diff fasta_to_tabular.py @ 0:9d189d08f2ad draft

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fasta_to_tabular.py	Mon May 19 12:34:27 2014 -0400
@@ -0,0 +1,57 @@
+#!/usr/bin/env python
+# This code exists in 2 places: ~/datatypes/converters and ~/tools/fasta_tools
+"""
+Input: fasta (input file), tabular (output file), int (truncation of id), int (columns from description)
+Output: tabular
+format convert: fasta to tabular
+"""
+
+import sys, os
+
+def stop_err( msg ):
+    sys.stderr.write( msg )
+    sys.exit()
+
+def __main__():
+    if len(sys.argv) != 5:
+        stop_err("Wrong number of argument. Expect four (fasta, tabular, truncation, columns)")
+    infile = sys.argv[1]
+    outfile = sys.argv[2]
+    keep_first = int( sys.argv[3] )
+    descr_split = int( sys.argv[4] )
+    fasta_title = fasta_seq = ''
+    if keep_first == 0:
+        keep_first = None
+    elif descr_split == 1:
+        #Added one for the ">" character
+        #(which is removed if using descr_split > 1)
+        keep_first += 1
+    if descr_split < 1:
+        stop_err("Bad description split value (should be 1 or more)")
+    out = open( outfile, 'w' )
+    for i, line in enumerate( open( infile ) ):
+        line = line.rstrip( '\r\n' )
+        if not line or line.startswith( '#' ):
+            continue
+        if line.startswith( '>' ):
+            #Don't want any existing tabs to trigger extra columns:
+            line = line.replace('\t', ' ')
+            if i > 0:
+                out.write('\n')
+            if descr_split == 1:
+                out.write(line[1:keep_first])
+            else:
+                words = line[1:].split(None, descr_split-1)
+                #apply any truncation to first word (the id)
+                words[0] = words[0][0:keep_first]
+                #pad with empty columns if required
+                words += [""]*(descr_split-len(words))
+                out.write("\t".join(words))
+            out.write('\t')
+        else:
+            out.write(line)
+    if i > 0:
+        out.write('\n')
+    out.close()
+
+if __name__ == "__main__" : __main__()