diff fasta_to_tabular.py @ 2:ff4751ce764d draft

"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_to_tabular commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"

--- a/fasta_to_tabular.py	Tue Oct 13 12:20:15 2015 -0400
+++ b/fasta_to_tabular.py	Sun Mar 01 12:23:22 2020 +0000
@@ -6,52 +6,53 @@
 format convert: fasta to tabular
 """
 
-import sys, os
+import sys
+
 
-def stop_err( msg ):
-    sys.stderr.write( msg )
-    sys.exit()
+def stop_err(msg):
+    sys.exit(msg)
+
 
 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 = ''
+    keep_first = int(sys.argv[3])
+    descr_split = int(sys.argv[4])
     if keep_first == 0:
         keep_first = None
     elif descr_split == 1:
-        #Added one for the ">" character
-        #(which is removed if using 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])
+    with open(outfile, 'w') as out, open(infile) as in_fh:
+        for i, line in enumerate(in_fh):
+            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:
-                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()
+                out.write(line)
+        if i > 0:
+            out.write('\n')
 
-if __name__ == "__main__" : __main__()
+
+if __name__ == "__main__":
+    __main__()