<s> import sys , subprocess , argparse <EOL> from smRtools import * <EOL> from collections import OrderedDict , defaultdict <EOL> import os <EOL> def Parser ( ) : <EOL> the_parser = argparse . ArgumentParser ( ) <EOL> the_parser . add_argument ( '<STR_LIT>' , action = "<STR_LIT:store>" , type = str , help = "<STR_LIT>" ) <EOL> the_parser . add_argument ( '<STR_LIT>' , action = "<STR_LIT:store>" , type = str , help = "<STR_LIT>" ) <EOL> the_parser . add_argument ( '<STR_LIT>' , action = '<STR_LIT:store>' , help = "<STR_LIT>" ) <EOL> the_parser . add_argument ( '<STR_LIT>' , nargs = '<STR_LIT:+>' , help = "<STR_LIT>" ) <EOL> the_parser . add_argument ( '<STR_LIT>' , nargs = '<STR_LIT:+>' , help = "<STR_LIT>" ) <EOL> the_parser . add_argument ( '<STR_LIT>' , nargs = '<STR_LIT:+>' , help = "<STR_LIT>" ) <EOL> the_parser . add_argument ( '<STR_LIT>' , nargs = '<STR_LIT:+>' , type = float , help = "<STR_LIT>" ) <EOL> the_parser . add_argument ( '<STR_LIT>' , type = str , help = "<STR_LIT>" ) <EOL> the_parser . add_argument ( '<STR_LIT>' , type = int , help = "<STR_LIT>" ) <EOL> the_parser . add_argument ( '<STR_LIT>' , type = int , help = "<STR_LIT>" ) <EOL> the_parser . add_argument ( '<STR_LIT>' , type = str , help = "<STR_LIT>" ) <EOL> the_parser . add_argument ( '<STR_LIT>' , action = "<STR_LIT:store_true>" , help = "<STR_LIT>" ) <EOL> the_parser . add_argument ( '<STR_LIT>' , action = "<STR_LIT:store_true>" , help = "<STR_LIT>" ) <EOL> args = the_parser . parse_args ( ) <EOL> return args <EOL> args = Parser ( ) <EOL> if args . reference_fasta : <EOL> genomeRefFormat = "<STR_LIT>" <EOL> genomeRefFile = args . reference_fasta <EOL> if args . reference_bowtie_index : <EOL> genomeRefFormat = "<STR_LIT>" <EOL> genomeRefFile = args . reference_bowtie_index <EOL> size_distribution_file = args . output_size_distribution <EOL> minquery = args . minquery <EOL> maxquery = args . maxquery <EOL> Rcode = args . rcode <EOL> filePath = args . input <EOL> fileExt = args . ext <EOL> fileLabel = args . label <EOL> normalization_factor = args . normalization_factor <EOL> global_size = args . global_size <EOL> collapse = args . collapse <EOL> if collapse : <EOL> pol = [ "<STR_LIT>" ] <EOL> else : <EOL> pol = [ "<STR_LIT:F>" , "<STR_LIT:R>" ] <EOL> MasterListOfGenomes = OrderedDict ( ) <EOL> def process_samples ( filePath ) : <EOL> for i , filePath in enumerate ( filePath ) : <EOL> norm = normalization_factor [ i ] <EOL> print fileLabel [ i ] <EOL> MasterListOfGenomes [ fileLabel [ i ] ] = HandleSmRNAwindows ( alignmentFile = filePath , alignmentFileFormat = fileExt [ i ] , genomeRefFile = genomeRefFile , genomeRefFormat = genomeRefFormat , biosample = fileLabel [ i ] , size_inf = minquery , size_sup = maxquery , norm = norm ) <EOL> return MasterListOfGenomes <EOL> def write_size_distribution_dataframe ( readDict , size_distribution_file , pol = [ "<STR_LIT>" ] ) : <EOL> '''<STR_LIT>''' <EOL> with open ( size_distribution_file , '<STR_LIT:w>' ) as size_distrib : <EOL> print >> size_distrib , "<STR_LIT>" <EOL> for sample in readDict . keys ( ) : <EOL> if args . gff : <EOL> dict = readDict [ sample ] <EOL> else : <EOL> dict = readDict [ sample ] . instanceDict <EOL> for gene in dict . keys ( ) : <EOL> histogram = dict [ gene ] . size_histogram ( ) <EOL> for polarity in pol : <EOL> for size , count in histogram [ polarity ] . iteritems ( ) : <EOL> print >> size_distrib , "<STR_LIT>" % ( gene , polarity , size , count , sample ) <EOL> def write_size_distribution_dataframe_global ( readDict , size_distribution_file , pol = [ "<STR_LIT>" ] ) : <EOL> with open ( size_distribution_file , '<STR_LIT:w>' ) as size_distrib : <EOL> print >> size_distrib , "<STR_LIT>" <EOL> for sample in readDict . keys ( ) : <EOL> histogram = readDict [ sample ] . size_histogram ( ) <EOL> gene = "<STR_LIT>" <EOL> for polarity in pol : <EOL> for size , count in histogram [ polarity ] . iteritems ( ) : <EOL> print >> size_distrib , "<STR_LIT>" % ( gene , polarity , size , count , sample ) <EOL> def gff_item_subinstances ( readDict , gff3 ) : <EOL> GFFinstanceDict = OrderedDict ( ) <EOL> with open ( gff3 ) as gff : <EOL> for line in gff : <EOL> if line [ <NUM_LIT:0> ] == "<STR_LIT:#>" : 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> item_polarity = gff_fields [ <NUM_LIT:6> ] <EOL> for sample in readDict . keys ( ) : <EOL> if not GFFinstanceDict . has_key ( sample ) : <EOL> GFFinstanceDict [ sample ] = { } <EOL> subinstance = extractsubinstance ( item_upstream_coordinate , item_downstream_coordinate , readDict [ sample ] . instanceDict [ chrom ] ) <EOL> if item_polarity == '<STR_LIT:->' : <EOL> subinstance . readDict = { key * - <NUM_LIT:1> : value for key , value in subinstance . readDict . iteritems ( ) } <EOL> subinstance . gene = gff_name <EOL> GFFinstanceDict [ sample ] [ gff_name ] = subinstance <EOL> return GFFinstanceDict <EOL> MasterListOfGenomes = process_samples ( filePath ) <EOL> if args . gff : <EOL> MasterListOfGenomes = gff_item_subinstances ( MasterListOfGenomes , args . gff ) <EOL> if global_size : <EOL> write_size_distribution_dataframe_global ( MasterListOfGenomes , size_distribution_file , pol ) <EOL> else : <EOL> write_size_distribution_dataframe ( MasterListOfGenomes , size_distribution_file , pol ) <EOL> R_command = "<STR_LIT>" + Rcode <EOL> process = subprocess . Popen ( R_command . split ( ) ) <EOL> process . wait ( ) </s>
