| Previous changeset 1:84849140a3bc (2021-04-23) Next changeset 3:c176164dc8a5 (2024-09-28) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8" |
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modified:
macros.xml readreduce.xml test-data/filter-out1.fasta tn93_cluster.py tn93_filter.py |
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| diff -r 84849140a3bc -r 1d2ec0b0a0a7 macros.xml --- a/macros.xml Fri Apr 23 03:04:45 2021 +0000 +++ b/macros.xml Wed Apr 20 16:59:27 2022 +0000 |
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| @@ -1,6 +1,12 @@ <?xml version="1.0"?> <macros> - <token name="@VERSION@">1.0.6</token> + <token name="@TOOL_VERSION@">1.0.6</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">tn93</requirement> + <yield /> + </requirements> + </xml> <xml name="citations"> <citations> <citation type="bibtex"> |
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| diff -r 84849140a3bc -r 1d2ec0b0a0a7 readreduce.xml --- a/readreduce.xml Fri Apr 23 03:04:45 2021 +0000 +++ b/readreduce.xml Wed Apr 20 16:59:27 2022 +0000 |
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| @@ -1,11 +1,9 @@ -<tool id="tn93_readreduce" name="Merge matching reads" version="@VERSION@"> +<tool id="tn93_readreduce" name="Merge matching reads" version="@TOOL_VERSION@+galaxy1"> <description>into clusters with TN-93</description> <macros> <import>macros.xml</import> </macros> - <requirements> - <requirement type="package" version="@VERSION@">tn93</requirement> - </requirements> + <expand macro="requirements" /> <version_command><![CDATA[tn93 --version]]></version_command> <command detect_errors="exit_code"><![CDATA[ readreduce |
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| diff -r 84849140a3bc -r 1d2ec0b0a0a7 test-data/filter-out1.fasta --- a/test-data/filter-out1.fasta Fri Apr 23 03:04:45 2021 +0000 +++ b/test-data/filter-out1.fasta Wed Apr 20 16:59:27 2022 +0000 |
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| b'@@ -13,3 +13,8 @@\n >gb_MW518841_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_220_2020_Segment_null_1\n ATGTTAGTTTTTCTTGTTTTATTGCCACTAGTCTCTAGTCAGTGTGTTAATCTTACAACCAGAACTCAATTACCCCCTGCATACACTAATTCTTTCACACGTGGTGTTTATTACCCTGACAAAGTTTTCAGATCCTCAGTTTTACATTCAACTCAGGACTTGTTCTTACCTTTCTTTTCCAATGTTACTTTGTTCCATGCTATACATGTCTCTGGGACCAATGGTACTAAGAGGTTTGATAACCCTGTCCTACCATTTAATGATGGTGTTTATTTTGCTTCCACTGAGAAGTCTAACATAATAAGAGGCTGGATTTTTGGTACTACTTTAGATTCGAAGACCCAGTCCCTACTTATTGTTAATAACGCTACTAATGTTGTTATTAAAGTCTGTGAATTTCAATTTTGTAATCATCCATTTTTGGGTGTTTATTACCACAAAAACAACAAAAGTTGGATGGAAAGTGAGTTCAGAGTTTATTCTAGTGCGAATAATTGCACTTTTGAATATGTCTCTCAGCCTTTTCTTATGGACCTTGAAGGAAAACAGGGTAATTTCAAAAATCTTAGGGAATTTGTGTTTAAGAATATTGATGGTTATTTTAAAATATATTCTAAGCACACGCCTATTAATTTAGTGCGTGATCTCCCTCAGGGTTTTTCGGCTTTAGAACCATTGGTAGATTTGCCAATAGGTATTAACATCACTAGGTTTCAAACTTTACTTGCTTTACATAGAAGTTATTTGACTCCTGGTGATTCTTCTTCAGGTTGGACAGCTGGTGCTGCAGCTTATTATGTGGGTTATCTTCAACCTAGGACTTTTCTATTAAAATATAATGAAAATGGAACCATTACAGATGCTGTAGACTGTGCACTTGACCCTCTCTCAGAAACAAAGTGTACGTTGAAATCCTTCACTGTAGAAAAAGGAATCTATCAAACTTCTAACTTTAGAGTCCAACCAACAGAATCTATTGTTAGATTTCCTAATATTACAAACTTGTGCCCTTTTGGTGAAGTTTTTAACGCCACCAGATTTGCATCTGTTTATGCTTGGAACAGGAAGAGAATCAGCAACTGTGTTGCTGATTATTCTGTCCTATATAATTCCGCATCATTTTCCACTTTTAAGTGTTATGGAGTGTCTCCTACTAAATTAAATGATCTCTGCTTTACTAATGTCTATGCAGATTCATTTGTAATTAGAGGTGATGAAGTCAGACAAATCGCTCCAGGGCAAACTGGAAAGATTGCTGATTATAATTATAAATTACCAGATGATTTTACAGGCTGCGTTATAGCTTGGAATTCTAACAATCTTGATTCTAAGGTTGGTGGTAATTATAATTACCTGTATAGATTGTTTAGGAAGTCTAATCTCAAACCTTTTGAGAGAGATATTTCAACTGAAATCTATCAGGCCGGTAGCACACCTTGTAATGGTGTTGAAGGTTTTAATTGTTACTTTCCTTTACAATCATATGGTTTCCAACCCACTAATGGTGTTGGTTACCAACCATACAGAGTAGTAGTACTTTCTTTTGAACTTCTACATGCACCAGCAACTGTTTGTGGACCTAAAAAGTCTACTAATTTGGTTAAAAACAAATGTGTCAATTTCAACTTTAATGGTTTAACAGGCACAGGTGTTCTTACTGAGTCTAACAAAAAGTTTCTGCCTTTCCAACAATTTGGCAGAGACATTGCTGACACTACTGATGCTGTCCGTGATCCACAGACACTTGAGATTCTTGACATTACACCATGTTCTTTTGGTGGTGTCAGTGTTATAACACCAGGAACAAATACTTCTAACCAGGTTGCTGTTCTTTATCAGGGTGTTAACTGCACAGAAGTCCCTGTTGCTATTCATGCAGATCAACTTACTCCTACTTGGCGTGTTTATTCTACAGGTTCTAATGTTTTTCAAACACGTGCAGGCTGTTTAATAGGGGCTGAACATGTCAACAACTCATATGAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTTATCAGACTCAGACTAATTCTCCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGTCACTTGGTGCAGAAAATTCAGTTGCTTACTCTAATAACTCTATTGCCATACCCACAAATTTTACTATTAGTGTTACCACAGAAATTCTACCAGTGTCTATGACCAAGACATCAGTAGATTGTACAATGTACATTTGTGGTGATTCAACTGAATGCAGCAATCTTTTGTTGCAATATGGCAGTTTTTGTACACAATTAAACCGTGCTTTAACTGGAATAGCTGTTGAACAAGACAAAAACACCCAAGAAGTTTTTGCACAAGTCAAACAAATTTACAAAACACCACCAATTAAAGATTTTGGTGGTTTTAATTTTTCACAAATATTACCAGATCCATCAAAACCAAGCAAGAGGTCATTTATTGAAGATCTACTTTTCAACAAAGTGACACTTGCAGATGCTGGCTTCATCAAACAATATGGTGATTGCCTTGGTGATATTGCTGCTAGAGACCTCATTTGTGCACAAAAGTTTAACGGCCTTACTGTTTTGCCACCTTTGCTCACAGATGAAATGATTGCTCAATACACTTCTGCACTGTTAGCGGGTACAATCACTTCTGGTTGGACCTTTGGTGCAGGTGCTGCATTACAAATACCATTTGCTATGCAAATGGCTTATAGGTTTAATGGTATTGGAGTTACACAGAATGTTCTCTATGAGAACCAAAAATTGATTGCCAACCAATTTAATAGTGCTATTGGCAAAATTCAAGACTCACTTTCTTCCACAGCAAGTGCACTTGGAAAACTTCAAGATGTGGTCAACCAAAATGCACAAGCTTTAAACACGCTTGTTAAACAACTTAGCTCCAATTTTGGTGCAATTTCAAGTGTTTTAAATGATATCCTTTCACGTCTTGACAAAGTTGAGGCTGAAGTGCAAATTGATAGGTTGATCACAGGCAGACTTCAAAGTTTGCAGACATATGTGACTCAACAATTAATTAGAGCTGCAGAAATCAGAGCTTCTGCTAATCTTGCTGCTACTAAAATGTCAGAGTGTGTACTTGGACAATCAAAAAGAGTTGATTTTTGTGGAAAGGGCTATCATCTTATGTCCTTCCCTCAGTCAGCACCTCATGGTGTAGTCTTCTTGCATGTGACTTATGTCCCTGCACAAGAAAAGAACTTCACAACTGCTCCTGCCATTTGTCATGATGGAAAAGCACACTTTCCTCGTGAAGGTGTCTTTGTTTCAAATGGCACACACTGGTTTGTAACACAAAGGAATTTTTATGAACCACAAATCATTACTACAGACAACACATTTGTGTCTGGTAACTGTGATGTTGTAATAGGAATTGTCAACAACACAGTTTATGATCCTTTGCAACCTGAATTAGACTCATTCAAGGAGGAGTTAGATAAATATTTTAAGAATCATACATCACCAGATGTTGATTTAGGTGACATCTCTGGCATTAATGCTTCAGTTGTAAACATTCAAAAAGAAATTGACCGCCTCAATGAGGTTGCCAAGAATTTAAATGAATCTCTCATCGATCTCCAAGAACTTGGAAAGTATGAGCAGTATATAAAATGGCCATGGTACATTTGGCTAGGTTTTATAGCTGGCTTGATTGCCATAGTAATGGTGACAATTATGCTTTGCTGTATGACCAGTTGCTGTAGTTGTCTCAAGGGCTGTTGTTCTTGTGGATCCTGCTGCAAATTTGATGAAGACGACTCTGAGCCAGTGCTCAAAGGAGTCAAATTACATTACACA\n \n+\n+>epi_isl_1041403'..b'-----------------------------------------------------------------------------------------------------------------------------------------\n+>REFERENCE\n+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAGACG\n\\ No newline at end of file\n' |
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| diff -r 84849140a3bc -r 1d2ec0b0a0a7 tn93_cluster.py --- a/tn93_cluster.py Fri Apr 23 03:04:45 2021 +0000 +++ b/tn93_cluster.py Wed Apr 20 16:59:27 2022 +0000 |
