# HG changeset patch # User greg # Date 1490626223 14400 # Node ID 3348b5ae153bcf746645738135aa228fe3b4d310 # Parent 9c6b468d8db237f919977665b4190c4e4d0ef8a2 Uploaded diff -r 9c6b468d8db2 -r 3348b5ae153b phylogenomics_analysis.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/phylogenomics_analysis.py Mon Mar 27 10:50:23 2017 -0400 @@ -0,0 +1,187 @@ +#!/usr/bin/env python +import argparse +import os +import shutil +import subprocess +import sys +import tempfile + +BUFF_SIZE = 1048576 +OUTPUT_DIR = 'phylogenomicsAnalysis_dir' + +parser = argparse.ArgumentParser() + +parser.add_argument('--alignments_method', dest='alignments_method', default=None, help='Multiple sequence alignments method') +parser.add_argument('--bootstrap_replicates', dest='bootstrap_replicates', type=int, default=None, help='Number of replicates for rapid bootstrap analysis') +parser.add_argument('--codon_alignments', dest='codon_alignments', default=None, help="Flag for constructing orthogroup multiple codon alignments") +parser.add_argument('--config_dir', dest='config_dir', help='Directory containing default configuration files') +parser.add_argument('--gap_trimming', dest='gap_trimming', default=None, type=float, help='Remove sites in alignments with gaps of') +parser.add_argument('--max_orthogroup_size', dest='max_orthogroup_size', type=int, default=None, help='Maximum number of sequences in orthogroup alignments') +parser.add_argument('--method', dest='method', help='Protein clustering method') +parser.add_argument('--min_orthogroup_size', dest='min_orthogroup_size', type=int, default=None, help='Minimum number of sequences in orthogroup alignments') +parser.add_argument('--num_threads', dest='num_threads', type=int, help='Number of threads to use for execution') +parser.add_argument('--output_aln', dest='output_aln', default=None, help='Output for orthogroups alignments') +parser.add_argument('--output_aln_dir', dest='output_aln_dir', default=None, help='output_aln.files_path') +parser.add_argument('--orthogroup_faa', dest='orthogroup_faa', help="Input dataset files_path") +parser.add_argument('--orthogroup_fna', dest='orthogroup_fna', default=None, help="Flag for coding sequences associated with orthogroups") +parser.add_argument('--output_ptortho', dest='output_ptortho', default=None, help='Output for orthogroups') +parser.add_argument('--output_ptorthocs', dest='output_ptorthocs', default=None, help='Output for orthogroups with corresponding coding sequences') +parser.add_argument('--output_ptorthocs_dir', dest='output_ptorthocs_dir', default=None, help='output_ptorthocs.files_path') +parser.add_argument('--output_ptortho_dir', dest='output_ptortho_dir', default=None, help='output_ptortho.files_path') +parser.add_argument('--output_tree', dest='output_tree', default=None, help='Output for phylogenetic trees') +parser.add_argument('--output_tree_dir', dest='output_tree_dir', default=None, help='output_tree.files_path') +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('--rooting_order', dest='rooting_order', default=None, help='Rooting order configuration for rooting trees') +parser.add_argument('--scaffold', dest='scaffold', default='mode', help='Orthogroups or gene families proteins scaffold') +parser.add_argument('--sequence_type', dest='sequence_type', default=None, help="Sequence type used in the phylogenetic inference") +parser.add_argument('--tree_inference', dest='tree_inference', default=None, help='Phylogenetic trees inference method') +parser.add_argument('--trim_type', dest='trim_type', default=None, help='Process used for gap trimming') + +args = parser.parse_args() + + +def get_stderr_exception(tmp_err, tmp_stderr, tmp_out, tmp_stdout, include_stdout=False): + tmp_stderr.close() + # Get stderr, allowing for case where it's very large. + tmp_stderr = open(tmp_err, 'rb') + stderr_str = '' + buffsize = BUFF_SIZE + try: + while True: + stderr_str += tmp_stderr.read(buffsize) + if not stderr_str or len(stderr_str) % buffsize != 0: + break + except OverflowError: + pass + tmp_stderr.close() + if include_stdout: + tmp_stdout = open(tmp_out, 'rb') + stdout_str = '' + buffsize = BUFF_SIZE + try: + while True: + stdout_str += tmp_stdout.read(buffsize) + if not stdout_str or len(stdout_str) % buffsize != 0: + break + except OverflowError: + pass + tmp_stdout.close() + if include_stdout: + return 'STDOUT\n%s\n\nSTDERR\n%s\n' % (stdout_str, stderr_str) + return stderr_str + + +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') + + +# Define command response buffers. +tmp_out = tempfile.NamedTemporaryFile().name +tmp_stdout = open(tmp_out, 'wb') +tmp_err = tempfile.NamedTemporaryFile().name +tmp_stderr = open(tmp_err, 'wb') +# Build the command line. +cmd = 'PhylogenomicsAnalysis' +cmd += ' --orthogroup_faa %s' % args.orthogroup_faa +cmd += ' --scaffold %s' % args.scaffold +cmd += ' --method %s' % args.method +cmd += ' --config_dir %s' % args.config_dir +cmd += ' --num_threads %d' % args.num_threads + +if args.codon_alignments is not None: + cmd += ' --codon_alignments' +if args.orthogroup_fna is not None: + cmd += ' --orthogroup_fna' +if args.sequence_type is not None: + cmd += ' --sequence_type %s' % args.sequence_type +if args.alignments_method is not None: + if args.alignments_method == 'create_alignments': + cmd += ' --create_alignments' + elif args.alignments_method == 'add_alignments': + cmd += ' --add_alignments' + elif args.alignments_method == 'pasta_alignments': + cmd += ' --pasta_alignments' + cmd += ' --pasta_script_path %s' % args.pasta_script_path + cmd += ' --pasta_iter_limit %d' % args.pasta_iter_limit +if args.tree_inference is not None: + cmd += ' --tree_inference %s' % args.tree_inference + if args.tree_inference == 'raxml': + if args.rooting_order is not None: + cmd += ' --rooting_order %s' % args.rooting_order + cmd += ' --bootstrap_replicates %d' % args.bootstrap_replicates +if args.max_orthogroup_size is not None: + cmd += ' --max_orthogroup_size %d' % args.max_orthogroup_size +if args.min_orthogroup_size is not None: + cmd += ' --min_orthogroup_size %d' % args.min_orthogroup_size +if args.remove_sequences is not None: + cmd += ' --remove_sequences %4f' % args.remove_sequences +if args.trim_type is not None: + if args.trim_type == 'automated_trimming': + cmd += ' --automated_trimming' + else: + cmd += ' --gap_trimming %4f' % args.gap_trimming +# Run the command. +proc = subprocess.Popen(args=cmd, stderr=tmp_stderr, stdout=tmp_stdout, shell=True) +rc = proc.wait() +# Handle execution errors. +if rc != 0: + error_message = get_stderr_exception(tmp_err, tmp_stderr, tmp_out, tmp_stdout) + stop_err( error_message ) +# Handle phylogenies for orthogroups outputs. +if args.orthogroup_fna is not None: + out_file = args.output_ptorthocs + orthogroups_dest_dir = args.output_ptorthocs_dir + title = 'Phylogenies files for orthogroups and corresponding coding sequences' +else: + out_file = args.output_ptortho + orthogroups_dest_dir = args.output_ptortho_dir + title = 'Phylogenies files for orthogroups' +orthogroups_src_dir = os.path.join(OUTPUT_DIR, 'orthogroups_fasta') +move_directory_files(orthogroups_src_dir, orthogroups_dest_dir) +write_html_output(out_file, title, orthogroups_dest_dir) +# Handle multiple sequences alignments for orthogroups outputs. +if args.output_aln is not None: + alignments_src_dir = os.path.join(OUTPUT_DIR, 'orthogroups_aln') + alignments_dest_dir = args.output_aln_dir + title = 'Multiple sequence alignments files for orthogroups' + move_directory_files(alignments_src_dir, alignments_dest_dir) + write_html_output(args.output_aln, title, alignments_dest_dir) +# Handle phylogenies for orthogroups outputs. +if args.output_tree is not None: + trees_src_dir = os.path.join(OUTPUT_DIR, 'orthogroups_tree') + trees_dest_dir = args.output_tree_dir + title = 'Phylogenetic tree files for orthogroups' + move_directory_files(trees_src_dir, trees_dest_dir) + write_html_output(args.output_tree, title, trees_dest_dir) diff -r 9c6b468d8db2 -r 3348b5ae153b plant_tribes_scaffolds.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/plant_tribes_scaffolds.loc.sample Mon Mar 27 10:50:23 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 9c6b468d8db2 -r 3348b5ae153b run_pasta.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/run_pasta.py Mon Mar 27 10:50:23 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 9c6b468d8db2 -r 3348b5ae153b tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Mon Mar 27 10:50:23 2017 -0400 @@ -0,0 +1,6 @@ + + + value, name, path, description + +
+