<s> import sys <EOL> import subprocess <EOL> from smRtools import * <EOL> IndexSource = sys . argv [ <NUM_LIT:1> ] <EOL> ExtractionDirective = sys . argv [ <NUM_LIT:2> ] <EOL> if ExtractionDirective == "<STR_LIT>" : <EOL> genomeRefFormat = "<STR_LIT>" <EOL> elif ExtractionDirective == "<STR_LIT>" : <EOL> genomeRefFormat = "<STR_LIT>" <EOL> OutputPre_mirs = sys . argv [ <NUM_LIT:3> ] <EOL> OutputMature_Mirs = sys . argv [ <NUM_LIT:4> ] <EOL> GFF3_file = sys . argv [ <NUM_LIT:5> ] <EOL> lattice = sys . argv [ <NUM_LIT:6> ] <EOL> Rcode = sys . argv [ <NUM_LIT:7> ] <EOL> latticePDF = sys . argv [ <NUM_LIT:8> ] <EOL> Triplets = [ sys . argv [ <NUM_LIT:9> : ] [ i : i + <NUM_LIT:3> ] for i in xrange ( <NUM_LIT:0> , len ( sys . argv [ <NUM_LIT:9> : ] ) , <NUM_LIT:3> ) ] <EOL> MasterListOfGenomes = { } <EOL> for [ filePath , FileExt , FileLabel ] in Triplets : <EOL> print FileLabel <EOL> MasterListOfGenomes [ FileLabel ] = HandleSmRNAwindows ( alignmentFile = filePath , <EOL> alignmentFileFormat = FileExt , <EOL> genomeRefFile = IndexSource , <EOL> genomeRefFormat = genomeRefFormat , <EOL> biosample = FileLabel ) <EOL> header = [ "<STR_LIT>" ] <EOL> for [ filePath , FileExt , FileLabel ] in Triplets : <EOL> header . append ( FileLabel ) <EOL> hit_table = [ "<STR_LIT:\t>" . join ( header ) ] <EOL> gff3 = open ( GFF3_file , "<STR_LIT:r>" ) <EOL> lattice_dataframe = [ ] <EOL> for line in gff3 : <EOL> if line [ <NUM_LIT:0> ] == "<STR_LIT:#>" : <EOL> continue <EOL> gff_fields = line [ : - <NUM_LIT:1> ] . split ( "<STR_LIT:\t>" ) <EOL> chrom = gff_fields [ <NUM_LIT:0> ] <EOL> gff_name = gff_fields [ - <NUM_LIT:1> ] . split ( "<STR_LIT>" ) [ - <NUM_LIT:1> ] . split ( "<STR_LIT:;>" ) [ <NUM_LIT:0> ] <EOL> item_upstream_coordinate = int ( gff_fields [ <NUM_LIT:3> ] ) <EOL> item_downstream_coordinate = int ( gff_fields [ <NUM_LIT:4> ] ) <EOL> if gff_fields [ <NUM_LIT:6> ] == "<STR_LIT:+>" : <EOL> item_polarity = "<STR_LIT>" <EOL> else : <EOL> item_polarity = "<STR_LIT>" <EOL> item_line = [ gff_name ] <EOL> for sample in header [ <NUM_LIT:1> : ] : <EOL> count = MasterListOfGenomes [ sample ] . instanceDict [ chrom ] . readcount ( upstream_coord = item_upstream_coordinate , <EOL> downstream_coord = item_downstream_coordinate , <EOL> polarity = item_polarity ) <EOL> item_line . append ( str ( count ) ) <EOL> if lattice != "<STR_LIT>" : <EOL> if ( "<STR_LIT>" not in gff_name ) and ( "<STR_LIT>" not in gff_name ) : <EOL> lattice_dataframe . append ( MasterListOfGenomes [ sample ] . instanceDict [ chrom ] . readcoverage ( <EOL> upstream_coord = item_upstream_coordinate , <EOL> downstream_coord = item_downstream_coordinate , <EOL> windowName = gff_name + "<STR_LIT:_>" + sample ) ) <EOL> hit_table . append ( "<STR_LIT:\t>" . join ( item_line ) ) <EOL> gff3 . close ( ) <EOL> Fpremirs = open ( OutputPre_mirs , "<STR_LIT:w>" ) <EOL> print >> Fpremirs , hit_table [ <NUM_LIT:0> ] <EOL> finalPreList = [ i for i in sorted ( hit_table [ <NUM_LIT:1> : ] ) if ( "<STR_LIT>" not in i ) and ( "<STR_LIT>" not in i ) ] <EOL> print >> Fpremirs , "<STR_LIT:\n>" . join ( finalPreList ) <EOL> Fpremirs . close ( ) <EOL> Fmaturemires = open ( OutputMature_Mirs , "<STR_LIT:w>" ) <EOL> print >> Fmaturemires , hit_table [ <NUM_LIT:0> ] <EOL> finalMatureList = [ i for i in sorted ( hit_table [ <NUM_LIT:1> : ] ) if ( "<STR_LIT>" in i ) or ( "<STR_LIT>" in i ) ] <EOL> print >> Fmaturemires , "<STR_LIT:\n>" . join ( finalMatureList ) <EOL> Fmaturemires . close ( ) <EOL> if lattice != "<STR_LIT>" : <EOL> Flattice = open ( lattice , "<STR_LIT:w>" ) <EOL> print >> Flattice , "<STR_LIT>" % ( "<STR_LIT>" , <EOL> "<STR_LIT>" , <EOL> "<STR_LIT>" , <EOL> "<STR_LIT>" , <EOL> "<STR_LIT>" , <EOL> "<STR_LIT>" , <EOL> "<STR_LIT>" ) <EOL> print >> Flattice , "<STR_LIT:\n>" . join ( lattice_dataframe ) <EOL> Flattice . close ( ) <EOL> R_command = "<STR_LIT>" + Rcode <EOL> process = subprocess . Popen ( R_command . split ( ) ) <EOL> process . wait ( ) </s>
