--- a/utils/fasta_to_len.py	Mon Mar 02 06:46:51 2020 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,47 +0,0 @@
-#!/usr/bin/env python
-"""
-Input: fasta, int
-Output: tabular
-Return titles with lengths of corresponding seq
-"""
-
-import sys
-
-
-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
-
-    # number of char to keep in the title
-    if keep_first_char == 0:
-        keep_first_char = None
-    else:
-        keep_first_char += 1
-
-    first_entry = True
-    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:
-                seq_len += len(line)
-
-        # 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)