changeset 5:3d9dd4b9fb09 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1-dirty

--- a/data_manager/data_manager_snpEff_databases.py	Tue Apr 04 18:14:37 2017 -0400
+++ b/data_manager/data_manager_snpEff_databases.py	Tue Apr 18 09:40:03 2017 -0400
@@ -6,33 +6,20 @@
 import sys
 
 
-def stop_err(msg):
-    sys.stderr.write(msg)
-    sys.exit(1)
-
-
-def fetch_databases(data_manager_dict, target_directory, jar_path):
-    (snpEff_dir, snpEff_jar) = os.path.split(jar_path)
+def fetch_databases(data_manager_dict, target_directory):
     if not os.path.exists(target_directory):
         os.makedirs(target_directory)
     databases_path = os.path.join( target_directory, '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()
+    args = ['snpEff', 'databases']
+    return_code = subprocess.call(args=args, shell=False, stdout=databases_output.fileno())
     if return_code:
         sys.exit( return_code )
     databases_output.close()
     data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
     data_manager_dict['data_tables']['snpeff4_databases'] = data_manager_dict['data_tables'].get( 'snpeff4_databases', [] )
     data_table_entries = []
-    try:
-        fh = open(databases_path, 'r')
+    with open(databases_path, 'r') as fh:
         for i, line in enumerate(fh):
             fields = line.split('\t')
             if len(fields) >= 2:
@@ -45,17 +32,11 @@
                 description = fields[1].strip() + ' : ' + genome_version
                 data_table_entries.append(dict(value=genome_version, name=description))
         data_manager_dict['data_tables']['snpeff4_databases'] = data_table_entries
-    except Exception as e:
-        stop_err( 'Error parsing %s %s\n' % (databases_path, str( e )) )
-    else:
-        fh.close()
     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' )
     (options, args) = parser.parse_args()
 
     filename = args[0]
@@ -66,7 +47,7 @@
     data_manager_dict = {}
 
     # Create Defuse Reference Data
-    data_manager_dict = fetch_databases( data_manager_dict, target_directory, options.jar_path)
+    data_manager_dict = fetch_databases( data_manager_dict, target_directory)
 
     # save info to json file
     open( filename, 'wb' ).write( json.dumps( data_manager_dict ) )

--- a/data_manager/data_manager_snpEff_databases.xml	Tue Apr 04 18:14:37 2017 -0400
+++ b/data_manager/data_manager_snpEff_databases.xml	Tue Apr 18 09:40:03 2017 -0400
@@ -1,44 +1,33 @@
-<tool id="data_manager_snpeff_databases" name="SnpEff Databases" version="4.1.0" tool_type="manage_data">
-	<description>Read the list of available snpEff databases</description>
-	<requirements>
-		<requirement type="package" version="4.1">snpEff</requirement>
-	</requirements>
-        <stdio>
-          <exit_code range=":-1"  level="fatal"   description="Error: Cannot open file" />
-          <exit_code range="1:"  level="fatal"   description="Error" />
-        </stdio>
-	<command interpreter="python">
-        data_manager_snpEff_databases.py --jar_path "\$SNPEFF_JAR_PATH/snpEff.jar" "$out_file"
-        </command>
-	<inputs>
-	</inputs>
-	<outputs>
-           <data name="out_file" format="data_manager_json"/>
-	</outputs>
-        <tests>
-            <test>
-                <output name="out_file">
-                    <assert_contents>
-                        <!-- Check that a genome was added -->
-                        <has_text text="GRCh38.76" />
-                    </assert_contents>
-                </output>
-            </test>
-        </tests>
-	<help>
+<tool id="data_manager_snpeff_databases" name="SnpEff Databases" version="4.3k" tool_type="manage_data">
+    <description>Read the list of available SnpEff databases</description>
+    <requirements>
+        <requirement type="package" version="4.3k">snpeff</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+python '$__tool_directory__/data_manager_snpEff_databases.py' '$out_file'
+    ]]></command>
+    <inputs>
+    </inputs>
+    <outputs>
+        <data name="out_file" format="data_manager_json"/>
+    </outputs>
+    <tests>
+        <test>
+            <output name="out_file">
+                <assert_contents>
+                    <!-- Check that a genome was added -->
+                    <has_text text="GRCh38.76" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+This tool updates the list of SnpEff databases for the SnpEff Download data manager.
+It should only need to be run once for a SnpEff version, since it populates the SnpEff Download data manager from the SnpEff config file.
 
