#!/usr/bin/env python

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## Created on July 4th 2018 to create IGV session file from file list
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import os
import errno
import argparse

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## PARSE ARGUMENTS
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Description = 'Create IGV session file from a list of files and associated colours - ".bed", ".bw", ".bigwig", ".tdf", ".gtf" files currently supported.'
Epilog = """Example usage: python igv_files_to_session.py <XML_OUT> <LIST_FILE> <GENOME>"""

argParser = argparse.ArgumentParser(description=Description, epilog=Epilog)

## REQUIRED PARAMETERS
argParser.add_argument('XML_OUT', help="XML output file.")
argParser.add_argument('LIST_FILE', help="Tab-delimited file containing two columns i.e. file_name\tcolour. Header isnt required.")
argParser.add_argument('GENOME', help="Full path to genome fasta file or shorthand for genome available in IGV e.g. hg19.")

## OPTIONAL PARAMETERS
argParser.add_argument('-pp', '--path_prefix', type=str, dest="PATH_PREFIX", default='', help="Path prefix to be added at beginning of all files in input list file.")
args = argParser.parse_args()

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## HELPER FUNCTIONS
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def makedir(path):

    if not len(path) == 0:
        try:
            os.makedirs(path)
        except OSError as exception:
            if exception.errno != errno.EEXIST:
                raise

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## MAIN FUNCTION
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def igv_files_to_session(XMLOut,ListFile,Genome,PathPrefix=''):

    makedir(os.path.dirname(XMLOut))

    fileList = []
    fin = open(ListFile,'r')
    while True:
        line = fin.readline()
        if line:
            ifile,colour = line.strip().split('\t')
            if len(colour.strip()) == 0:
                colour = '0,0,178'
            fileList.append((PathPrefix.strip()+ifile,colour))
        else:
            break
            fout.close()

    ## ADD RESOURCES SECTION
    XMLStr =  '<?xml version="1.0" encoding="UTF-8" standalone="no"?>\n'
    XMLStr += '<Session genome="%s" hasGeneTrack="true" hasSequenceTrack="true" locus="All" version="8">\n' % (Genome)
    XMLStr += '\t<Resources>\n'
    for ifile,colour in fileList:
        XMLStr += '\t\t<Resource path="%s"/>\n' % (ifile)
    XMLStr += '\t</Resources>\n'

    ## ADD PANEL SECTION
    XMLStr += '\t<Panel height="1160" name="DataPanel" width="1897">\n'
    for ifile,colour in fileList:
        extension = os.path.splitext(ifile)[1].lower()
        if extension in ['.bed','.broadpeak','.narrowpeak']:
            XMLStr += '\t\t<Track altColor="0,0,178" autoScale="false" clazz="org.broad.igv.track.FeatureTrack" color="%s" ' % (colour)
            XMLStr += 'displayMode="SQUISHED" featureVisibilityWindow="-1" fontSize="12" height="20" '
            XMLStr += 'id="%s" name="%s" renderer="BASIC_FEATURE" sortable="false" visible="true" windowFunction="count"/>\n' % (ifile,os.path.basename(ifile))
        elif extension in ['.bw', '.bigwig', '.tdf']:
            XMLStr += '\t\t<Track altColor="0,0,178" autoScale="true" clazz="org.broad.igv.track.DataSourceTrack" color="%s" ' % (colour)
            XMLStr += 'displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="12" height="100" '
            XMLStr += 'id="%s" name="%s" normalize="false" renderer="BAR_CHART" sortable="true" visible="true" windowFunction="mean">\n' % (ifile,os.path.basename(ifile))
            XMLStr += '\t\t\t<DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="10" minimum="0.0" type="LINEAR"/>\n'
            XMLStr += '\t\t</Track>\n'
        elif extension in ['.gtf']:
            XMLStr += '\t\t<Track altColor="0,0,178" autoScale="false" clazz="org.broad.igv.track.FeatureTrack" color="%s" ' % (colour)
            XMLStr += 'displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="12" '
            XMLStr += 'id="%s" name="%s" renderer="BASIC_FEATURE" sortable="false" visible="true" windowFunction="count"/>\n' % (ifile,os.path.basename(ifile))
        elif extension in ['.gff']:
            XMLStr += '\t\t<Track altColor="0,0,178" autoScale="false" clazz="org.broad.igv.track.FeatureTrack" color="%s" ' % (colour)
            XMLStr += 'displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="12" '
            XMLStr += 'id="%s" name="%s" renderer="BASIC_FEATURE" sortable="false" visible="true" windowFunction="count"/>\n' % (ifile,os.path.basename(ifile))
        elif extension in ['.bam']:
            pass
        else:
            XMLStr += '\t\t<Track altColor="0,0,178" autoScale="false" clazz="org.broad.igv.track.FeatureTrack" color="%s" ' % (colour)
            XMLStr += 'displayMode="SQUISHED" featureVisibilityWindow="-1" fontSize="10" height="20" '
            XMLStr += 'id="%s" name="%s" renderer="BASIC_FEATURE" sortable="false" visible="true" windowFunction="count"/>\n' % (ifile,os.path.basename(ifile))

    XMLStr += '\t</Panel>\n'
    #XMLStr += '\t<HiddenAttributes>\n\t\t<Attribute name="DATA FILE"/>\n\t\t<Attribute name="DATA TYPE"/>\n\t\t<Attribute name="NAME"/>\n\t</HiddenAttributes>\n'
    XMLStr += '</Session>'
    XMLOut = open(XMLOut,'w')
    XMLOut.write(XMLStr)
    XMLOut.close()

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## RUN FUNCTION
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igv_files_to_session(XMLOut=args.XML_OUT,ListFile=args.LIST_FILE,Genome=args.GENOME,PathPrefix=args.PATH_PREFIX)

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