# HG changeset patch # User greg # Date 1491831465 14400 # Node ID 529f4635ddb4d10eb275fa9c1b82032957ca5f6c # Parent badd2d0f168955fed80614c63061cde059dceff3 Uploaded diff -r badd2d0f1689 -r 529f4635ddb4 .shed.yml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/.shed.yml Mon Apr 10 09:37:45 2017 -0400 @@ -0,0 +1,13 @@ +name: plant_tribes_gene_family_aligner +owner: greg +description: | + Contains a tool that integrates de novo assembly sequences with scaffold gene family sequences. +homepage_url: https://github.com/dePamphilis/PlantTribes +long_description: | + Contains a tool that tool is one of the PlantTribes collection of automated modular analysis pipelines that + utilize objective classifications of complete protein sequences from sequenced plant genomes to perform + comparative evolutionary studies. This tool aligns gene family sequences. +remote_repository_url: https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/plant_tribes/gene_family_aligner +type: unrestricted +categories: +- Phylogenetics diff -r badd2d0f1689 -r 529f4635ddb4 gene_family_aligner.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gene_family_aligner.py Mon Apr 10 09:37:45 2017 -0400 @@ -0,0 +1,59 @@ +#!/usr/bin/env python +import argparse +import os +import subprocess + +import utils + +OUTPUT_DIR = 'geneFamilyAlignments_dir' + +parser = argparse.ArgumentParser() +parser.add_argument('--alignment_method', dest='alignment_method', help='Multiple sequence alignments method') +parser.add_argument('--automated_trimming', dest='automated_trimming', default=None, help="Trims alignments using trimAl's ML heuristic trimming approach") +parser.add_argument('--codon_alignments', dest='codon_alignments', default=None, help="Flag for constructing orthogroup multiple codon alignments") +parser.add_argument('--gap_trimming', dest='gap_trimming', default=None, type=float, help='Remove sites in alignments with gaps of') +parser.add_argument('--iterative_realignment', dest='iterative_realignment', type=int, default=None, help='"Maximum number of iterations') +parser.add_argument('--method', dest='method', help='Protein clustering method') +parser.add_argument('--num_threads', dest='num_threads', type=int, help='Number of threads to use for execution') +parser.add_argument('--orthogroup_faa', dest='orthogroup_faa', help="Directory of input fasta datasets") +parser.add_argument('--output', dest='output', help="Output dataset") +parser.add_argument('--output_dir', dest='output_dir', help="Output dataset file_path directory") +parser.add_argument('--pasta_iter_limit', dest='pasta_iter_limit', type=int, default=None, help='"Maximum number of iteration that the PASTA algorithm will execute') +parser.add_argument('--pasta_script_path', dest='pasta_script_path', default=None, help='Path to script for executing pasta') +parser.add_argument('--remove_sequences', dest='remove_sequences', default=None, type=float, help='Remove sequences with gaps of') +parser.add_argument('--scaffold', dest='scaffold', help='Orthogroups or gene families proteins scaffold') + +args = parser.parse_args() + +# Build the command line. +cmd = 'GeneFamilyAligner' +cmd += ' --orthogroup_faa %s' % args.orthogroup_faa +cmd += ' --scaffold %s' % args.scaffold +cmd += ' --method %s' % args.method +cmd += ' --alignment_method %s' % args.alignment_method +if args.alignment_method == 'pasta': + if args.pasta_script_path is not None: + cmd += ' --pasta_script_path %s' % args.pasta_script_path + if args.pasta_iter_limit is not None: + cmd += ' --pasta_iter_limit %d' % args.pasta_iter_limit +cmd += ' --num_threads %d' % args.num_threads +if args.codon_alignments is not None: + cmd += ' --codon_alignments' +if args.automated_trimming is not None: + cmd += ' --automated_trimming' +if args.gap_trimming is not None: + cmd += ' --gap_trimming %4f' % args.gap_trimming +if args.remove_sequences is not None: + cmd += ' --remove_sequences %4f' % args.remove_sequences +if args.iterative_realignment is not None: + cmd += ' --iterative_realignment %d' % args.iterative_realignment +# Run the command. +proc = subprocess.Popen(args=cmd, stderr=subprocess.PIPE, stdout=subprocess.PIPE, shell=True) +rc = proc.wait() +utils.check_execution_errors(rc, proc.stderr) +if args.codon_alignments is None: + src_output_dir = OUTPUT_DIR +else: + src_output_dir = os.path.join(OUTPUT_DIR, 'orthogroups_aln') +utils.move_directory_files(src_output_dir, args.output_dir) +utils.write_html_output(args.output, 'Aligned gene family sequences', args.output_dir) diff -r badd2d0f1689 -r 529f4635ddb4 plant_tribes_scaffolds.