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diff karyotype-from-fasta.py @ 7:4b519282a05b draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit ef20b4968a6d00c49209de6b723f8b96d8bd128a"
author iuc
date Mon, 25 May 2020 10:52:02 -0400
parents
children e6cbe3190642
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/karyotype-from-fasta.py	Mon May 25 10:52:02 2020 -0400
@@ -0,0 +1,12 @@
+#!/usr/bin/env python
+import sys
+from Bio import SeqIO
+
+
+# Process fasta data, extracting only headers
+for idx, seq in enumerate(SeqIO.parse(sys.argv[1], "fasta")):
+    sys.stdout.write(
+        "chr	-	{seq_id}	{seq_id}	0	{length}	chr{idx}color\n".format(
+            seq_id=seq.id, idx=idx, length=len(seq)
+        )
+    )