.rst .pdf

repository open issue suggest edit

Contents

ALLCools._open

• read and write allc file

• parallel writing

• read region from allc

• separate process gives better performance

This file is modified from xopen 0.3.4 Here is the licence

Copyright (c) 2010-2018 Marcel Martin <mail@marcelm.net>

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

Module Contents

PIGZ = True

BGZIP = True

class Closing

Bases: object

Inherit from this class and implement a close() method to offer context manager functionality.

abstract close(self)

__enter__(self)

__exit__(self, *exc_info)

__del__(self)

class PipedGzipWriter(path, mode='wt', compresslevel=6, threads=1)

Bases: Closing

Write gzip-compressed files by running an external gzip or pigz process and piping into it. On Python 2, this is faster than using gzip.open(). On Python 3, it allows to run the compression in a separate process and can therefore also be faster.

write(self, arg)

close(self)

class PipedGzipReader(path, region=None, mode='r')

Bases: Closing

Inherit from this class and implement a close() method to offer context manager functionality.

close(self)

__iter__(self)

readline(self)

_raise_if_error(self)

Raise IOError if process is not running anymore and the exit code is nonzero.

read(self, *args)

class PipedBamReader(path, region=None, mode='r', include_header=True, samtools_parms_str=None)

Bases: Closing

Inherit from this class and implement a close() method to offer context manager functionality.

close(self)

__iter__(self)

readline(self)

_raise_if_error(self)

Raise IOError if process is not running anymore and the exit code is nonzero.

read(self, *args)

class PipedBamWriter(path, mode='wt', threads=1)

Bases: Closing

Inherit from this class and implement a close() method to offer context manager functionality.

write(self, arg)

close(self)

open_bam(file_path, mode='r', region=None, include_header=True, samtools_parms_str=None, threads=1)

open_gz(file_path, mode='r', compresslevel=3, threads=1, region=None)

open_allc(file_path, mode='r', compresslevel=3, threads=1, region=None)

A replacement for the “open” function that can also open files that have been compressed with gzip, bzip2 or xz. If the file_path is ‘-‘, standard output (mode ‘w’) or input (mode ‘r’) is returned.

The file type is determined based on the file_path: .gz is gzip, .bz2 is bzip2 and .xz is xz/lzma.

When writing a gzip-compressed file, the following methods are tried in order to get the best speed 1) using a pigz (parallel gzip) subprocess; 2) using a gzip subprocess; 3) gzip.open. A single gzip subprocess can be faster than gzip.open because it runs in a separate process.

Uncompressed files are opened with the regular open().

mode can be: ‘rt’, ‘rb’, ‘at’, ‘ab’, ‘wt’, or ‘wb’. Also, the ‘t’ can be omitted, so instead of ‘rt’, ‘wt’ and ‘at’, the abbreviations ‘r’, ‘w’ and ‘a’ can be used.

threads is the number of threads for pigz. If None, then the pigz default is used. multi-thread only apply to writer, reader (decompression) can’t be paralleled

has_tabix(filename)

has_bai(filename)

previous

ALLCools._merge_allc

next

ALLCools._version