Mercurial > repos > devteam > filter_transcripts_via_tracking
view filter_transcripts_via_tracking.py @ 1:447a704766ba draft default tip
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
author | devteam |
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date | Tue, 13 Oct 2015 12:21:22 -0400 |
parents | 0601d9a817c7 |
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#!/usr/bin/env python import os, sys, tempfile assert sys.version_info[:2] >= ( 2, 4 ) def __main__(): """ Utility script for analyzing Cufflinks data: uses a tracking file (produced by cuffcompare) to filter a GTF file of transcripts (usually the transcripts produced by cufflinks). Filtering is done by extracting transcript IDs from tracking file and then filtering the GTF so that the output GTF contains only transcript found in the tracking file. Because a tracking file has multiple samples, a sample number is used to filter transcripts for a particular sample. """ # Read parms. tracking_file_name = sys.argv[1] transcripts_file_name = sys.argv[2] output_file_name = sys.argv[3] sample_number = int ( sys.argv[4] ) # Open files. transcripts_file = open( transcripts_file_name, 'r' ) output_file = open( output_file_name, 'w' ) # Read transcript IDs from tracking file. transcript_ids = {} for i, line in enumerate( file( tracking_file_name ) ) : # Split line into elements. Line format is # [Transfrag ID] [Locus ID] [Ref Gene ID] [Ref Transcript ID] [Class code] [qJ:<gene_id>|<transcript_id>|<FMI>|<FPKM>|<conf_lo>|<conf_hi>] line = line.rstrip( '\r\n' ) elems = line.split( '\t' ) # Get transcript info. if sample_number == 1: transcript_info = elems[4] elif sample_number == 2: transcript_info = elems[5] if not transcript_info.startswith('q'): # No transcript for this sample. continue # Get and store transcript id. transcript_id = transcript_info.split('|')[1] transcript_id = transcript_id.strip('"') transcript_ids[transcript_id] = "" # Filter transcripts file using transcript_ids for i, line in enumerate( file( transcripts_file_name ) ): # GTF format: chrom source, name, chromStart, chromEnd, score, strand, frame, attributes. elems = line.split( '\t' ) # Get attributes. attributes_list = elems[8].split(";") attributes = {} for name_value_pair in attributes_list: pair = name_value_pair.strip().split(" ") name = pair[0].strip() if name == '': continue # Need to strip double quote from values value = pair[1].strip(" \"") attributes[name] = value # Get element's transcript id. transcript_id = attributes['transcript_id'] if transcript_id in transcript_ids: output_file.write(line) # Clean up. output_file.close() if __name__ == "__main__": __main__()