From fd6c5364aa2fc453b19454fbd3e6e343b8721504 Mon Sep 17 00:00:00 2001
From: "christoph.stritt@unibas.ch" <christoph.stritt@unibas.ch>
Date: Wed, 30 Oct 2024 13:46:22 +0100
Subject: [PATCH] ... and from the rename rule
---
workflow/rules/circularize.smk | 22 ++++++++++------------
1 file changed, 10 insertions(+), 12 deletions(-)
diff --git a/workflow/rules/circularize.smk b/workflow/rules/circularize.smk
index d5e731c..2e7e496 100755
--- a/workflow/rules/circularize.smk
+++ b/workflow/rules/circularize.smk
@@ -51,6 +51,8 @@ rule circlator_removeduplicates:
else:
if not skip:
output_handle.write(line)
+
+ output_handle.close()
rule circlator_localassembly:
@@ -112,26 +114,22 @@ rule rename:
run:
- import os
- import sys
- from Bio import SeqIO
-
contig_NR = 1
fasta_handle = open(output[0], "w")
with open(input.assembly) as original:
- records = SeqIO.parse(original, 'fasta')
+ for line in original:
+ if line.startswith('>'):
- for record in records:
+ seq_name = line.split(' ')[0][1:].strip()
+ seq_name_new = '>' + params.prefix + '_' + str(contig_NR)
+ fasta_handle.write(seq_name_new + '\n')
+ contig_NR += 1
- record.id = params.prefix + "_" + str(contig_NR)
- record.description = ""
-
- SeqIO.write(record, fasta_handle, 'fasta')
-
- contig_NR += 1
+ else:
+ fasta_handle.write(line)
fasta_handle.close()
--
GitLab