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104 lines
2.9 KiB
Python
Executable File
104 lines
2.9 KiB
Python
Executable File
#!/usr/bin/env python
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"""
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usage: %prog bed_file_1 bed_file_2 out_file
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-1, --cols1=N,N,N,N: Columns for chr, start, end, strand in first file
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-2, --cols2=N,N,N,N,N: Columns for chr, start, end, strand, name/value in second file
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"""
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from galaxy import eggs
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import collections
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import sys, string
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#import numpy
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from galaxy import eggs
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import pkg_resources
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pkg_resources.require( "bx-python" )
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import sys, traceback, fileinput
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from warnings import warn
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from galaxy.tools.util.galaxyops import *
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from bx.cookbook import doc_optparse
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#export PYTHONPATH=~/galaxy/lib/
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#running command python WeightedAverage.py interval_interpolate.bed value_interpolate.bed interpolate_result.bed
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def stop_err(msg):
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sys.stderr.write(msg)
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sys.exit()
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def FindRate(chromosome,start_stop,dictType):
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OverlapList=[]
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for tempO in dictType[chromosome]:
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DatabaseInterval=[tempO[0],tempO[1]]
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Overlap=GetOverlap(start_stop,DatabaseInterval)
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if Overlap>0:
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OverlapList.append([Overlap,tempO[2]])
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if len(OverlapList)>0:
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SumRecomb=0
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SumOverlap=0
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for member in OverlapList:
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SumRecomb+=member[0]*member[1]
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SumOverlap+=member[0]
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averageRate=SumRecomb/SumOverlap
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return averageRate
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else:
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return 'NA'
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def GetOverlap(a,b):
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return min(a[1],b[1])-max(a[0],b[0])
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options, args = doc_optparse.parse( __doc__ )
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try:
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chr_col_1, start_col_1, end_col_1, strand_col1 = parse_cols_arg( options.cols1 )
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chr_col_2, start_col_2, end_col_2, strand_col2, name_col_2 = parse_cols_arg( options.cols2 )
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input1, input2, input3 = args
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except Exception, eee:
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print eee
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stop_err( "Data issue: click the pencil icon in the history item to correct the metadata attributes." )
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fd2=open(input2)
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lines2=fd2.readlines()
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RecombChrDict=collections.defaultdict(list)
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skipped=0
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for line in lines2:
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temp=line.strip().split()
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try:
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assert float(temp[int(name_col_2)])
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except:
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skipped+=1
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continue
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tempIndex=[int(temp[int(start_col_2)]),int(temp[int(end_col_2)]),float(temp[int(name_col_2)])]
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RecombChrDict[temp[int(chr_col_2)]].append(tempIndex)
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print "Skipped %d features with invalid values" %(skipped)
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fd1=open(input1)
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lines=fd1.readlines()
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finalProduct=''
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for line in lines:
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temp=line.strip().split('\t')
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chromosome=temp[int(chr_col_1)]
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start=int(temp[int(start_col_1)])
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stop=int(temp[int(end_col_1)])
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start_stop=[start,stop]
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RecombRate=FindRate(chromosome,start_stop,RecombChrDict)
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try:
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RecombRate="%.4f" %(float(RecombRate))
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except:
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RecombRate=RecombRate
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finalProduct+=line.strip()+'\t'+str(RecombRate)+'\n'
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fdd=open(input3,'w')
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fdd.writelines(finalProduct)
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fdd.close()
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