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changeset 1:112d80c9ccca draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
author iuc
date Wed, 20 Apr 2022 17:00:11 +0000
parents af03f3398f03
children eb6f0ec5b95e
files macros.xml test-data/filter-out1.fasta tn93_cluster.py tn93_cluster.xml tn93_filter.py
diffstat 5 files changed, 39 insertions(+), 25 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Fri Apr 23 03:04:15 2021 +0000
+++ b/macros.xml	Wed Apr 20 17:00:11 2022 +0000
@@ -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">
--- a/test-data/filter-out1.fasta	Fri Apr 23 03:04:15 2021 +0000
+++ b/test-data/filter-out1.fasta	Wed Apr 20 17:00:11 2022 +0000
@@ -13,3 +13,8 @@
 >gb_MW518841_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_220_2020_Segment_null_1
 ATGTTAGTTTTTCTTGTTTTATTGCCACTAGTCTCTAGTCAGTGTGTTAATCTTACAACCAGAACTCAATTACCCCCTGCATACACTAATTCTTTCACACGTGGTGTTTATTACCCTGACAAAGTTTTCAGATCCTCAGTTTTACATTCAACTCAGGACTTGTTCTTACCTTTCTTTTCCAATGTTACTTTGTTCCATGCTATACATGTCTCTGGGACCAATGGTACTAAGAGGTTTGATAACCCTGTCCTACCATTTAATGATGGTGTTTATTTTGCTTCCACTGAGAAGTCTAACATAATAAGAGGCTGGATTTTTGGTACTACTTTAGATTCGAAGACCCAGTCCCTACTTATTGTTAATAACGCTACTAATGTTGTTATTAAAGTCTGTGAATTTCAATTTTGTAATCATCCATTTTTGGGTGTTTATTACCACAAAAACAACAAAAGTTGGATGGAAAGTGAGTTCAGAGTTTATTCTAGTGCGAATAATTGCACTTTTGAATATGTCTCTCAGCCTTTTCTTATGGACCTTGAAGGAAAACAGGGTAATTTCAAAAATCTTAGGGAATTTGTGTTTAAGAATATTGATGGTTATTTTAAAATATATTCTAAGCACACGCCTATTAATTTAGTGCGTGATCTCCCTCAGGGTTTTTCGGCTTTAGAACCATTGGTAGATTTGCCAATAGGTATTAACATCACTAGGTTTCAAACTTTACTTGCTTTACATAGAAGTTATTTGACTCCTGGTGATTCTTCTTCAGGTTGGACAGCTGGTGCTGCAGCTTATTATGTGGGTTATCTTCAACCTAGGACTTTTCTATTAAAATATAATGAAAATGGAACCATTACAGATGCTGTAGACTGTGCACTTGACCCTCTCTCAGAAACAAAGTGTACGTTGAAATCCTTCACTGTAGAAAAAGGAATCTATCAAACTTCTAACTTTAGAGTCCAACCAACAGAATCTATTGTTAGATTTCCTAATATTACAAACTTGTGCCCTTTTGGTGAAGTTTTTAACGCCACCAGATTTGCATCTGTTTATGCTTGGAACAGGAAGAGAATCAGCAACTGTGTTGCTGATTATTCTGTCCTATATAATTCCGCATCATTTTCCACTTTTAAGTGTTATGGAGTGTCTCCTACTAAATTAAATGATCTCTGCTTTACTAATGTCTATGCAGATTCATTTGTAATTAGAGGTGATGAAGTCAGACAAATCGCTCCAGGGCAAACTGGAAAGATTGCTGATTATAATTATAAATTACCAGATGATTTTACAGGCTGCGTTATAGCTTGGAATTCTAACAATCTTGATTCTAAGGTTGGTGGTAATTATAATTACCTGTATAGATTGTTTAGGAAGTCTAATCTCAAACCTTTTGAGAGAGATATTTCAACTGAAATCTATCAGGCCGGTAGCACACCTTGTAATGGTGTTGAAGGTTTTAATTGTTACTTTCCTTTACAATCATATGGTTTCCAACCCACTAATGGTGTTGGTTACCAACCATACAGAGTAGTAGTACTTTCTTTTGAACTTCTACATGCACCAGCAACTGTTTGTGGACCTAAAAAGTCTACTAATTTGGTTAAAAACAAATGTGTCAATTTCAACTTTAATGGTTTAACAGGCACAGGTGTTCTTACTGAGTCTAACAAAAAGTTTCTGCCTTTCCAACAATTTGGCAGAGACATTGCTGACACTACTGATGCTGTCCGTGATCCACAGACACTTGAGATTCTTGACATTACACCATGTTCTTTTGGTGGTGTCAGTGTTATAACACCAGGAACAAATACTTCTAACCAGGTTGCTGTTCTTTATCAGGGTGTTAACTGCACAGAAGTCCCTGTTGCTATTCATGCAGATCAACTTACTCCTACTTGGCGTGTTTATTCTACAGGTTCTAATGTTTTTCAAACACGTGCAGGCTGTTTAATAGGGGCTGAACATGTCAACAACTCATATGAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTTATCAGACTCAGACTAATTCTCCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGTCACTTGGTGCAGAAAATTCAGTTGCTTACTCTAATAACTCTATTGCCATACCCACAAATTTTACTATTAGTGTTACCACAGAAATTCTACCAGTGTCTATGACCAAGACATCAGTAGATTGTACAATGTACATTTGTGGTGATTCAACTGAATGCAGCAATCTTTTGTTGCAATATGGCAGTTTTTGTACACAATTAAACCGTGCTTTAACTGGAATAGCTGTTGAACAAGACAAAAACACCCAAGAAGTTTTTGCACAAGTCAAACAAATTTACAAAACACCACCAATTAAAGATTTTGGTGGTTTTAATTTTTCACAAATATTACCAGATCCATCAAAACCAAGCAAGAGGTCATTTATTGAAGATCTACTTTTCAACAAAGTGACACTTGCAGATGCTGGCTTCATCAAACAATATGGTGATTGCCTTGGTGATATTGCTGCTAGAGACCTCATTTGTGCACAAAAGTTTAACGGCCTTACTGTTTTGCCACCTTTGCTCACAGATGAAATGATTGCTCAATACACTTCTGCACTGTTAGCGGGTACAATCACTTCTGGTTGGACCTTTGGTGCAGGTGCTGCATTACAAATACCATTTGCTATGCAAATGGCTTATAGGTTTAATGGTATTGGAGTTACACAGAATGTTCTCTATGAGAACCAAAAATTGATTGCCAACCAATTTAATAGTGCTATTGGCAAAATTCAAGACTCACTTTCTTCCACAGCAAGTGCACTTGGAAAACTTCAAGATGTGGTCAACCAAAATGCACAAGCTTTAAACACGCTTGTTAAACAACTTAGCTCCAATTTTGGTGCAATTTCAAGTGTTTTAAATGATATCCTTTCACGTCTTGACAAAGTTGAGGCTGAAGTGCAAATTGATAGGTTGATCACAGGCAGACTTCAAAGTTTGCAGACATATGTGACTCAACAATTAATTAGAGCTGCAGAAATCAGAGCTTCTGCTAATCTTGCTGCTACTAAAATGTCAGAGTGTGTACTTGGACAATCAAAAAGAGTTGATTTTTGTGGAAAGGGCTATCATCTTATGTCCTTCCCTCAGTCAGCACCTCATGGTGTAGTCTTCTTGCATGTGACTTATGTCCCTGCACAAGAAAAGAACTTCACAACTGCTCCTGCCATTTGTCATGATGGAAAAGCACACTTTCCTCGTGAAGGTGTCTTTGTTTCAAATGGCACACACTGGTTTGTAACACAAAGGAATTTTTATGAACCACAAATCATTACTACAGACAACACATTTGTGTCTGGTAACTGTGATGTTGTAATAGGAATTGTCAACAACACAGTTTATGATCCTTTGCAACCTGAATTAGACTCATTCAAGGAGGAGTTAGATAAATATTTTAAGAATCATACATCACCAGATGTTGATTTAGGTGACATCTCTGGCATTAATGCTTCAGTTGTAAACATTCAAAAAGAAATTGACCGCCTCAATGAGGTTGCCAAGAATTTAAATGAATCTCTCATCGATCTCCAAGAACTTGGAAAGTATGAGCAGTATATAAAATGGCCATGGTACATTTGGCTAGGTTTTATAGCTGGCTTGATTGCCATAGTAATGGTGACAATTATGCTTTGCTGTATGACCAGTTGCTGTAGTTGTCTCAAGGGCTGTTGTTCTTGTGGATCCTGCTGCAAATTTGATGAAGACGACTCTGAGCCAGTGCTCAAAGGAGTCAAATTACATTACACA
 
+
+>epi_isl_1041403/hCoV-19/USA/NY-PRL-2021_02_08_05H08/2021
+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>REFERENCE
+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAGACG
\ No newline at end of file
--- a/tn93_cluster.py	Fri Apr 23 03:04:15 2021 +0000
+++ b/tn93_cluster.py	Wed Apr 20 17:00:11 2022 +0000
@@ -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
 
 
