changeset 102:3348b5ae153b draft

Uploaded

--- /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('<html><head><h3>%s</h3></head>\n' % title)
+        fh.write('<body><p/><table cellpadding="2">\n')
+        fh.write('<tr><th>Size</th><th>Name</th></tr>\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 = '<a href="%s" type="text/plain">%s</a>\n' % (fname, fname)
+            fh.write('<tr bgcolor="%s"><td>%s</td><td>%s</td></tr>\n' % (bgcolor, size, link))
+        fh.write('</table></body></html>\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)

--- /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)

--- /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 <http://www.gnu.org/licenses/>.
+
+# 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)

--- /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 @@
+<tables>
+    <table name="plant_tribes_scaffolds" comment_char="#">
+        <columns>value, name, path, description</columns>
+        <file path="tool-data/plant_tribes_scaffolds.loc" />
+    </table>
+</tables>