-This tool updatess the list of SnpEff databases for the SnpEff Download data manager.
-It should only need to be run once for a snpEff version, 
-since it populates the SnpEff Download data manager from the snpEff config file.
-
-For information about snpEff:    http://snpEff.sourceforge.net
-
-Please cite:
-"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly (Austin). 2012 Apr-Jun;6(2):80-92. PMID: 22728672 [PubMed - in process]
-
-	</help>
-      <citations>
+For information about SnpEff: http://snpeff.sourceforge.net
+    ]]></help>
+    <citations>
         <citation type="doi">10.4161/fly.19695</citation>
-      </citations>
+    </citations>
 </tool>
-

--- a/data_manager/data_manager_snpEff_download.py	Tue Apr 04 18:14:37 2017 -0400
+++ b/data_manager/data_manager_snpEff_download.py	Tue Apr 18 09:40:03 2017 -0400
@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-import gzip
 import json
 import optparse
 import os
@@ -13,19 +12,12 @@
     sys.exit(1)
 
 
-def fetch_databases(jar_path, genome_list=None):
+def fetch_databases(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()
+    args = ['snpEff', 'databases']
+    return_code = subprocess.call(args=args, shell=False, stdout=databases_output.fileno())
     if return_code:
         sys.exit( return_code )
     databases_output.close()
@@ -48,28 +40,24 @@
     return snpDBs
 
 
-def getOrganismNames(jar_path, genomes, organisms):
+def getOrganismNames(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)
+        snpDBdict = fetch_databases(genome_list=genome_list)
         for genome in snpDBdict:
             descriptions.append(snpDBdict[genome] if genome in snpDBdict else genome)
         return ','.join(descriptions)
     return organisms
 
 
-def getSnpeffVersion(jar_path):
+def getSnpeffVersion():
     snpeff_version = 'SnpEff ?.?'
-    (snpEff_dir, snpEff_jar) = os.path.split(jar_path)
     stderr_path = 'snpeff.err'
     stderr_fh = open(stderr_path, 'w')
-    args = [ 'java', '-jar' ]
-    args.append( snpEff_jar )
-    args.append( '-h' )
-    proc = subprocess.Popen( args=args, shell=False, cwd=snpEff_dir, stderr=stderr_fh.fileno() )
-    return_code = proc.wait()
+    args = ['snpEff', '-h']
+    return_code = subprocess.call(args=args, shell=False, stderr=stderr_fh.fileno())
     if return_code != 255:
         sys.exit( return_code )
     stderr_fh.close()
@@ -83,27 +71,6 @@
     return snpeff_version
 
 
-# Starting with SnpEff 4.1 the .bin files contain the SnpEff version:
-# Example - the first 3 line of GRCh37.75/snpEffectPredictor.bin (uncompressed):
-#
-# SnpEff  4.1
-# CHROMOSOME      2       1       0       179197  GL000219.1      false
-# CHROMOSOME      3       1       0       81347269        HSCHR17_1       false
-def getSnpeffVersionFromFile(path):
-    snpeff_version = None
-    try:
-        fh = gzip.open(path, 'rb')
-        buf = fh.read(100)
-        lines = buf.splitlines()
-        m = re.match('^(SnpEff)\s+(\d+\.\d+).*$', lines[0].strip())
-        if m:
-            snpeff_version = m.groups()[0] + m.groups()[1]
-        fh.close()
-    except Exception as e:
-        stop_err( 'Error parsing SnpEff version from: %s %s\n' % (path, str( e )) )
-    return snpeff_version
-
-
 # Download human database 'hg19'
 # java -jar snpEff.jar download -v hg19
 #
@@ -112,36 +79,24 @@
 # snpEffectPredictor.bin
 # regulation_HeLa-S3.bin
 # regulation_pattern = 'regulation_(.+).bin'
-def download_database(data_manager_dict, target_directory, jar_path, config, genome_version, organism):
+def download_database(data_manager_dict, target_directory, 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()
+    args = ['snpEff', 'download', '-dataDir', data_dir, '-v', genome_version]
+    return_code = subprocess.call(args=args, shell=False)
     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'}
+    #  annotation files that are included in SnpEff by a flag
+    annotations_dict = {'nextProt.bin': '-nextprot', 'motif.bin': '-motif', 'interactions.bin': '-interaction'}
     genome_path = os.path.join(data_dir, genome_version)
-    snpeff_version = getSnpeffVersion(jar_path)
+    snpeff_version = getSnpeffVersion()
     key = snpeff_version + '_' + genome_version
     if os.path.isdir(genome_path):
         for root, dirs, files in os.walk(genome_path):
@@ -149,7 +104,6 @@
                 if fname.startswith('snpEffectPredictor'):
                     # if snpEffectPredictor.bin download succeeded
                     name = genome_version + (' : ' + organism if organism else '')
-                    # version = getSnpeffVersionFromFile(os.path.join(root,fname))
                     data_table_entry = dict(key=key, version=snpeff_version, value=genome_version, name=name, path=data_dir)
                     _add_data_table_entry( data_manager_dict, 'snpeffv_genomedb', data_table_entry )
                 else:
@@ -174,10 +128,7 @@
 
