changeset 0:ba049ce65693 draft

Initial upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_fetch_motifs.py	Sun Jan 11 19:21:52 2015 -0500
@@ -0,0 +1,73 @@
+#!/usr/bin/env python
+#Dan Blankenberg
+
+import sys
+import os
+import tempfile
+import shutil
+import optparse
+import urllib2
+#import uuid
+from ftplib import FTP
+import tarfile
+import zipfile
+import gzip
+import bz2
+
+from galaxy.util.json import from_json_string, to_json_string
+
+CHUNK_SIZE = 2**20 #1mb
+
+def download_motif_databases( data_manager_dict, params, target_directory, motif_db ):
+    TEST_DOWNLOAD_URL = 'http://gehlenborg.com/wp-content/uploads/motif/pouya_test_motifs.bed.bgz'
+    #TO DO: Add tbi file
+
+    url = TEST_DOWNLOAD_URL
+    fasta_reader = urllib2.urlopen( url )
+    
+    data_table_entry = _stream_fasta_to_file( fasta_reader, target_directory, params )
+    _add_data_table_entry( data_manager_dict, data_table_entry )
+
+def _add_data_table_entry( data_manager_dict, data_table_entry ):
+    data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
+    data_manager_dict['data_tables']['all_fasta'] = data_manager_dict['data_tables'].get( 'all_fasta', [] )
+    data_manager_dict['data_tables']['all_fasta'].append( data_table_entry )
+    return data_manager_dict
+
+def _stream_fasta_to_file( fasta_stream, target_directory, params, close_stream=True ):
+    fasta_base_filename = "pouya_test_motifs.bed.bgz"
+    fasta_filename = os.path.join( target_directory, fasta_base_filename )
+    fasta_writer = open( fasta_filename, 'wb+' )
+    
+    while True:
+        buffer = fasta_stream.read(CHUNK_SIZE)
+        if not buffer:
+            break
+
+        fasta_writer.write(buffer)
+
+    fasta_stream.close()
+    fasta_writer.close()
+    
+    return dict( value="test", name="Test Pouya Subset (hg19)", path=fasta_base_filename )
+
+def main():
+    #Parse Command Line
+    parser = optparse.OptionParser()
+    parser.add_option( '-m', '--motif_db', dest='motif_db', action='store', type="string", default=None, help='motif_db' )
+    (options, args) = parser.parse_args()
+    
+    filename = args[0]
+    
+    params = from_json_string( open( filename ).read() )
+    target_directory = params[ 'output_data' ][0]['extra_files_path']
+    os.mkdir( target_directory )
+    data_manager_dict = {}
+    
+    #Fetch the Motif Database
+    download_motif_databases( data_manager_dict, params, target_directory, motif_db )
+    
+    #save info to json file
+    open( filename, 'wb' ).write( to_json_string( data_manager_dict ) )
+        
+if __name__ == "__main__": main()

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_fetch_motifs.xml	Sun Jan 11 19:21:52 2015 -0500
@@ -0,0 +1,22 @@
+<tool id="data_manager_fetch_motifs" name="Motif Database" version="1.0.0" tool_type="manage_data">
+    <description>fetching</description>
+    <command interpreter="python">data_manager_fetch_motifs.py "${out_file}" --motif_db ${motif_db_selector}</command>
+    <inputs>
+        <param name="motif_db_selector" type="select" label="Choose the source for the motif db">
+            <option value="test" selected="True">Test Pouya Subset (hg19)</option>
+            <option value="pouya">Pouya Encode Motifs (hg19)</option>
+            <option value="jaspar">Jaspar and Jolma Motifs (hg19)</option>
+            <option value="mouse">Mouse Motifs (mm9)</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="out_file" format="data_manager_json"/>
+    </outputs>
+    <help>
+        **What it does**
+
+        Fetches a reference genome from various sources (UCSC, NCBI, URL, Galaxy History, or a server directory) and populates the "all_fasta" data table.
+
+        **Notice:** If you leave name, description, or id blank, it will be generated automatically. 
+    </help>
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/test.py	Sun Jan 11 19:21:52 2015 -0500
@@ -0,0 +1,13 @@
+#!/usr/bin/env python
+import optparse
+
+def main():
+    #Parse Command Line
+    parser = optparse.OptionParser()
+    parser.add_option( '-d', '--dbkey_description', dest='dbkey_description', action='store', type="string", default=None, help='dbkey_description' )
+    (options, args) = parser.parse_args()
+    
+    filename = args[0]
+    print(args)
+
+main()
\ No newline at end of file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml	Sun Jan 11 19:21:52 2015 -0500
@@ -0,0 +1,21 @@
+<?xml version="1.0"?>
+<data_managers>
+    
+    <data_manager tool_file="data_manager/data_manager_fetch_motifs.xml" id="data_manager_fetch_motifs">
+        <data_table name="motif_databases">
+            <output>
+                <column name="value" />
+                <column name="name" />
+                <column name="path" output_ref="out_file" >
+                    <move type="file">
+                        <source>${path}</source>
+                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">motifs/${path}</target>
+                    </move>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/motifs/${path}</value_translation>
+                    <value_translation type="function">abspath</value_translation>
+                </column>
+            </output>
+        </data_table>
+    </data_manager>
+    
+</data_managers>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/all_fasta.loc.sample	Sun Jan 11 19:21:52 2015 -0500
@@ -0,0 +1,18 @@
+#This file lists the locations and dbkeys of all the fasta files
+#under the "genome" directory (a directory that contains a directory
+#for each build). The script extract_fasta.py will generate the file
+#all_fasta.loc. This file has the format (white space characters are
+#TAB characters):
+#
+#<unique_build_id>	<dbkey>		<display_name>	<file_path>
+#
+#So, all_fasta.loc could look something like this:
+#
+#apiMel3	apiMel3	Honeybee (Apis mellifera): apiMel3		/path/to/genome/apiMel3/apiMel3.fa
+#hg19canon	hg19		Human (Homo sapiens): hg19 Canonical		/path/to/genome/hg19/hg19canon.fa
+#hg19full	hg19		Human (Homo sapiens): hg19 Full			/path/to/genome/hg19/hg19full.fa
+#
+#Your all_fasta.loc file should contain an entry for each individual
+#fasta file. So there will be multiple fasta files for each build,
+#such as with hg19 above.
+#

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Sun Jan 11 19:21:52 2015 -0500
@@ -0,0 +1,7 @@
+<tables>
+    <!-- Locations of all fasta files under genome directory -->
+    <table name="motif_databases" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="tool-data/motif_databases.loc" />
+    </table>
+</tables>