diff fastqsolexa_to_fasta_qual.py @ 0:b471da1d7303 draft default tip

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fastqsolexa_to_fasta_qual.py	Mon May 19 10:59:35 2014 -0400
@@ -0,0 +1,109 @@
+#!/usr/bin/env python
+
+"""
+convert fastqsolexa file to separated sequence and quality files.
+
+assume each sequence and quality score are contained in one line
+the order should be:
+1st line: @title_of_seq
+2nd line: nucleotides
+3rd line: +title_of_qualityscore (might be skipped)
+4th line: quality scores 
+(in three forms: a. digits, b. ASCII codes, the first char as the coding base, c. ASCII codes without the first char.)
+
+Usage:
+%python fastqsolexa_to_fasta_qual.py <your_fastqsolexa_filename> <output_seq_filename> <output_score_filename>
+"""
+
+import sys, os
+from math import *
+
+assert sys.version_info[:2] >= ( 2, 4 )
+
+def stop_err( msg ):
+    sys.stderr.write( "%s" % msg )
+    sys.exit()
+
+def __main__():
+    infile_name = sys.argv[1]
+    outfile_seq = open( sys.argv[2], 'w' )
+    outfile_score = open( sys.argv[3], 'w' )
+    datatype = sys.argv[4]
+    seq_title_startswith = ''
+    qual_title_startswith = ''
+    default_coding_value = 64
+    fastq_block_lines = 0
+    
+    for i, line in enumerate( file( infile_name ) ):
+        line = line.rstrip()
+        if not line or line.startswith( '#' ):
+            continue
+        fastq_block_lines = ( fastq_block_lines + 1 ) % 4
+        line_startswith = line[0:1]
+        if fastq_block_lines == 1:
+            # first line is @title_of_seq
+            if not seq_title_startswith:
+                seq_title_startswith = line_startswith
+            if line_startswith != seq_title_startswith:
+                outfile_seq.close()
+                outfile_score.close()
+                stop_err( 'Invalid fastqsolexa format at line %d: %s.' % ( i + 1, line ) )
+            read_title = line[1:]
+            outfile_seq.write( '>%s\n' % line[1:] )
+        elif fastq_block_lines == 2:
+            # second line is nucleotides
+            read_length = len( line )
+            outfile_seq.write( '%s\n' % line )
+        elif fastq_block_lines == 3:
+            # third line is +title_of_qualityscore ( might be skipped )
+            if not qual_title_startswith:
+                qual_title_startswith = line_startswith
+            if line_startswith != qual_title_startswith:
+                outfile_seq.close()
+                outfile_score.close()
+                stop_err( 'Invalid fastqsolexa format at line %d: %s.' % ( i + 1, line ) )    
+            quality_title = line[1:]
+            if quality_title and read_title != quality_title:
+                outfile_seq.close()
+                outfile_score.close()
+                stop_err( 'Invalid fastqsolexa format at line %d: sequence title "%s" differes from score title "%s".' % ( i + 1, read_title, quality_title ) )
+            if not quality_title:
+                outfile_score.write( '>%s\n' % read_title )
+            else:
+                outfile_score.write( '>%s\n' % line[1:] )
+        else:
+            # fourth line is quality scores
+            qual = ''
+            fastq_integer = True
+            # peek: ascii or digits?
+            val = line.split()[0]
+            try: 
+                check = int( val )
+                fastq_integer = True
+            except:
+                fastq_integer = False
+                
+            if fastq_integer:
+                # digits
+                qual = line
+            else:
+                # ascii
+                quality_score_length = len( line )
+                if quality_score_length == read_length + 1:
+                    # first char is qual_score_startswith
+                    qual_score_startswith = ord( line[0:1] )
+                    line = line[1:]
+                elif quality_score_length == read_length:
+                    qual_score_startswith = default_coding_value
+                else:
+                    stop_err( 'Invalid fastqsolexa format at line %d: the number of quality scores ( %d ) is not the same as bases ( %d ).' % ( i + 1, quality_score_length, read_length ) )
+                for j, char in enumerate( line ):
+                    score = ord( char ) - qual_score_startswith    # 64
+                    qual = "%s%s " % ( qual, str( score ) )
+            outfile_score.write( '%s\n' % qual )
+              
+    outfile_seq.close()
+    outfile_score.close()
+
+if __name__ == "__main__": __main__() 
+    
\ No newline at end of file