#!/usr/bin/env python
# -*- coding: utf-8 -*-
import os
import shutil
import tempfile
import numpy as np
import sys
# NGS packages
import pyBigWig
# own module
from deeptools import mapReduce
from deeptools.utilities import getCommonChrNames, toBytes
from deeptools.writeBedGraph import *
from deeptools import bamHandler
old_settings = np.seterr(all='ignore')
[docs]def getCoverageFromBigwig(bigwigHandle, chrom, start, end, tileSize,
missingDataAsZero=False):
try:
coverage = np.asarray(bigwigHandle.values(chrom, start, end))
except TypeError:
# this error happens when chromosome
# is not into the bigwig file
return []
if coverage is None:
return []
if missingDataAsZero is True:
coverage[np.isnan(coverage)] = 0
# average the values per bin
cov = np.array(
[np.mean(coverage[x:x + tileSize])
for x in range(0, len(coverage), tileSize)])
return cov
[docs]def writeBedGraph_wrapper(args):
return writeBedGraph_worker(*args)
[docs]def writeBedGraph_worker(
chrom, start, end, tileSize, defaultFragmentLength,
bamOrBwFileList, func, funcArgs, extendPairedEnds=True, smoothLength=0,
missingDataAsZero=False, fixed_step=False):
r"""
Writes a bedgraph having as base a number of bam files.
The given func is called to compute the desired bedgraph value
using the funcArgs
tileSize
"""
if start > end:
raise NameError("start position ({0}) bigger than "
"end position ({1})".format(start, end))
coverage = []
for indexFile, fileFormat in bamOrBwFileList:
if fileFormat == 'bam':
bamHandle = bamHandler.openBam(indexFile)
coverage.append(getCoverageFromBam(
bamHandle, chrom, start, end, tileSize,
defaultFragmentLength, extendPairedEnds,
True))
bamHandle.close()
elif fileFormat == 'bigwig':
bigwigHandle = pyBigWig.open(indexFile)
coverage.append(
getCoverageFromBigwig(
bigwigHandle, chrom, start, end,
tileSize, missingDataAsZero))
bigwigHandle.close()
# is /dev/shm available?
# working in this directory speeds the process
try:
_file = tempfile.NamedTemporaryFile(dir="/dev/shm", delete=False)
except OSError:
_file = tempfile.NamedTemporaryFile(delete=False)
previousValue = None
lengthCoverage = len(coverage[0])
for tileIndex in range(lengthCoverage):
tileCoverage = []
for index in range(len(bamOrBwFileList)):
if smoothLength > 0:
vectorStart, vectorEnd = getSmoothRange(
tileIndex, tileSize, smoothLength, lengthCoverage)
tileCoverage.append(
np.mean(coverage[index][vectorStart:vectorEnd]))
else:
try:
tileCoverage.append(coverage[index][tileIndex])
except IndexError:
sys.exit("Chromosome {} probably not in one of the bigwig "
"files. Remove this chromosome from the bigwig file "
"to continue".format(chrom))
# if zerosToNans == True and sum(tileCoverage) == 0.0:
# continue
value = func(tileCoverage, funcArgs)
if fixed_step:
writeStart = start + tileIndex * tileSize
writeEnd = min(writeStart + tileSize, end)
try:
_file.write(toBytes("%s\t%d\t%d\t%.2f\n" % (chrom, writeStart,
writeEnd, value)))
except TypeError:
_file.write(toBytes("{}\t{}\t{}\t{}\n".format(chrom, writeStart,
writeEnd, value)))
else:
if previousValue is None:
writeStart = start + tileIndex * tileSize
writeEnd = min(writeStart + tileSize, end)
previousValue = value
elif previousValue == value:
writeEnd = min(writeEnd + tileSize, end)
elif previousValue != value:
if not np.isnan(previousValue):
_file.write(
toBytes("{0}\t{1}\t{2}\t{3:g}\n".format(chrom, writeStart,
writeEnd, previousValue)))
previousValue = value
writeStart = writeEnd
writeEnd = min(writeStart + tileSize, end)
if not fixed_step:
# write remaining value if not a nan
if previousValue and writeStart != end and \
not np.isnan(previousValue):
_file.write(toBytes("{0}\t{1}\t{2}\t{3:g}\n".format(chrom, writeStart,
end, previousValue)))
tempFileName = _file.name
_file.close()
return(tempFileName)
[docs]def writeBedGraph(
bamOrBwFileList, outputFileName, fragmentLength,
func, funcArgs, tileSize=25, region=None, blackListFileName=None, numberOfProcessors=None,
format="bedgraph", extendPairedEnds=True, missingDataAsZero=False,
smoothLength=0, fixed_step=False, verbose=False):
r"""
Given a list of bamfiles, a function and a function arguments,
this method writes a bedgraph file (or bigwig) file
for a partition of the genome into tiles of given size
and a value for each tile that corresponds to the given function
and that is related to the coverage underlying the tile.
"""
bamHandlers = [bamHandler.openBam(indexedFile) for
indexedFile,
fileFormat in bamOrBwFileList if fileFormat == 'bam']
if len(bamHandlers):
genomeChunkLength = getGenomeChunkLength(bamHandlers, tileSize)
# check if both bam files correspond to the same species
# by comparing the chromosome names:
chromNamesAndSize, __ = getCommonChrNames(bamHandlers, verbose=verbose)
else:
genomeChunkLength = int(10e6)
cCommon = []
chromNamesAndSize = {}
for fileName, fileFormat in bamOrBwFileList:
if fileFormat == 'bigwig':
fh = pyBigWig.open(fileName)
else:
continue
for chromName, size in list(fh.chroms().items()):
if chromName in chromNamesAndSize:
cCommon.append(chromName)
if chromNamesAndSize[chromName] != size:
print("\nWARNING\n"
"Chromosome {} length reported in the "
"input files differ.\n{} for {}\n"
"{} for {}.\n\nThe smallest "
"length will be used".format(
chromName, chromNamesAndSize[chromName],
bamOrBwFileList[0][0], size, fileName))
chromNamesAndSize[chromName] = min(
chromNamesAndSize[chromName], size)
else:
chromNamesAndSize[chromName] = size
fh.close()
# get the list of common chromosome names and sizes
chromNamesAndSize = [(k, v) for k, v in chromNamesAndSize.items()
if k in cCommon]
if region:
# in case a region is used, append the tilesize
region += ":{}".format(tileSize)
res = mapReduce.mapReduce((tileSize, fragmentLength, bamOrBwFileList,
func, funcArgs, extendPairedEnds, smoothLength,
missingDataAsZero, fixed_step),
writeBedGraph_wrapper,
chromNamesAndSize,
genomeChunkLength=genomeChunkLength,
region=region,
blackListFileName=blackListFileName,
numberOfProcessors=numberOfProcessors,
verbose=verbose)
# concatenate intermediary bedgraph files
outFile = open(outputFileName + ".bg", 'wb')
for tempFileName in res:
if tempFileName:
# concatenate all intermediate tempfiles into one
# bedgraph file
_foo = open(tempFileName, 'rb')
shutil.copyfileobj(_foo, outFile)
_foo.close()
os.remove(tempFileName)
bedGraphFile = outFile.name
outFile.close()
if format == 'bedgraph':
os.rename(bedGraphFile, outputFileName)
if debug:
print("output file: %s" % (outputFileName))
else:
bedGraphToBigWig(
chromNamesAndSize, bedGraphFile, outputFileName, True)
if debug:
print("output file: %s" % (outputFileName))
os.remove(bedGraphFile)