| Previous changeset 3:b12ff7a3ee41 (2019-10-16) Next changeset 5:79261884facd (2021-11-27) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 3a3bb179f4f3c99b25ef082996720c62aedb6200" |
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modified:
convert_gff.xml macros.xml |
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removed:
gff_to_prot.py |
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| diff -r b12ff7a3ee41 -r 2aea122fbd25 convert_gff.xml --- a/convert_gff.xml Wed Oct 16 04:33:13 2019 -0400 +++ b/convert_gff.xml Fri Jan 31 10:49:13 2020 -0500 |
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| @@ -1,10 +1,11 @@ <?xml version="1.0"?> -<tool id="gff_to_prot" name="Convert GFF3" version="1.0.0"> +<tool id="gff_to_prot" name="Convert GFF3" version="@VERSION@+galaxy0"> <description>to prot_table for TRANSIT</description> <macros> <import>macros.xml</import> </macros> - <command detect_errors="exit_code">$__tool_directory__/gff_to_prot.py '$input' '$output'</command> + <expand macro="requirements" /> + <command detect_errors="exit_code">transit convert gff_to_prot_table '$input' '$output'</command> <inputs> <param name="input" type="data" format="gff3" label="GenBank GFF file" /> </inputs> |
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| diff -r b12ff7a3ee41 -r 2aea122fbd25 gff_to_prot.py --- a/gff_to_prot.py Wed Oct 16 04:33:13 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,65 +0,0 @@ -#!/usr/bin/env python -import csv -import os -import sys - - -def get_description(line, parent): - cols = line.split('\t') - labels = {} - for pair in cols[8].split(";"): - k, v = pair.split('=') - labels[k] = v - - if (cols[2]) == "CDS" and labels["Parent"] == parent: - return labels.get("Note", '-') - return '-' - - -def convert_to_prot_table(fname, output_name): - gff_file = open(fname) - output_file = open(output_name, 'w') - writer = csv.writer(output_file, delimiter='\t') - lines = gff_file.readlines() - gff_file.close() - for i, line in enumerate(lines): - line = line.strip() - if line.startswith('#'): - continue - cols = line.split('\t') - if (len(cols) < 9): - print("Ignoring invalid row with entries: {0}".format(cols)) - elif (cols[2]) == "region": - continue - elif (cols[2]) == "CDS": - continue - elif (cols[2]) == "gene": - start = int(cols[3]) - end = int(cols[4]) - strand = cols[6].strip() - labels = {} - diff = int(abs(end - start) / 3) # What is this called? - for pair in cols[8].split(";"): - k, v = pair.split('=') - labels[k.strip()] = v.strip() - - Rv = labels["locus_tag"].strip() # error out if not found - gene = labels.get('Name', '') - desc = get_description(lines[i + 1], labels.get("ID", "")) if (i + 1) < len(lines) else '-' - vals = [desc, start, end, strand, diff, '-', '-', gene, Rv, '-'] - writer.writerow(vals) - output_file.close() - - -if __name__ == "__main__": - usage_string = "Usage: python gff-prot-converter.py <gff filename> <output filename>" - - if len(sys.argv) < 3: - print(usage_string) - sys.exit(0) - file_name = sys.argv[1] - if not os.path.exists(file_name): - print("File not found. Exiting...") - print(usage_string) - sys.exit(0) - convert_to_prot_table(file_name, sys.argv[2]) |
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| diff -r b12ff7a3ee41 -r 2aea122fbd25 macros.xml --- a/macros.xml Wed Oct 16 04:33:13 2019 -0400 +++ b/macros.xml Fri Jan 31 10:49:13 2020 -0500 |
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| @@ -9,11 +9,10 @@ <xml name="requirements"> <requirements> <requirement type="package" version="@VERSION@">transit</requirement> - <requirement type="package" version="3.7">python</requirement> <yield /> </requirements> </xml> - <token name="@VERSION@">3.0.1</token> + <token name="@VERSION@">3.0.2</token> <xml name="outputs"> <yield /> <data name="sites" from_work_dir="transit_out.txt" format="tabular" label="${tool.name} on ${on_string} Sites" /> |