diff tools/fasta_tools/tabular_to_fasta.py @ 0:9071e359b9a3

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/fasta_tools/tabular_to_fasta.py	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,68 @@
+#!/usr/bin/env python
+"""
+Input: fasta, minimal length, maximal length
+Output: fasta
+Return sequences whose lengths are within the range.
+"""
+import sys, os
+
+assert sys.version_info[:2] >= ( 2, 4 )
+
+def stop_err( msg ):
+    sys.stderr.write( msg )
+    sys.exit()
+
+def __main__():
+    infile = sys.argv[1]
+    title_col = sys.argv[2]
+    seq_col = sys.argv[3]
+    outfile = sys.argv[4]        
+
+    if title_col == None or title_col == 'None' or seq_col == None or seq_col == 'None':
+        stop_err( "Columns not specified." )
+    try:
+        seq_col = int( seq_col ) - 1
+    except:
+        stop_err( "Invalid Sequence Column: %s." %str( seq_col ) )
+
+    title_col_list = title_col.split( ',' )
+    out = open( outfile, 'w' )
+    skipped_lines = 0
+    first_invalid_line = 0
+    invalid_line = ""
+    i = 0
+    
+    for i, line in enumerate( open( infile ) ):
+        error = False
+        line = line.rstrip( '\r\n' )
+        if line and not line.startswith( '#' ):
+            fields = line.split( '\t' )
+            fasta_title = []
+            for j in title_col_list:
+                try:
+                    j = int( j ) - 1
+                    fasta_title.append( fields[j] )
+                except:
+                    skipped_lines += 1
+                    if not invalid_line:
+                        first_invalid_line = i + 1
+                        invalid_line = line
+                    error = True
+                    break
+            if not error:
+                try:
+                    fasta_seq = fields[seq_col]
+                    if fasta_title[0].startswith( ">" ):
+                        fasta_title[0] = fasta_title[0][1:]
+                    print >> out, ">%s\n%s" % ( "_".join( fasta_title ), fasta_seq )
+                except:
+                    skipped_lines += 1
+                    if not invalid_line:
+                        first_invalid_line = i + 1
+                        invalid_line = line
+    out.close()    
+
+    if skipped_lines > 0:
+        print 'Data issue: skipped %d blank or invalid lines starting at #%d: "%s"' % ( skipped_lines, first_invalid_line, invalid_line )
+
+if __name__ == "__main__" : __main__()
\ No newline at end of file