/usr/lib/python2.7/dist-packages/pbalign/bampostservice.py is in python-pbalign 0.3.0-1.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 | #!/usr/bin/env python
###############################################################################
# Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
#
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright
# notice, this list of conditions and the following disclaimer in the
# documentation and/or other materials provided with the distribution.
# * Neither the name of Pacific Biosciences nor the names of its
# contributors may be used to endorse or promote products derived from
# this software without specific prior written permission.
#
# NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE GRANTED BY
# THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC BIOSCIENCES AND ITS
# CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT
# NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR
# ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
###############################################################################
"""This script defines BamPostService, which
* calls 'samtools sort' to sort out.bam, and
* calls 'samtools index' to make out.bai index, and
* calls 'makePbi.py' to make out.pbi index file.
"""
# Author: Yuan Li
from __future__ import absolute_import
import logging
from pbalign.service import Service
from pbalign.utils.progutil import Execute
class BamPostService(Service):
"""Sort a bam, makes bam index and PacBio index."""
@property
def name(self):
"""Name of bam post service."""
return "BamPostService"
@property
def progName(self):
return "samtools"
@property
def cmd(self):
return ""
def __init__(self, filenames):
"""Initialize a BamPostService object.
Input - unsortedBamFile: a filtered, unsorted bam file
refFasta : a reference fasta file
Output - sortedBamFile: sorted BAM file
outBaiFile: index BAI file
"""
self.refFasta = filenames.targetFileName
# filtered, unsorted bam file.
self.unsortedBamFile = filenames.filteredSam
self.outBamFile = filenames.outBamFileName
self.outBaiFile = filenames.outBaiFileName
self.outPbiFile = filenames.outPbiFileName
def _sortbam(self, unsortedBamFile, sortedBamFile):
"""Sort unsortedBamFile and output sortedBamFile."""
if not sortedBamFile.endswith(".bam"):
raise ValueError("sorted bam file name %s must end with .bam" %
sortedBamFile)
sortedPrefix = sortedBamFile[0:-4]
cmd = 'samtools --version'
_samtoolsversion = ["0","1","19"]
try:
_out, _code, _msg = Execute(self.name, cmd)
if "samtools" in _out[0]:
_samtoolsversion = str(_out[0][8:]).strip().split('.')
else:
pass
except Exception:
pass
_stvmajor = int(_samtoolsversion[0])
if _stvmajor >= 1:
cmd = 'samtools sort -m 4G -o {sortedBamFile} {unsortedBamFile}'.format(
sortedBamFile=sortedBamFile, unsortedBamFile=unsortedBamFile)
else:
cmd = 'samtools sort -m 4G {unsortedBamFile} {prefix}'.format(
unsortedBamFile=unsortedBamFile, prefix=sortedPrefix)
Execute(self.name, cmd)
def _makebai(self, sortedBamFile, outBaiFile):
"""Build *.bai index file."""
cmd = 'samtools --version'
_samtoolsversion = ["0","1","19"]
try:
_out, _code, _msg = Execute(self.name, cmd)
if "samtools" in _out[0]:
_samtoolsversion = str(_out[0][8:]).strip().split('.')
else:
pass
except Exception:
pass
_stvmajor = int(_samtoolsversion[0])
_stvminor = int(_samtoolsversion[1])
if _stvmajor == 1 and _stvminor == 2:
# only for 1.2
cmd = "samtools index {sortedBamFile}".format(
sortedBamFile=sortedBamFile)
else:
cmd = "samtools index {sortedBamFile} {outBaiFile}".format(
sortedBamFile=sortedBamFile, outBaiFile=outBaiFile)
Execute(self.name, cmd)
def _makepbi(self, sortedBamFile):
"""Generate *.pbi PacBio BAM index."""
cmd = "pbindex %s" % sortedBamFile
Execute(self.name, cmd)
def run(self):
""" Run the BAM post-processing service. """
logging.info(self.name + ": Sort and build index for a bam file.")
self._sortbam(unsortedBamFile=self.unsortedBamFile,
sortedBamFile=self.outBamFile)
self._makebai(sortedBamFile=self.outBamFile,
outBaiFile=self.outBaiFile)
self._makepbi(sortedBamFile=self.outBamFile)
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