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"""
Utils that support fringe DataSet features.
"""
import os
import tempfile
import logging
import json
import shutil
import pysam
from pbcore.util.Process import backticks
log = logging.getLogger(__name__)
def consolidateBams(inFiles, outFile, filterDset=None, useTmp=True):
"""Take a list of infiles, an outFile to produce, and optionally a dataset
(filters) to provide the definition and content of filtrations."""
# check space available
if useTmp:
tmpout = tempfile.mkdtemp(suffix="consolidation-filtration")
local_free_space = disk_free(os.path.split(outFile)[0])
tmp_free_space = disk_free(tmpout)
projected_size = sum(file_size(infn) for infn in inFiles)
log.debug("Projected size: {p}".format(p=projected_size))
log.debug("In place free space: {f}".format(f=local_free_space))
log.debug("Tmp free space: {f}".format(f=tmp_free_space))
if tmp_free_space > projected_size:
log.debug("Using tmp storage: " + tmpout)
tmpInFiles = _tmpFiles(inFiles, tmpout)
origOutFile = outFile
origInFiles = inFiles[:]
inFiles = tmpInFiles
outFile = os.path.join(tmpout, "outfile.bam")
elif local_free_space > projected_size:
log.debug("Using in place storage")
useTmp = False
else:
raise RuntimeError("No space available to consolidate")
if filterDset and filterDset.filters:
finalOutfile = outFile
outFile = _infixFname(outFile, "_unfiltered")
_mergeBams(inFiles, outFile)
if filterDset and filterDset.filters:
_filterBam(outFile, finalOutfile, filterDset)
outFile = finalOutfile
_indexBam(outFile)
_pbindexBam(outFile)
if useTmp:
shutil.copy(outFile, origOutFile)
shutil.copy(outFile + ".bai", origOutFile + ".bai")
shutil.copy(outFile + ".pbi", origOutFile + ".pbi")
# cleanup:
shutil.rmtree(os.path.split(outFile)[0])
def _tmpFiles(inFiles, tmpout=None):
tmpInFiles = []
if tmpout is None:
tmpout = tempfile.mkdtemp(suffix="consolidation-filtration")
for i, fname in enumerate(inFiles):
newfn = _infixFname(os.path.join(tmpout, os.path.basename(fname)), i)
shutil.copy(fname, newfn)
tmpInFiles.append(newfn)
return tmpInFiles
def disk_free(path):
if path == '':
path = os.getcwd()
space = os.statvfs(path)
return space.f_bavail * space.f_frsize
def file_size(path):
return os.stat(path).st_size
def _pbindexBam(fname):
cmd = "pbindex {i}".format(i=fname)
log.info(cmd)
o, r, m = backticks(cmd)
if r != 0:
raise RuntimeError(m)
return fname + ".pbi"
# Singleton so we don't need to check and parse repeatedly
class BamtoolsVersion:
class __BamtoolsVersion:
def __init__(self):
cmd = "bamtools -v"
o, r, m = backticks(cmd)
if r == 127:
self.good = False
return
version = ''
for line in o:
if line.startswith("bamtools"):
version = line.split(' ')[-1]
break
self.number = version
if map(int, version.split('.')) >= [2, 4, 0]:
self.good = True
else:
self.good = False
instance = None
def __init__(self):
if not BamtoolsVersion.instance:
BamtoolsVersion.instance = BamtoolsVersion.__BamtoolsVersion()
def __getattr__(self, name):
return getattr(self.instance, name)
def check(self):
if not self.good:
raise RuntimeError("Bamtools version >= 2.4.0 required for "
"consolidation")
def _sortBam(fname):
BamtoolsVersion().check()
tmpname = _infixFname(fname, "_sorted")
cmd = "bamtools sort -in {i} -out {o}".format(i=fname, o=tmpname)
log.info(cmd)
o, r, m = backticks(cmd)
if r != 0:
raise RuntimeError(m)
shutil.move(tmpname, fname)
def _indexBam(fname):
pysam.samtools.index(fname, catch_stdout=False)
return fname + ".bai"
def _indexFasta(fname):
pysam.samtools.faidx(fname, catch_stdout=False)
return fname + ".fai"
def _mergeBams(inFiles, outFile):
BamtoolsVersion().check()
if len(inFiles) > 1:
cmd = "bamtools merge -in {i} -out {o}".format(i=' -in '.join(inFiles),
o=outFile)
log.info(cmd)
o, r, m = backticks(cmd)
if r != 0:
raise RuntimeError(m)
else:
shutil.copy(inFiles[0], outFile)
def _filterBam(inFile, outFile, filterDset):
BamtoolsVersion().check()
tmpout = tempfile.mkdtemp(suffix="consolidation-filtration")
filtScriptName = os.path.join(tmpout, "filtScript.json")
_emitFilterScript(filterDset, filtScriptName)
cmd = "bamtools filter -in {i} -out {o} -script {s}".format(
i=inFile, o=outFile, s=filtScriptName)
log.info(cmd)
o, r, m = backticks(cmd)
if r != 0:
raise RuntimeError(m)
def _infixFname(fname, infix):
prefix, extension = os.path.splitext(fname)
return prefix + str(infix) + extension
def _emitFilterScript(filterDset, filtScriptName):
"""Use the filter script feature of bamtools. Use with specific filters if
all that are needed are available, otherwise filter by readname (easy but
uselessly expensive)"""
filterMap = {'rname': 'reference',
'pos': 'position',
'length': 'queryBases',
'qname': 'name',
'rq': 'mapQuality'}
cheapFilters = True
for filt in filterDset.filters:
for req in filt:
if not filterMap.get(req.name):
cheapFilters = False
if cheapFilters:
script = {"filters":[]}
for filt in filterDset.filters:
filtDict = {}
for req in filt:
name = filterMap[req.name]
if name == 'reference':
if req.operator == '=' or req.operator == '==':
filtDict[name] = req.value
else:
raise NotImplementedError()
else:
filtDict[name] = req.operator + req.value
script['filters'].append(filtDict)
else:
names = [rec.qName for rec in filterDset]
script = {"filters":[{"name": name} for name in names]}
with open(filtScriptName, 'w') as scriptFile:
scriptFile.write(json.dumps(script))
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