--- a/tn93_cluster.xml	Fri Apr 23 03:04:15 2021 +0000
+++ b/tn93_cluster.xml	Wed Apr 20 17:00:11 2022 +0000
@@ -1,12 +1,11 @@
-<tool id="tn93_cluster" name="TN93 Cluster" version="@VERSION@">
+<tool id="tn93_cluster" name="TN93 Cluster" version="@TOOL_VERSION@+galaxy1">
     <description>sequences that lie within a specific distance of each other</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <requirements>
-        <requirement type="package" version="@VERSION@">tn93</requirement>
+    <expand macro="requirements">
         <requirement type="package" version="3.9">python</requirement>
-    </requirements>
+    </expand>
     <version_command><![CDATA[tn93 --version]]></version_command>
     <command detect_errors="exit_code"><![CDATA[
     python '$__tool_directory__/tn93_cluster.py' --input '$input_fasta' --reference '$reference' --output '$tn93_clusters'
@@ -25,7 +24,7 @@
         <param name="reference" type="data" format="fasta" label="Reference in FASTA format" />
         <param argument="--compress" type="boolean" truevalue="--compress" falsevalue="" label="Output additional fasta dataset with compressed clusters" />
         <param argument="--cluster-count" type="integer" value="200" label="Only retain this many clusters" />
-        <param argument="--threshold" type="float" min="0" value="0.0005" label="Distance threshold" help="Sequences which lie within this distance will be clustered" />
+        <param argument="--threshold" type="float" value="0.0005" min="0" max="1" label="Distance threshold" help="Sequences which lie within this distance will be clustered" />
         <param argument="--ambigs" type="select" label="Strategy for ambiguous nucleotides">
             <option value="resolve" selected="true">resolve</option>
             <option value="average">average</option>
@@ -42,8 +41,8 @@
             label="Maximum tolerated fraction of ambiguous characters" />
     </inputs>
     <outputs>
-        <data format="json" name="tn93_clusters" />
-        <data format="fasta" name="tn93_compressed_clusters">
+        <data format="json" name="tn93_clusters" from_work_dir="clusters.json" />
+        <data format="fasta" name="tn93_compressed_clusters" from_work_dir="clusters.fa">
             <filter>compress</filter>
         </data>
     </outputs>
--- a/tn93_filter.py	Fri Apr 23 03:04:15 2021 +0000
+++ b/tn93_filter.py	Wed Apr 20 17:00:11 2022 +0000
@@ -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)