# HG changeset patch
# User iuc
# Date 1408201437 14400
# Node ID a47cd0bacb6759e24ce00f2a9c6ad269a20586ba
Uploaded
diff -r 000000000000 -r a47cd0bacb67 data_manager/data_manager_gemini_download.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_gemini_download.py Sat Aug 16 11:03:57 2014 -0400
@@ -0,0 +1,158 @@
+#!/usr/bin/env python
+
+import sys
+import os
+import re
+import tempfile
+import subprocess
+import fileinput
+import shutil
+import optparse
+import urllib2
+from ftplib import FTP
+import tarfile
+
+from galaxy.util.json import from_json_string, to_json_string
+
+def stop_err(msg):
+ sys.stderr.write(msg)
+ sys.exit(1)
+
+
+def fetch_databases(jar_path,genome_list=None):
+ snpDBs = dict()
+ (snpEff_dir,snpEff_jar) = os.path.split(jar_path)
+ databases_path = 'databases.out'
+ databases_output = open(databases_path,'w')
+ args = [ 'java','-jar', ]
+ args.append( snpEff_jar )
+ args.append( 'databases' )
+ # tmp_stderr = tempfile.NamedTemporaryFile( prefix = "tmp-data-manager-snpEff-stderr" )
+ # databases_output = open(databases_path)
+ # proc = subprocess.Popen( args=args, shell=False, cwd=snpEff_dir, stdout=databases_output.fileno(), stderr=tmp_stderr.fileno() )
+ proc = subprocess.Popen( args=args, shell=False, cwd=snpEff_dir, stdout=databases_output.fileno() )
+ return_code = proc.wait()
+ if return_code:
+ sys.exit( return_code )
+ databases_output.close()
+ try:
+ fh = open(databases_path,'r')
+ for i,line in enumerate(fh):
+ fields = line.split('\t')
+ if len(fields) >= 2:
+ genome_version = fields[0].strip()
+ if genome_list and genome_version not in genome_list:
+ continue
+ if genome_version.startswith("Genome") or genome_version.startswith("-"):
+ continue
+ description = fields[1].strip()
+ snpDBs[genome_version] = description;
+ except Exception, e:
+ stop_err( 'Error parsing %s %s\n' % (config,str( e )) )
+ else:
+ fh.close()
+ return snpDBs
+
+def getOrganismNames(jar_path,genomes,organisms) :
+ genome_list = genomes.split(',')
+ organism_list = organisms.split(',') if organisms else []
+ if len(genome_list) != len(organism_list):
+ descriptions = []
+ snpDBdict = fetch_databases(jar_path,genome_list=genome_list);
+ for genome in snpDBdict:
+ descriptions.append(snpDBdict[genome] if genome in snpDBdict else genome)
+ return ','.join(descriptions)
+ return organisms
+
+"""
+# Download human database 'hg19'
+java -jar snpEff.jar download -v hg19
+
+ java -jar \$SNPEFF_JAR_PATH/snpEff.jar download -c \$JAVA_JAR_PATH/snpEff.config $genomeVersion > $logfile
+
+snpEffectPredictor.bin
+regulation_HeLa-S3.bin
+regulation_pattern = 'regulation_(.+).bin'
+"""
+def download_database(data_manager_dict, target_directory, jar_path,config,genome_version,organism):
+ ## get data_dir from config
+ ##---
+ ## Databases are stored here
+ ## E.g.: Information for 'hg19' is stored in data_dir/hg19/
+ ##
+ ## Note: Since version 2.1 you can use tilde ('~') as first character to refer to your home directory
+ ##---
+ #data_dir = ~/snpEff/data/
+ data_dir = target_directory
+ (snpEff_dir,snpEff_jar) = os.path.split(jar_path)
+ args = [ 'java','-jar' ]
+ args.append( jar_path )
+ args.append( 'download' )
+ args.append( '-c' )
+ args.append( config )
+ args.append( '-dataDir' )
+ args.append( data_dir )
+ args.append( '-v' )
+ args.append( genome_version )
+ proc = subprocess.Popen( args=args, shell=False, cwd=snpEff_dir )
+ return_code = proc.wait()
+ if return_code:
+ sys.exit( return_code )
+ ## search data_dir/genome_version for files
+ regulation_pattern = 'regulation_(.+).bin'
+ # annotation files that are included in snpEff by a flag
+ annotations_dict = {'nextProt.bin' : '-nextprot','motif.bin': '-motif'}
+ genome_path = os.path.join(data_dir,genome_version)
+ if os.path.isdir(genome_path):
+ for root, dirs, files in os.walk(genome_path):
+ for fname in files:
+ if fname.startswith('snpEffectPredictor'):
+ # if snpEffectPredictor.bin download succeeded
+ name = genome_version + (' : ' + organism if organism else '')
+ data_table_entry = dict(value=genome_version, name=name, path=data_dir)
+ _add_data_table_entry( data_manager_dict, 'snpeff_genomedb', data_table_entry )
+ else:
+ m = re.match(regulation_pattern,fname)
+ if m:
+ name = m.groups()[0]
+ data_table_entry = dict(genome=genome_version,value=name, name=name)
