Mercurial > repos > iuc > trycycler_reconcile_msa
annotate trycycler.py @ 4:59bd28f6265d draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit e093c3f4fa599c1cb5cfc6f98e11ff1070ce440f"
author | iuc |
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date | Mon, 13 Dec 2021 21:16:05 +0000 |
parents | 4ac81df20c74 |
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4ac81df20c74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
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1 #!/usr/bin/env python3 |
4ac81df20c74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
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2 |
4ac81df20c74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
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3 from os import path, walk |
4ac81df20c74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
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4 from sys import argv |
4ac81df20c74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
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5 |
4ac81df20c74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
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6 |
4ac81df20c74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
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7 def cluster(output_folder): |
4ac81df20c74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
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8 counter = 1 |
4ac81df20c74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
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9 for root, dir, files in walk(output_folder): |
4ac81df20c74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
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10 if root.endswith('1_contigs'): |
4ac81df20c74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
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11 output_path = path.join(output_folder, f"cluster_0{counter}.fasta") |
4ac81df20c74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
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12 with open(output_path, "a") as out_cluster: |
4ac81df20c74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
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13 for fasta in files: |
4ac81df20c74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
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14 fasta_path = path.join(root, fasta) |
4ac81df20c74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
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15 fasta = open(fasta_path).read() |
4ac81df20c74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
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16 out_cluster.write(fasta) |
4ac81df20c74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
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17 counter += 1 |
4ac81df20c74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
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18 |
4ac81df20c74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
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19 |
4ac81df20c74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
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20 def reconcile(input_file): |
4ac81df20c74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
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21 number_cluster = [x for x in input_file[-1:0:-1] if x.isdigit()][0] |
4ac81df20c74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
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22 full_path = f"selected_cluster/cluster_0{number_cluster}/1_contigs/" |
4ac81df20c74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
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23 with open(input_file) as tmp: |
4ac81df20c74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
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24 for line in tmp: |
4ac81df20c74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
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25 if ">" in line: |
4ac81df20c74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
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26 filename = line[1:].strip() |
4ac81df20c74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
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27 output_fasta = f"{full_path}{filename}.fasta" |
4ac81df20c74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
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28 with open(output_fasta, "a") as handle: |
4ac81df20c74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
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29 handle.write(line) |
4ac81df20c74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
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30 |
4ac81df20c74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
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31 |
4ac81df20c74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
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32 def main(): |
4ac81df20c74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
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33 if argv[1] == "cluster": |
4ac81df20c74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
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34 cluster(argv[2]) |
4ac81df20c74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
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35 if argv[1] == "reconcile": |
4ac81df20c74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
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36 reconcile(argv[2]) |
4ac81df20c74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
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37 |
4ac81df20c74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
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38 |
4ac81df20c74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
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39 if __name__ == "__main__": |
4ac81df20c74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
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40 main() |