diff fasta_affixer.py @ 0:a4cd8608ef6b draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fasta_affixer.py	Mon Apr 01 07:56:36 2019 -0400
@@ -0,0 +1,35 @@
+#!/usr/bin/env python3
+''' fasta affixer - adding prefixes and suffixes to fasta sequence names'''
+import argparse
+
+parser = argparse.ArgumentParser()
+parser.add_argument("-f", "--fasta", type=str, help="fasta file")
+parser.add_argument("-o", "--output", type=str, help="output fasta file")
+parser.add_argument(
+    "-p", "--prefix",
+    type=str, help="prefix to be added to names")
+parser.add_argument(
+    "-s", "--suffix",
+    type=str, help="suffix to be added",
+    default='')
+parser.add_argument("-n",
+                    "--nspace",
+                    type=int,
+                    help="number of spaces to ignore",
+                    default='0')
+
+args = parser.parse_args()
+
+with open(args.fasta, "r") as f, open(args.output, "w") as out:
+    for oneline in f:
+        if oneline == "":
+            continue
+        if not oneline:
+            break
+        if oneline[0] == ">":
+            header = " ".join(oneline.split()[:1 + args.nspace])
+            header_out = header[0] + args.prefix + header[1:] + args.suffix + "\n"
+            out.write(header_out)
+        else:
+            out.write(oneline)
+