 @@ if sys.version_info > (3, ):
dna_bases = re.compile(r'([ACTGNactgnYRWSKMDVHBXyrwskmdvhbx]+)')
-__version__ = '0.5.9.5'
+__version__ = '0.6.2'
class KeyFunctionError(ValueError):
@@ -437,8 +438,8 @@ class Faidx(object):
self.read_fai()
except FastaIndexingError:
- os.remove(self.indexname)
self.file.close()
+ os.remove(self.indexname + '.tmp')
raise
except Exception:
# Handle potential exceptions other than 'FastaIndexingError'
@@ -515,7 +516,7 @@ class Faidx(object):
def build_index(self):
try:
with self._fasta_opener(self.filename, 'rb') as fastafile:
- with open(self.indexname, 'w') as indexfile:
+ with open(self.indexname + '.tmp', 'w') as indexfile:
rname = None # reference sequence name
offset = 0 # binary offset of end of current line
rlen = 0 # reference character length
@@ -596,6 +597,7 @@ class Faidx(object):
"Inconsistent line found in >{0} at "
"line {1:n}.".format(rname,
bad_lines[0][0] + 1))
+ shutil.move(self.indexname + '.tmp', self.indexname)
except (IOError, FastaIndexingError) as e:
if isinstance(e, IOError):
raise IOError(
=====================================
pyfaidx/cli.py
=====================================
@@ -117,6 +117,10 @@ def split_regions(args):
def transform_sequence(args, fasta, name, start=None, end=None):
line_len = fasta.faidx.index[name].lenc
s = fasta[name][start:end]
+ if args.complement:
+ s = s.complement
+ if args.reverse:
+ s = s.reverse
if args.no_output:
return
if args.transform == 'bed':
@@ -148,7 +152,7 @@ def main(ext_args=None):
_input = parser.add_argument_group('input options')
output = parser.add_argument_group('output options')
header = parser.add_argument_group('header options')
- _input.add_argument('-b', '--bed', type=argparse.FileType('r'), help="bed file of regions")
+ _input.add_argument('-b', '--bed', type=argparse.FileType('r'), help="bed file of regions (zero-based start coordinate)")
output.add_argument('-o', '--out', type=argparse.FileType('w'), help="output file name (default: stdout)")
output.add_argument('-i', '--transform', type=str, choices=('bed', 'chromsizes', 'nucleotide', 'transposed'), help="transform the requested regions into another format. default: %(default)s")
output.add_argument('-c', '--complement', action="store_true", default=False, help="complement the sequence. default: %(default)s")
=====================================
setup.cfg
=====================================
@@ -1,3 +1,4 @@
[nosetests]
with-doctest=1
verbosity=2
+with-ignore-docstrings=1
\ No newline at end of file
View it on GitLab: https://salsa.debian.org/med-team/python-pyfaidx/-/commit/17438b7c77cd39a202a0da600c9a6ce837edd4bd
--
View it on GitLab: https://salsa.debian.org/med-team/python-pyfaidx/-/commit/17438b7c77cd39a202a0da600c9a6ce837edd4bd
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