Mercurial > repos > iuc > trycycler_reconcile_msa

comparison trycycler.py @ 0:4ac81df20c74 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
author iuc
date Thu, 11 Feb 2021 19:26:05 +0000
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-1:000000000000 0:4ac81df20c74
1 #!/usr/bin/env python3
2
3 from os import path, walk
4 from sys import argv
5
6
7 def cluster(output_folder):
8 counter = 1
9 for root, dir, files in walk(output_folder):
10 if root.endswith('1_contigs'):
11 output_path = path.join(output_folder, f"cluster_0{counter}.fasta")
12 with open(output_path, "a") as out_cluster:
13 for fasta in files:
14 fasta_path = path.join(root, fasta)
15 fasta = open(fasta_path).read()
16 out_cluster.write(fasta)
17 counter += 1
18
19
20 def reconcile(input_file):
21 number_cluster = [x for x in input_file[-1:0:-1] if x.isdigit()][0]
22 full_path = f"selected_cluster/cluster_0{number_cluster}/1_contigs/"
23 with open(input_file) as tmp:
24 for line in tmp:
25 if ">" in line:
26 filename = line[1:].strip()
27 output_fasta = f"{full_path}{filename}.fasta"
28 with open(output_fasta, "a") as handle:
29 handle.write(line)
30
31
32 def main():
33 if argv[1] == "cluster":
34 cluster(argv[2])
35 if argv[1] == "reconcile":
36 reconcile(argv[2])
37
38
39 if __name__ == "__main__":
40 main()