Mercurial > repos > devteam > data_manager_gatk_picard_index_builder

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_gatk_picard_index_builder.py	Tue Apr 01 10:48:03 2014 -0400
@@ -0,0 +1,179 @@
+#!/usr/bin/env python
+# Dave B.
+# Uses fasta sorting functions written by Dan Blankenberg.
+
+import json
+import optparse
+import os
+import shutil
+import subprocess
+import sys
+import tempfile
+
+CHUNK_SIZE = 2**20
+
+DEFAULT_DATA_TABLE_NAME = "fasta_indexes"
+
+def get_id_name( params, dbkey, fasta_description=None):
+    #TODO: ensure sequence_id is unique and does not already appear in location file
+    sequence_id = params['param_dict']['sequence_id']
+    if not sequence_id:
+        sequence_id = dbkey
+
+    sequence_name = params['param_dict']['sequence_name']
+    if not sequence_name:
+        sequence_name = fasta_description
+        if not sequence_name:
+            sequence_name = dbkey
+    return sequence_id, sequence_name
+
+def build_picard_index( data_manager_dict, fasta_filename, target_directory, dbkey, sequence_id, sequence_name, jar, data_table_name=DEFAULT_DATA_TABLE_NAME ):
+    fasta_base_name = os.path.split( fasta_filename )[-1]
+    gatk_sorted_fasta_filename = os.path.join( target_directory, fasta_base_name )
+    shutil.copy( fasta_filename, gatk_sorted_fasta_filename )
+    _sort_fasta_gatk( gatk_sorted_fasta_filename )
+    sam_index_filename = '%s.fai' % gatk_sorted_fasta_filename
+    if not os.path.exists( sam_index_filename ):
+        sam_command = [ 'samtools', 'faidx', gatk_sorted_fasta_filename ]
+        _run_command( sam_command, target_directory )
+    args = [ 'java', '-jar', jar, 'R=%s' % gatk_sorted_fasta_filename, 'O=%s.dict' % sequence_id ]
+    _run_command( args, target_directory )
+    data_table_entry = dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_name )
+    _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry )
+
+def _run_command( command, target_directory ):
+    tmp_stderr = tempfile.NamedTemporaryFile( prefix = "tmp-data-manager-gatk_picard_index_builder-stderr" )
+    proc = subprocess.Popen( args=command, shell=False, cwd=target_directory, stderr=tmp_stderr.fileno() )
+    return_code = proc.wait()
+    if return_code:
+        tmp_stderr.flush()
+        tmp_stderr.seek( 0 )
+        sys.stderr.write( "Error building index:\n" )
+        while True:
+            chunk = tmp_stderr.read( CHUNK_SIZE )
+            if not chunk:
+                break
+            sys.stderr.write( chunk )
+        sys.exit( return_code )
+    tmp_stderr.close()
+
+def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ):
+    data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
+    data_manager_dict['data_tables'][ data_table_name ] = data_manager_dict['data_tables'].get( data_table_name, [] )
+    data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry )
+    return data_manager_dict
+
+def _move_and_index_fasta_for_sorting( fasta_filename ):
+    unsorted_filename = tempfile.NamedTemporaryFile().name
+    shutil.move( fasta_filename, unsorted_filename )
+    fasta_offsets = {}
+    unsorted_fh = open( unsorted_filename )
+    while True:
+        offset = unsorted_fh.tell()
+        line = unsorted_fh.readline()
+        if not line:
+            break
+        if line.startswith( ">" ):
+            line = line.split( None, 1 )[0][1:]
+            fasta_offsets[ line ] = offset
+    unsorted_fh.close()
+    current_order = map( lambda x: x[1], sorted( map( lambda x: ( x[1], x[0] ), fasta_offsets.items() ) ) )
+    return ( unsorted_filename, fasta_offsets, current_order )
+
+def _write_sorted_fasta( sorted_names, fasta_offsets, sorted_fasta_filename, unsorted_fasta_filename ):
+    unsorted_fh = open( unsorted_fasta_filename )
+    sorted_fh = open( sorted_fasta_filename, 'wb+' )
+
+    for name in sorted_names:
+        offset = fasta_offsets[ name ]
+        unsorted_fh.seek( offset )
+        sorted_fh.write( unsorted_fh.readline() )
+        while True:
+            line = unsorted_fh.readline()
+            if not line or line.startswith( ">" ):
+                break
+            sorted_fh.write( line )
+    unsorted_fh.close()
+    sorted_fh.close()
+
+def _int_to_roman( integer ):