+ _add_data_table_entry( data_manager_dict, 'snpeff_regulationdb', data_table_entry )
+ elif fname in annotations_dict:
+ value = annotations_dict[fname]
+ name = value.lstrip('-')
+ data_table_entry = dict(genome=genome_version,value=value, name=name)
+ _add_data_table_entry( data_manager_dict, 'snpeff_annotations', data_table_entry )
+ return data_manager_dict
+
+def _add_data_table_entry( data_manager_dict, data_table, data_table_entry ):
+ data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
+ data_manager_dict['data_tables'][data_table] = data_manager_dict['data_tables'].get( data_table, [] )
+ data_manager_dict['data_tables'][data_table].append( data_table_entry )
+ return data_manager_dict
+
+def main():
+ #Parse Command Line
+ parser = optparse.OptionParser()
+ parser.add_option( '-j', '--jar_path', dest='jar_path', action='store', type="string", default=None, help='snpEff.jar path' )
+ parser.add_option( '-c', '--config', dest='config', action='store', type="string", default=None, help='snpEff.config path' )
+ parser.add_option( '-g', '--genome_version', dest='genome_version', action='store', type="string", default=None, help='genome_version' )
+ parser.add_option( '-o', '--organism', dest='organism', action='store', type="string", default=None, help='organism name' )
+ (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 = {}
+
+
+ #Create SnpEff Reference Data
+ for genome_version, organism in zip(options.genome_version.split(','), getOrganismNames(options.jar_path,options.genome_version,options.organism).split(',')):
+ download_database( data_manager_dict, target_directory, options.jar_path, options.config, genome_version, organism )
+
+ #save info to json file
+ open( filename, 'wb' ).write( to_json_string( data_manager_dict ) )
+
+if __name__ == "__main__": main()
+
diff -r 000000000000 -r a47cd0bacb67 data_manager/data_manager_gemini_download.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_gemini_download.xml Sat Aug 16 11:03:57 2014 -0400
@@ -0,0 +1,62 @@
+
+ Download a new database
+
+ gemini
+
+
+ #from galaxy.util.json import from_json_string, to_json_string
+
+ ##\$GEMINI_ROOT_DIR/gemini/gemini/install-data.py /home/bag/test/gdata/ $gerp_bp $cadd_score
+
+ #set $params = from_json_string( open( '$out_file' ).read() )
+ #set $target_directory = $params[ 'output_data' ][0]['extra_files_path']
+ mkdir $target_directory
+ #set $data_manager_dict = { 'data_tables': {'data_table': [ {'value': 'bar', 'name': 'foo', 'path': '$target_directory'] } }
+
+ data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
+ data_manager_dict['data_tables'][data_table] = data_manager_dict['data_tables'].get( data_table, [] )
+ data_manager_dict['data_tables'][data_table].append( data_table_entry )
+
+
+ #silent open( '$out_file', 'wb' ).write( to_json_string( $data_manager_dict ) )
+
+## data_manager_snpEff_download.py --jar_path \$SNPEFF_JAR_PATH/snpEff.jar --config \$SNPEFF_JAR_PATH/snpEff.config
+## #if $snpDb.genomeSrc == "named":
+## --genome_version "${snpDb.genome_version}"
+## #else
+## --genome_version "${snpDb.genome_databases.fields.value}"
+## --organism "${snpDb.genome_databases.fields.name}"
+## #end if
+## "$out_file"
+
+
+
+
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+
+
+This tool downloads the GEMINI databases.
+
+For details about this tool, please go to http://http://gemini.readthedocs.org
+
+
+
+ 10.1371/journal.pcbi.1003153
+
+
+
+
diff -r 000000000000 -r a47cd0bacb67 data_manager_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml Sat Aug 16 11:03:57 2014 -0400
@@ -0,0 +1,20 @@
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diff -r 000000000000 -r a47cd0bacb67 tool-data/gemini_databases.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/gemini_databases.loc.sample Sat Aug 16 11:03:57 2014 -0400
@@ -0,0 +1,3 @@
+## GEMINI databases
+#Version Description Path
+#08_08_2014 Database (08-08-2014) /data/0/gemini/08_08_2014/
diff -r 000000000000 -r a47cd0bacb67 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Sat Aug 16 11:03:57 2014 -0400
@@ -0,0 +1,7 @@
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diff -r 000000000000 -r a47cd0bacb67 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Sat Aug 16 11:03:57 2014 -0400
@@ -0,0 +1,6 @@
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