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/plant_tribes_scaffolds.loc.sample Mon Apr 10 09:37:45 2017 -0400 @@ -0,0 +1,4 @@ +## Plant Tribes scaffolds +#Value Name Path Description +#22Gv1.0 22Gv1.0 /plant_tribes/scaffolds/22Gv1.0 22 plant genomes (Angiosperms clusters, version 1.0; 22Gv1.0) +#22Gv1.1 22Gv1.1 /plant_tribes/scaffolds/22Gv1.1 22 plant genomes (Angiosperms clusters, version 1.1; 22Gv1.1) diff -r badd2d0f1689 -r 529f4635ddb4 run_pasta.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/run_pasta.py Mon Apr 10 09:37:45 2017 -0400 @@ -0,0 +1,63 @@ +#! /usr/bin/env python + +"""Main script of PASTA in command-line mode - this simply invokes the main + function found in pasta/mainpasta.py +""" + +# This file is part of PASTA which is forked from SATe + +# PASTA like SATe is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . + +# Jiaye Yu and Mark Holder, University of Kansas + +if __name__ == "__main__": + import os + import sys + from pasta.mainpasta import pasta_main + from pasta import MESSENGER + sys.setrecursionlimit(100000) + _PASTA_DEBUG = os.environ.get('PASTA_DEBUG') + _DEVELOPER = _PASTA_DEBUG and _PASTA_DEBUG != '0' + + if not _DEVELOPER: + _PASTA_DEVELOPER = os.environ.get('PASTA_DEVELOPER') + _DEVELOPER = _PASTA_DEVELOPER and _PASTA_DEVELOPER != '0' + try: + rc, temp_dir, temp_fs = pasta_main() + if not rc: + raise ValueError("Unknown PASTA execution error") + if (temp_dir is not None) and (os.path.exists(temp_dir)): + MESSENGER.send_info("Note that temporary files from the run have not been deleted, they can be found in:\n '%s'\n" % temp_dir) + if sys.platform.lower().startswith('darwin') and ("'" not in temp_dir): + MESSENGER.send_info(''' +If you cannot see this directory in the Finder application, you may want to use +the 'open' command executed from a Terminal. You can do this by launching the +/Applications/Utilities/Terminal program and then typing + +open '%s' + +followed by a return at the prompt. If the argument to the open command is a +directory, then it should open a Finder window in the directory (even if that +directory is hidden by default). +''' % temp_dir) + except Exception, x: + if _DEVELOPER: + raise + message = "PASTA is exiting because of an error:\n%s " % str(x) + try: + from pasta import MESSENGER + MESSENGER.send_error(message) + except: + sys.stderr.write(message) + sys.exit(1) diff -r badd2d0f1689 -r 529f4635ddb4 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Mon Apr 10 09:37:45 2017 -0400 @@ -0,0 +1,6 @@ + + + value, name, path, description + +
+ diff -r badd2d0f1689 -r 529f4635ddb4 utils.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/utils.py Mon Apr 10 09:37:45 2017 -0400 @@ -0,0 +1,42 @@ +import os +import shutil +import sys + + +def check_execution_errors(rc, stderr): + if rc != 0: + stop_err(stderr.read()) + + +def move_directory_files(source_dir, destination_dir): + source_directory = os.path.abspath(source_dir) + destination_directory = os.path.abspath(destination_dir) + if not os.path.isdir(destination_directory): + os.makedirs(destination_directory) + for dir_entry in os.listdir(source_directory): + source_entry = os.path.join(source_directory, dir_entry) + shutil.move(source_entry, destination_directory) + + +def stop_err(msg): + sys.stderr.write(msg) + sys.exit(1) + + +def write_html_output(output, title, dir): + with open(output, 'w') as fh: + fh.write('

%s

\n' % title) + fh.write('

\n') + fh.write('\n') + for index, fname in enumerate(sorted(os.listdir(dir))): + if index % 2 == 0: + bgcolor = '#D8D8D8' + else: + bgcolor = '#FFFFFF' + try: + size = str(os.path.getsize(os.path.join(dir, fname))) + except: + size = 'unknown' + link = '%s\n' % (fname, fname) + fh.write('\n' % (bgcolor, size, link)) + fh.write('
SizeName
%s%s
\n')