+    if not isinstance( integer, int ):
+        raise TypeError, "expected integer, got %s" % type( integer )
+    if not 0 < integer < 4000:
+        raise ValueError, "Argument must be between 1 and 3999, got %s" % str( integer )
+    ints = ( 1000, 900, 500, 400, 100, 90, 50, 40, 10, 9, 5, 4, 1 )
+    nums = ( 'M', 'CM', 'D', 'CD', 'C', 'XC', 'L', 'XL', 'X', 'IX', 'V', 'IV', 'I' )
+    result = ""
+    for i in range( len( ints ) ):
+        count = int( integer / ints[ i ] )
+        result += nums[ i ] * count
+        integer -= ints[ i ] * count
+    return result
+
+def _sort_fasta_gatk( fasta_filename ):
+    ( unsorted_filename, fasta_offsets, current_order ) = _move_and_index_fasta_for_sorting( fasta_filename )
+    sorted_names = map( str, range( 1, 100 ) ) + map( _int_to_roman, range( 1, 100 ) ) + [ 'X', 'Y', 'M' ]
+    #detect if we have chrN, or just N
+    has_chr = False
+    for chrom in sorted_names:
+        if "chr%s" % chrom in current_order:
+            has_chr = True
+            break
+
+    if has_chr:
+        sorted_names = map( lambda x: "chr%s" % x, sorted_names)
+    else:
+        sorted_names.insert( 0, "MT" )
+    sorted_names.extend( map( lambda x: "%s_random" % x, sorted_names ) )
+
+    existing_sorted_names = []
+    for name in sorted_names:
+        # Append each chromosome only once.
+        if name in current_order and name not in existing_sorted_names:
+            existing_sorted_names.append( name )
+    for name in current_order:
+        #TODO: confirm that non-canonical names do not need to be sorted specially
+        if name not in existing_sorted_names:
+            existing_sorted_names.append( name )
+
+    if existing_sorted_names == current_order:
+        shutil.move( unsorted_filename, fasta_filename )
+    else:
+        _write_sorted_fasta( existing_sorted_names, fasta_offsets, fasta_filename, unsorted_filename )
+
+def main():
+    #Parse Command Line
+    parser = optparse.OptionParser()
+    parser.add_option( '-f', '--fasta_filename', dest='fasta_filename', action='store', type="string", default=None, help='fasta_filename' )
+    parser.add_option( '-d', '--fasta_dbkey', dest='fasta_dbkey', action='store', type="string", default=None, help='fasta_dbkey' )
+    parser.add_option( '-t', '--fasta_description', dest='fasta_description', action='store', type="string", default=None, help='fasta_description' )
+    parser.add_option( '-n', '--data_table_name', dest='data_table_name', action='store', type="string", default=None, help='data_table_name' )
+    parser.add_option( '-j', '--jar', dest='jar', action='store', type="string", default=None, help='GATK .jar file' )
+    (options, args) = parser.parse_args()
+
+    filename = args[0]
+
+    params = json.loads( open( filename ).read() )
+    target_directory = params[ 'output_data' ][0]['extra_files_path']
+    os.mkdir( target_directory )
+    data_manager_dict = {}
+
+    if options.fasta_dbkey in [ None, '', '?' ]:
+        raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( options.fasta_dbkey ) )
+
+    sequence_id, sequence_name = get_id_name( params, dbkey=options.fasta_dbkey, fasta_description=options.fasta_description )
+
+    #build the index
+    build_picard_index( data_manager_dict,
+                        options.fasta_filename,
+                        target_directory,
+                        options.fasta_dbkey,
+                        sequence_id,
+                        sequence_name,
+                        options.jar,
+                        data_table_name=options.data_table_name or DEFAULT_DATA_TABLE_NAME )
+
+    #save info to json file
+    open( filename, 'wb' ).write( json.dumps( data_manager_dict ) )
+
+if __name__ == "__main__": main()
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_gatk_picard_index_builder.xml	Tue Apr 01 10:48:03 2014 -0400
@@ -0,0 +1,33 @@
+<tool id="gatk_picard_index_builder" name="Generate GATK-sorted Picard indexes" tool_type="manage_data" version="0.0.1">
+    <description>builder</description>
+    <requirements>
+        <requirement type="package" version="0.1.18">samtools</requirement>
+        <requirement type="package" version="1.56.0">picard</requirement>
+    </requirements>
+    <command interpreter="python">
