diff utils/fasta_to_len.py @ 4:e12f68d2cc4e draft

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

--- a/utils/fasta_to_len.py	Wed Sep 11 09:41:59 2019 -0400
+++ b/utils/fasta_to_len.py	Sun Mar 01 07:24:10 2020 -0500
@@ -5,16 +5,13 @@
 Return titles with lengths of corresponding seq
 """
 
-import sys, os
+import sys
 
-assert sys.version_info[:2] >= ( 2, 4 )
+assert sys.version_info[:2] >= (2, 4)
 
-def compute_fasta_length( fasta_file, out_file, keep_first_char, keep_first_word=False ):
 
-    infile = fasta_file
-    out = open( out_file, 'w')
-    keep_first_char = int( keep_first_char )
-
+def compute_fasta_length(fasta_file, out_file, keep_first_char, keep_first_word=False):
+    keep_first_char = int(keep_first_char)
     fasta_title = ''
     seq_len = 0
 
@@ -25,28 +22,28 @@
         keep_first_char += 1
 
     first_entry = True
-
-    for line in open( infile ):
-        line = line.strip()
-        if not line or line.startswith( '#' ):
-            continue
-        if line[0] == '>':
-            if first_entry == False:
-                if keep_first_word:
-                    fasta_title = fasta_title.split()[0]
-                out.write( "%s\t%d\n" % ( fasta_title[ 1:keep_first_char ], seq_len ) )
+    with open(fasta_file) as in_fh, open(out_file, 'w') as out_fh:
+        for line in in_fh:
+            line = line.strip()
+            if not line or line.startswith('#'):
+                continue
+            if line[0] == '>':
+                if first_entry is False:
+                    if keep_first_word:
+                        fasta_title = fasta_title.split()[0]
+                    out_fh.write("%s\t%d\n" % (fasta_title[1:keep_first_char], seq_len))
+                else:
+                    first_entry = False
+                fasta_title = line
+                seq_len = 0
             else:
-                first_entry = False
-            fasta_title = line
-            seq_len = 0
-        else:
-            seq_len += len(line)
+                seq_len += len(line)
 
-    # last fasta-entry
-    if keep_first_word:
-        fasta_title = fasta_title.split()[0]
-    out.write( "%s\t%d\n" % ( fasta_title[ 1:keep_first_char ], seq_len ) )
-    out.close()
+        # last fasta-entry
+        if keep_first_word:
+            fasta_title = fasta_title.split()[0]
+        out_fh.write("%s\t%d\n" % (fasta_title[1:keep_first_char], seq_len))
 
-if __name__ == "__main__" :
-    compute_fasta_length( sys.argv[1], sys.argv[2], sys.argv[3], True )
\ No newline at end of file
+
+if __name__ == "__main__":
+    compute_fasta_length(sys.argv[1], sys.argv[2], sys.argv[3], True)