bamToGFF_turbo.py

#!/usr/bin/python
#bamToGFF_turbo.py

'''
The MIT License (MIT)

Copyright (c) 2013 Charles Lin

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.
'''

#20130716

#script to grab reads from a bam that align to a .gff file

#uses the bamliquidator super fast uber thingy written by Xin Zhou

import os
import string
import subprocess
import utils

def mapBamToGFF(bamFile,gff,sense = '.',extension = 200,rpm = False,clusterGram = None,matrix = None):
    '''maps reads from a bam to a gff'''

    #creating a new gff to output
    newGFF = []
    #reading in the bam
    bam = utils.Bam(bamFile)

    #getting RPM normalization
    if rpm:    
        MMR= round(float(bam.getTotalReads('mapped'))/1000000,4)
    else:
        MMR = 1

    print('using a MMR value of %s' % (MMR))

    #creating a sense trans 
    senseTrans = string.maketrans('-+.','+-+')
    
    #reading in the gff
    if type(gff) == str:
        gff = utils.parseTable(gff,'\t')

    #setting up a clustergram table
    if clusterGram:
        binSize = int(clusterGram)
        binSizeList = []
        #now go through each line of the gff and make sure they're all the same length
        for i in range(0,len(gff),1):
            line = gff[i]
            gffLocus = utils.Locus(line[0],int(line[3]),int(line[4]),line[6],line[1])
            binSizeList.append(gffLocus.len()/binSize)
        binSizeList = utils.uniquify(binSizeList)
        if len(binSizeList) > 1: 
            print('WARNING: lines in gff are of different length. Output clustergram will have variable row length')
        newGFF.append(['GENE_ID','locusLine'] + [str(x*binSize)+'_'+bamFile.split('/')[-1] for x in range(1,max(binSizeList)+1,1)])        
        
    #setting up a maxtrix table
    if matrix:
        newGFF.append(['GENE_ID','locusLine'] + ['bin_'+str(n)+'_'+bamFile.split('/')[-1] for n in range(1,int(matrix)+1,1)])
        nBin = int(matrix)

    # Try to use the bamliquidatior script on cluster, otherwise, failover to local (in path), otherwise fail.
    bamliquidatorString = '/usr/bin/bamliquidator'
    if not os.path.isfile(bamliquidatorString):
        bamliquidatorString = './bamliquidator'
        if not os.path.isfile(bamliquidatorString):
            raise ValueError('bamliquidator not found in path')

    #getting and processing reads for gff lines
    ticker = 0
    print('Number lines processed')
    for line in gff:
        line = line[0:9]
        if ticker%100 == 0:
            print(ticker)
        ticker+=1
        gffLocus = utils.Locus(line[0],int(line[3]),int(line[4]),line[6],line[1])
        
        #get the nBin and binSize
        if clusterGram:
            nBin =gffLocus.len()/int(clusterGram)
            binSize = int(clusterGram)
        if matrix:
            nBin = int(matrix)
            binSize = gffLocus.len()/nBin
            #some regions will be too short to get info on
            if binSize == 0:
                clusterLine = [gffLocus.ID(),gffLocus.__str__()] + ['NA']*nBin
                newGFF.append(clusterLine)
                continue


        #flippy flip if sense is negative
        if sense == '-':
            bamSense = string.translate(gffLocus.sense(),senseTrans)
        elif sense == '+':
            bamSense = gffLocus.sense()
        else:
            bamSense = '.'
        #using the bamLiquidator to get the readstring            
        #print('using nBin of %s' % nBin)
        bamCommand = "%s %s %s %s %s %s %s %s" % (bamliquidatorString,bamFile,line[0],gffLocus.start(),gffLocus.end(),bamSense,nBin,extension)
        #print(bamCommand)
        getReads = subprocess.Popen(bamCommand,stdin = subprocess.PIPE,stderr = subprocess.PIPE,stdout = subprocess.PIPE,shell = True)
        readString, stderr = getReads.communicate()
        if stderr:
            print("STDERR out: %s" % (stderr))
        denList = readString.split('\n')[:-1]
        #print("denlist is: %s" % denList)
        #flip the denList if the actual gff region is -
        if gffLocus.sense() == '-':
            denList = denList[::-1]

        #converting from units of total bp of read sequence per bin to rpm/bp
        
        denList = [round(float(x)/binSize/MMR,4) for x in denList]
        
