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249 lines
8.8 KiB
Python
Executable File
249 lines
8.8 KiB
Python
Executable File
#!/usr/bin/env python
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#Guruprasad Ananda
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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, os, tempfile
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import traceback
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import 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.intervals.io import *
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from bx.intervals.operations import quicksect
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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 counter(node, start, end, sort_col):
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global full, blk_len, blk_list
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if node.start < start:
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if node.right:
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counter(node.right, start, end, sort_col)
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elif start <= node.start <= end and start <= node.end <= end:
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full += 1
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if node.other[0] not in blk_list:
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blk_list.append(node.other[0])
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blk_len += int(node.other[sort_col+2])
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if node.left and node.left.maxend > start:
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counter(node.left, start, end, sort_col)
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if node.right:
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counter(node.right, start, end, sort_col)
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elif node.start > end:
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if node.left:
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counter(node.left, start, end, sort_col)
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infile = sys.argv[1]
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fout = open(sys.argv[2],'w')
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int_file = sys.argv[3]
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if int_file != "None": #User has specified an interval file
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try:
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fint = open(int_file, 'r')
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dbkey_i = sys.argv[4]
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chr_col_i, start_col_i, end_col_i, strand_col_i = parse_cols_arg( sys.argv[5] )
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except:
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stop_err("Unable to open input Interval file")
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def main():
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for i, line in enumerate( file ( infile )):
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line = line.rstrip('\r\n')
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if len( line )>0 and not line.startswith( '#' ):
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elems = line.split( '\t' )
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break
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if i == 30:
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break # Hopefully we'll never get here...
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if len( elems ) != 18:
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stop_err( "This tool only works on tabular data output by 'Fetch Indels from 3-way alignments' tool. The data in your input dataset is either missing or not formatted properly." )
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for i, line in enumerate( file ( infile )):
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line = line.rstrip('\r\n')
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elems = line.split('\t')
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try:
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assert int(elems[0])
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assert len(elems) == 18
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if int_file != "None":
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if dbkey_i not in elems[3] and dbkey_i not in elems[8] and dbkey_i not in elems[13]:
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stop_err("The species build corresponding to your interval file is not present in the Indel file.")
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if dbkey_i in elems[3]:
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sort_col = 4
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elif dbkey_i in elems[8]:
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sort_col = 9
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elif dbkey_i in elems[13]:
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sort_col = 14
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else:
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species = []
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species.append( elems[3].split('.')[0] )
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species.append( elems[8].split('.')[0] )
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species.append( elems[13].split('.')[0] )
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sort_col = 0 #Based on block numbers
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break
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except:
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continue
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fin = open(infile, 'r')
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skipped = 0
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if int_file == "None":
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sorted_infile = tempfile.NamedTemporaryFile()
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cmdline = "sort -n -k"+str(1)+" -o "+sorted_infile.name+" "+infile
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try:
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os.system(cmdline)
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except:
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stop_err("Encountered error while sorting the input file.")
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print >>fout, "#Block\t%s_InsRate\t%s_InsRate\t%s_InsRate\t%s_DelRate\t%s_DelRate\t%s_DelRate" %(species[0],species[1],species[2],species[0],species[1],species[2])
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prev_bnum = -1
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sorted_infile.seek(0)
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for line in sorted_infile.readlines():
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line = line.rstrip('\r\n')
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elems = line.split('\t')
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try:
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assert int(elems[0])
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assert len(elems) == 18
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new_bnum = int(elems[0])
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if new_bnum != prev_bnum:
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if prev_bnum != -1:
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irate = []
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drate = []
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for i,elem in enumerate(inserts):
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try:
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irate.append(str("%.2e" %(inserts[i]/blen[i])))
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except:
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irate.append('0')
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try:
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drate.append(str("%.2e" %(deletes[i]/blen[i])))
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except:
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drate.append('0')
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print >>fout, "%s\t%s\t%s" %(prev_bnum, '\t'.join(irate) , '\t'.join(drate))
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inserts = [0.0, 0.0, 0.0]
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deletes = [0.0, 0.0, 0.0]
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blen = []
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blen.append( int(elems[6]) )
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blen.append( int(elems[11]) )
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blen.append( int(elems[16]) )
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line_sp = elems[1].split('.')[0]
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sp_ind = species.index(line_sp)
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if elems[1].endswith('insert'):
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inserts[sp_ind] += 1
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elif elems[1].endswith('delete'):
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deletes[sp_ind] += 1
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prev_bnum = new_bnum
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except Exception, ei:
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#print >>sys.stderr, ei
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continue
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irate = []
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drate = []
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for i,elem in enumerate(inserts):
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try:
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irate.append(str("%.2e" %(inserts[i]/blen[i])))
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except:
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irate.append('0')
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try:
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drate.append(str("%.2e" %(deletes[i]/blen[i])))
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except:
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drate.append('0')
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print >>fout, "%s\t%s\t%s" %(prev_bnum, '\t'.join(irate) , '\t'.join(drate))
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sys.exit()
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inf = open(infile, 'r')
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start_met = False
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end_met = False
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sp_file = tempfile.NamedTemporaryFile()
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for n, line in enumerate(inf):
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line = line.rstrip('\r\n')
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elems = line.split('\t')
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try:
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assert int(elems[0])
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assert len(elems) == 18
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if dbkey_i not in elems[1]:
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if not(start_met):
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continue
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else:
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sp_end = n
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break
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else:
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print >>sp_file, line
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if not(start_met):
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start_met = True
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sp_start = n
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except:
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continue
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try:
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assert sp_end
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except:
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sp_end = n+1
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sp_file.seek(0)
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win = NiceReaderWrapper( fileinput.FileInput( int_file ),
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chrom_col=chr_col_i,
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start_col=start_col_i,
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end_col=end_col_i,
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strand_col=strand_col_i,
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fix_strand=True)
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indel = NiceReaderWrapper( fileinput.FileInput( sp_file.name ),
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chrom_col=1,
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start_col=sort_col,
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end_col=sort_col+1,
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strand_col=-1,
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fix_strand=True)
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indelTree = quicksect.IntervalTree()
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for item in indel:
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if type( item ) is GenomicInterval:
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indelTree.insert( item, indel.linenum, item.fields )
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result=[]
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global full, blk_len, blk_list
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for interval in win:
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if type( interval ) is Header:
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pass
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if type( interval ) is Comment:
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pass
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elif type( interval ) == GenomicInterval:
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chrom = interval.chrom
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start = int(interval.start)
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end = int(interval.end)
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if start > end:
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warn( "Interval start after end!" )
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ins_chr = "%s.%s_insert" %(dbkey_i,chrom)
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del_chr = "%s.%s_delete" %(dbkey_i,chrom)
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irate = 0
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drate = 0
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if ins_chr not in indelTree.chroms and del_chr not in indelTree.chroms:
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pass
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else:
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if ins_chr in indelTree.chroms:
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full = 0.0
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blk_len = 0
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blk_list = []
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root = indelTree.chroms[ins_chr] #root node for the chrom insertion tree
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counter(root, start, end, sort_col)
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if blk_len:
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irate = full/blk_len
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if del_chr in indelTree.chroms:
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full = 0.0
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blk_len = 0
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blk_list = []
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root = indelTree.chroms[del_chr] #root node for the chrom insertion tree
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counter(root, start, end, sort_col)
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if blk_len:
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drate = full/blk_len
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interval.fields.append(str("%.2e" %irate))
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interval.fields.append(str("%.2e" %drate))
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print >>fout, "\t".join(interval.fields)
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fout.flush()
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if __name__ == "__main__":
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main() |