 
 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()
@@ -190,8 +141,8 @@
     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 )
+    for genome_version, organism in zip(options.genome_version.split(','), getOrganismNames(options.genome_version, options.organism).split(',')):
+        download_database( data_manager_dict, target_directory, genome_version, organism )
 
     # save info to json file
     open( filename, 'wb' ).write( json.dumps( data_manager_dict ) )

--- a/data_manager/data_manager_snpEff_download.xml	Tue Apr 04 18:14:37 2017 -0400
+++ b/data_manager/data_manager_snpEff_download.xml	Tue Apr 18 09:40:03 2017 -0400
@@ -1,25 +1,21 @@
-<tool id="data_manager_snpeff_download" name="SnpEff Download" version="4.1.0" tool_type="manage_data">
+<tool id="data_manager_snpeff_download" name="SnpEff Download" version="4.3k" tool_type="manage_data">
     <description>Download a new database</description>
     <requirements>
-        <requirement type="package" version="4.1">snpEff</requirement>
+        <requirement type="package" version="4.3k">snpeff</requirement>
     </requirements>
-    <stdio>
-        <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
-        <exit_code range="1:" level="fatal" description="Error" />
-    </stdio>
-    <command interpreter="python">
-        data_manager_snpEff_download.py --jar_path "\$SNPEFF_JAR_PATH/snpEff.jar" --config "\$SNPEFF_JAR_PATH/snpEff.config"
-          --genome_version "$genome_version" "$out_file"
-        </command>
+    <command detect_errors="exit_code"><![CDATA[
+python '$__tool_directory__/data_manager_snpEff_download.py'
+--genome_version '$genome_version'
+'$out_file'
+    ]]></command>
     <inputs>
-        <param name="genome_version" type="text" value="" label="Snpff Genome Version Name (e.g. GRCh38.76)">
-            <help>https://snpeff-data.galaxyproject.org/databases/</help>
+        <param name="genome_version" type="text" value="" label="Snpff Genome Version Name (e.g. GRCh38.76)" help="https://snpeff-data.galaxyproject.org/databases/">
             <validator type="regex" message="A genome version name is required">\S+</validator>
         </param>
     </inputs>
 
     <outputs>
-           <data name="out_file" format="data_manager_json" label="${tool.name}"/>
+        <data name="out_file" format="data_manager_json" label="${tool.name}"/>
     </outputs>
     <tests>
         <test>
@@ -34,23 +30,16 @@
             </output>
         </test>
     </tests>
-    <help>
-
-This tool downloads a SnpEff database and populates data tables: snpeffv_genomedb, snpeffv_regulationdb, and snpeffv_annotations.
+    <help><![CDATA[
+This tool downloads a SnpEff database and populates the data tables: snpeffv_genomedb, snpeffv_regulationdb, and snpeffv_annotations.
 
 To see the list of available SnpEff genomes run the "SnpEff Databases" data manager which records the available genome databases in data table: snpeff4_databases
 
 The SnpEff genome databases are at: http://sourceforge.net/projects/snpeff/files/databases/
 
-
-For details about this tool, please go to http://snpEff.sourceforge.net
-
-Please cite:
-"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly (Austin). 2012 Apr-Jun;6(2):80-92. PMID: 22728672 [PubMed - in process]
-
-    </help>
-      <citations>
+For details about this tool, please go to http://snpeff.sourceforge.net
+    ]]></help>
+    <citations>
         <citation type="doi">10.4161/fly.19695</citation>
-      </citations>
+    </citations>
 </tool>
-

--- a/data_manager_conf.xml	Tue Apr 04 18:14:37 2017 -0400
+++ b/data_manager_conf.xml	Tue Apr 18 09:40:03 2017 -0400
@@ -19,9 +19,9 @@
         <column name="name" />  <!-- columns that are going to be specified by the Data Manager Tool -->
         <column name="path" output_ref="out_file" >
           <move type="directory" relativize_symlinks="True">
-            <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">snpEff/v4_1/data</target>
+            <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">snpEff/v4_3/data</target>
           </move>
-          <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/snpEff/v4_1/data</value_translation>
+          <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/snpEff/v4_3/data</value_translation>
           <value_translation type="function">abspath</value_translation>
         </column>
       </output>

--- a/tool_dependencies.xml	Tue Apr 04 18:14:37 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="snpEff" version="4.1">
-        <repository changeset_revision="374c7f8421fb" name="package_snpeff_4_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>