+        data_manager_gatk_picard_index_builder.py "${out_file}" \
+            --jar "\$JAVA_JAR_PATH/CreateSequenceDictionary.jar" \
+            --fasta_filename "${all_fasta_source.fields.path}" \
+            --fasta_dbkey "${all_fasta_source.fields.dbkey}" \
+            --fasta_description "${all_fasta_source.fields.name}" \
+            --data_table_name "gatk_picard_indexes"
+    </command>
+    <inputs>
+        <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
+            <options from_data_table="all_fasta"/>
+        </param>
+        <param type="text" name="sequence_name" value="" label="Name of sequence" />
+        <param type="text" name="sequence_id" value="" label="ID for sequence" />
+    </inputs>
+    <outputs>
+        <data name="out_file" format="data_manager_json"/>
+    </outputs>
+
+    <help>
+
+.. class:: infomark
+
+**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_conf.xml	Tue Apr 01 10:48:03 2014 -0400
@@ -0,0 +1,20 @@
+<?xml version="1.0"?>
+<data_managers>
+    <data_manager tool_file="data_manager/data_manager_gatk_picard_index_builder.xml" id="gatk_picard_index_builder" version="0.0.1">
+        <data_table name="gatk_picard_indexes">
+            <output>
+                <column name="value" />
+                <column name="dbkey" />
+                <column name="name" />
+                <column name="path" output_ref="out_file" >
+                    <move type="directory" relativize_symlinks="True">
+                        <!-- <source>${path}</source>--> <!-- out_file.extra_files_path is used as base by default --> <!-- if no source, eg for type=directory, then refers to base -->
+                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${dbkey}/gatk_picard_index/${value}</target>
+                    </move>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/gatk_picard_index/${value}/${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	Tue Apr 01 10:48:03 2014 -0400
@@ -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/gatk_sorted_picard_index.loc.sample	Tue Apr 01 10:48:03 2014 -0400
@@ -0,0 +1,26 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of Picard dict and associated files. You will need
+#to create these data files and then create a picard_index.loc file
+#similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The picard_index.loc
+#file has this format (longer white space is the TAB character):
+#
+#<unique_build_id>	<dbkey>		<display_name>		<fasta_file_path>
+#
+#So, for example, if you had hg18 indexed and stored in
+#/depot/data2/galaxy/srma/hg18/,
+#then the srma_index.loc entry would look like this:
+#
+#hg18	hg18	hg18 Pretty		/depot/data2/galaxy/picard/hg18/hg18.fa
+#
+#and your /depot/data2/galaxy/srma/hg18/ directory
+#would contain the following three files:
+#hg18.fa
+#hg18.dict
+#hg18.fa.fai
+#
+#The dictionary file for each reference (ex. hg18.dict) must be
+#created via Picard (http://picard.sourceforge.net). Note that
+#the dict file does not have the .fa extension although the
+#path list in the loc file does include it.
+#
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Tue Apr 01 10:48:03 2014 -0400
@@ -0,0 +1,13 @@
+<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc-->
+<tables>
+    <!-- Locations of all fasta files under genome directory -->
+    <table name="all_fasta" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/all_fasta.loc" />
+    </table>
+    <!-- Location of Picard dict files valid for GATK -->
+    <table name="gatk_picard_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/gatk_sorted_picard_index.loc" />
+    </table>
+</tables>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Apr 01 10:48:03 2014 -0400
@@ -0,0 +1,9 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  <package name="picard" version="1.56.0">
+      <repository changeset_revision="7206dbf34dcd" name="package_picard_1_56_0" owner="devteam" prior_installation_required="False" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="samtools" version="0.1.18">
+      <repository changeset_revision="c0f72bdba484" name="package_samtools_0_1_18" owner="devteam" prior_installation_required="False" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>