        #if the gff region is - strand, flip the

        clusterLine = [gffLocus.ID(),gffLocus.__str__()] + denList
        newGFF.append(clusterLine)

    return newGFF
        

    
def convertEnrichedRegionsToGFF(enrichedRegionFile):
    '''converts a young lab enriched regions file into a gff'''
    newGFF = []
    enrichedRegions = open(enrichedRegionFile,'r')
    header = enrichedRegions.readline()
    i = 0
    for line in enrichedRegions:
        line = line[:-1].split('\t')
        newLine = ['chr'+line[0],'row_'+str(i),line[4],line[1],line[2],'','.','','row_'+str(i),'']
        newGFF.append(newLine)
        i+=1
    return newGFF

        
#python bamToGFF.py --density --floor 0 -b test.sam.sorted.bam -g pol2_sample.gff -o pol2_sample_mapped.gff

def main():
    from optparse import OptionParser
    usage = "usage: %prog [options] -b [SORTED BAMFILE] -i [INPUTFILE] -o [OUTPUTFILE]"
    parser = OptionParser(usage = usage)
    #required flags
    parser.add_option("-b","--bam", dest="bam",nargs = 1, default=None,
                      help = "Enter .bam file to be processed.")
    parser.add_option("-i","--input", dest="input",nargs = 1, default=None,
                      help = "Enter .gff or ENRICHED REGION file to be processed.")
    #output flag
    parser.add_option("-o","--output", dest="output",nargs = 1, default=None,
                      help = "Enter the output filename.")
    #additional options
    parser.add_option("-s","--sense", dest="sense",nargs = 1, default='.',
                      help = "Map to '+','-' or 'both' strands. Default maps to both.")
    parser.add_option("-e","--extension", dest="extension",nargs = 1, default=200,
                      help = "Extends reads by n bp. Default value is 200bp")
    parser.add_option("-r","--rpm", dest="rpm",action = 'store_true', default=False,
                      help = "Normalizes density to reads per million (rpm)")
    parser.add_option("-c","--cluster", dest="cluster",nargs = 1, default=None,
                      help = "Outputs a fixed bin size clustergram. user must specify bin size.")
    parser.add_option("-m","--matrix", dest="matrix",nargs = 1, default=None,
                      help = "Outputs a variable bin sized matrix. User must specify number of bins.")
    (options,args) = parser.parse_args()

    print(options)
    print(args)

   
    if options.sense:
        if ['+','-','.','both'].count(options.sense) == 0:
            print('ERROR: sense flag must be followed by +,-,.,both')
            parser.print_help()
            exit()

    if options.cluster and options.matrix:
        print('ERROR: Cannot specify both matrix and clustergram flags.')
        parser.print_help()
        exit()

    if options.matrix:
        try:
            int(options.matrix)
        except:
            print('ERROR: User must specify an integer bin number for matrix (try 50)')
            parser.print_help()
            exit()
            
    if options.cluster:
        try:
            int(options.cluster)
        except:
            print('ERROR: User must specify an integer bin size for clustergram (try 25)')
            parser.print_help()
            exit()

    
    
    if options.input and options.bam:
        inputFile = options.input
        if inputFile.split('.')[-1] != 'gff':
            print('converting file to a .gff')
            gffFile = convertEnrichedRegionsToGFF(inputFile)
        else:
            gffFile = inputFile

        bamFile = options.bam
        
        if options.output == None:
            output = os.getcwd() + inputFile.split('/')[-1]+'.mapped'
        else:
            output = options.output
        if options.cluster:
            print('mapping to GFF and making clustergram with fixed bin width')
            newGFF = mapBamToGFF(bamFile,gffFile,options.sense,int(options.extension),options.rpm,int(options.cluster),None)
        elif options.matrix:
            print('mapping to GFF and making a matrix with fixed bin number')
            newGFF = mapBamToGFF(bamFile,gffFile,options.sense,int(options.extension),options.rpm,None,int(options.matrix))

        print('bamToGFF_turbo writing output to: %s' % (output))
        # Hackjob to make subdirectories for ROSE integration
        try:
            os.mkdir(os.path.dirname(output))
        except OSError:
            pass
        utils.unParseTable(newGFF,output,'\t')

    else:
        parser.print_help()
        

        
if __name__ == "__main__":
    main()