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| @@ -2,7 +2,6 @@ import json import os import shlex -import shutil import subprocess import sys @@ -41,27 +40,22 @@ def main(arguments): threshold = arguments.threshold step = threshold * 0.25 - shutil.copy(arguments.input, os.path.join(os.getcwd(), 'reference_msa.fa')) - shutil.copy(arguments.input, os.path.join(os.getcwd(), 'reference_msa.fa.bak')) with open(arguments.reference) as fh: for line in fh: if line[0] == '>': _ref_seq_name = line[1:].split(' ')[0].strip() break - while True and threshold <= 1: - command = 'tn93-cluster -o clusters.json -t %g -a %s -c %s -m json -l %d -g %f reference_msa.fa' % (threshold, arguments.ambigs, arguments.cluster_type, arguments.overlap, arguments.fraction) + while threshold <= 1: + command = 'tn93-cluster -o clusters.json -t %g -a %s -c %s -m json -l %d -g %f %s' % (threshold, arguments.ambigs, arguments.cluster_type, arguments.overlap, arguments.fraction, arguments.input) return_code = run_command(command) if return_code != 0: return return_code - input_stamp, cluster_count = cluster_to_fasta('clusters.json', 'reference_msa.fa.bak', _ref_seq_name) - if cluster_count <= arguments.cluster_count or threshold == 1: + input_stamp, cluster_count = cluster_to_fasta('clusters.json', 'clusters.fa', _ref_seq_name) + if cluster_count <= arguments.cluster_count: break else: threshold += step print('Found %d clusters at threshold %f' % (cluster_count, threshold)) - shutil.copy('reference_msa.fa.bak', arguments.compressed) - shutil.copy('clusters.json', arguments.output) - os.remove('reference_msa.fa.bak') return 0 |
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| diff -r 84849140a3bc -r 1d2ec0b0a0a7 tn93_filter.py --- a/tn93_filter.py Fri Apr 23 03:04:45 2021 +0000 +++ b/tn93_filter.py Wed Apr 20 16:59:27 2022 +0000 |
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| @@ -1,5 +1,6 @@ import argparse import csv +import random from Bio import SeqIO @@ -8,15 +9,22 @@ arguments.add_argument('-f', '--reference', help='Reference sequence', required=True, type=str) arguments.add_argument('-d', '--distances', help='Calculated pairwise distances', required=True, type=str) arguments.add_argument('-r', '--reads', help='Output file for filtered reads', required=True, type=str) -arguments.add_argument('-q', '--clusters', help='Compressed clusters', required=True, type=str) +arguments.add_argument('-q', '--clusters', help='Compressed background clusters', required=True, type=str) settings = arguments.parse_args() reference_name = 'REFERENCE' reference_seq = '' + +def unique_id(new_id, existing_ids): + while new_id in existing_ids: + new_id += '_' + ''.join(random.choices('0123456789abcdef', k=10)) + return new_id + + with open(settings.reference) as seq_fh: for seq_record in SeqIO.parse(seq_fh, 'fasta'): - reference_name = seq_record.name + reference_name = seq_record.name.split(' ')[0] reference_seq = seq_record.seq break @@ -27,17 +35,19 @@ for line in reader: if line[1] not in seqs_to_filter: seqs_to_filter.add(line[1]) + else: + seqs_to_filter.add(unique_id(line[1], seqs_to_filter)) if reference_name in seqs_to_filter: seqs_to_filter.remove(reference_name) with open(settings.reads, "a+") as fh: seqs_filtered = list() for seq_record in SeqIO.parse(settings.clusters, "fasta"): + if seq_record.name.split(' ')[0] == reference_name: + continue if seq_record.name not in seqs_to_filter: - if seq_record.name == reference_name: - if seq_record.name not in seqs_filtered: - seqs_filtered.append(seq_record.name) - else: - continue + unique_name = unique_id(seq_record.name, seqs_filtered) + fh.write('\n>%s\n%s' % (unique_name, seq_record.seq)) + seqs_filtered.append(unique_name) if reference_name not in seqs_filtered: fh.write('\n>REFERENCE\n%s' % reference_seq) |