# HG changeset patch
# User bgruening
# Date 1423407920 18000
# Node ID ce62d0912b10ef664d6b4f04a562a43ab61bd182
Imported from capsule None
diff -r 000000000000 -r ce62d0912b10 .shed.yml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/.shed.yml Sun Feb 08 10:05:20 2015 -0500
@@ -0,0 +1,2 @@
+owner: bgruening
+name: data_manager_diamond_database_builder
diff -r 000000000000 -r ce62d0912b10 README
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README Sun Feb 08 10:05:20 2015 -0500
@@ -0,0 +1,2 @@
+Diamond database builder
+========================
diff -r 000000000000 -r ce62d0912b10 data_manager/data_manager_diamond_database_builder.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_diamond_database_builder.py Sun Feb 08 10:05:20 2015 -0500
@@ -0,0 +1,238 @@
+#!/usr/bin/env python
+import sys
+import os
+import tempfile
+import shutil
+import optparse
+import urllib2
+import subprocess
+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 cleanup_before_exit( tmp_dir ):
+ if tmp_dir and os.path.exists( tmp_dir ):
+ shutil.rmtree( tmp_dir )
+
+
+def stop_err(msg):
+ sys.stderr.write(msg)
+ sys.exit(1)
+
+
+def _get_files_in_ftp_path( ftp, path ):
+ path_contents = []
+ ftp.retrlines( 'MLSD %s' % ( path ), path_contents.append )
+ return [ line.split( ';' )[ -1 ].lstrip() for line in path_contents ]
+
+
+def _get_stream_readers_for_tar( file_obj, tmp_dir ):
+ fasta_tar = tarfile.open( fileobj=file_obj, mode='r:*' )
+ return [ fasta_tar.extractfile( member ) for member in fasta_tar.getmembers() ]
+
+
+def _get_stream_readers_for_zip( file_obj, tmp_dir ):
+ fasta_zip = zipfile.ZipFile( file_obj, 'r' )
+ rval = []
+ for member in fasta_zip.namelist():
+ fasta_zip.extract( member, tmp_dir )
+ rval.append( open( os.path.join( tmp_dir, member ), 'rb' ) )
+ return rval
+
+
+def _get_stream_readers_for_gzip( file_obj, tmp_dir ):
+ return [ gzip.GzipFile( fileobj=file_obj, mode='rb' ) ]
+
+
+def _get_stream_readers_for_bz2( file_obj, tmp_dir ):
+ return [ bz2.BZ2File( file_obj.name, 'rb' ) ]
+
+
+def download_from_ncbi( data_manager_dict, params, target_directory, database_id, database_name ):
+ NCBI_FTP_SERVER = 'ftp.ncbi.nlm.nih.gov'
+ NCBI_DOWNLOAD_PATH = '/blast/db/FASTA/'
+ COMPRESSED_EXTENSIONS = [ ( '.tar.gz', _get_stream_readers_for_tar ), ( '.tar.bz2', _get_stream_readers_for_tar ), ( '.zip', _get_stream_readers_for_zip ), ( '.gz', _get_stream_readers_for_gzip ), ( '.bz2', _get_stream_readers_for_bz2 ) ]
+
+ ncbi_identifier = params['param_dict']['reference_source']['requested_identifier']
+ ftp = FTP( NCBI_FTP_SERVER )
+ ftp.login()
+
+ path_contents = _get_files_in_ftp_path( ftp, NCBI_DOWNLOAD_PATH )
+
+ ncbi_file_name = None
+ get_stream_reader = None
+ ext = None
+ for ext, get_stream_reader in COMPRESSED_EXTENSIONS:
+ if "%s%s" % ( ncbi_identifier, ext ) in path_contents:
+ ncbi_file_name = "%s%s%s" % ( NCBI_DOWNLOAD_PATH, ncbi_identifier, ext )
+ break
+
+ if not ncbi_file_name:
+ raise Exception( 'Unable to determine filename for NCBI database for %s: %s' % ( ncbi_identifier, path_contents ) )
+
+ tmp_dir = tempfile.mkdtemp( prefix='tmp-data-manager-ncbi-' )
+ ncbi_fasta_filename = os.path.join( tmp_dir, "%s%s" % ( ncbi_identifier, ext ) )
+
+ fasta_base_filename = "%s.fa" % database_id
+ fasta_filename = os.path.join( target_directory, fasta_base_filename )
+ fasta_writer = open( fasta_filename, 'wb+' )
+
+ tmp_extract_dir = os.path.join ( tmp_dir, 'extracted_fasta' )
+ os.mkdir( tmp_extract_dir )
+
+ tmp_fasta = open( ncbi_fasta_filename, 'wb+' )
+
+ ftp.retrbinary( 'RETR %s' % ncbi_file_name, tmp_fasta.write )
+
+ tmp_fasta.flush()
+ tmp_fasta.seek( 0 )
+
+ fasta_readers = get_stream_reader( tmp_fasta, tmp_extract_dir )
+
+ data_table_entry = _stream_fasta_to_file( fasta_readers, target_directory, database_id, database_name, params )
+ _add_data_table_entry( data_manager_dict, data_table_entry )
+
+ for fasta_reader in fasta_readers:
+ fasta_reader.close()
+ tmp_fasta.close()
+ cleanup_before_exit( tmp_dir )
+
+
+def download_from_url( data_manager_dict, params, target_directory, database_id, database_name ):
+ #TODO: we should automatically do decompression here
+ urls = filter( bool, map( lambda x: x.strip(), params['param_dict']['reference_source']['user_url'].split( '\n' ) ) )
+ fasta_reader = [ urllib2.urlopen( url ) for url in urls ]
+
+ data_table_entry = _stream_fasta_to_file( fasta_reader, target_directory, database_id, database_name, params )
+ _add_data_table_entry( data_manager_dict, data_table_entry )
+
+
+def download_from_history( data_manager_dict, params, target_directory, database_id, database_name ):
+ #TODO: allow multiple FASTA input files
+ input_filename = params['param_dict']['reference_source']['input_fasta']
+ if isinstance( input_filename, list ):
+ fasta_reader = [ open( filename, 'rb' ) for filename in input_filename ]
+ else:
+ fasta_reader = open( input_filename )
+
+ data_table_entry = _stream_fasta_to_file( fasta_reader, target_directory, database_id, database_name, params )
+ _add_data_table_entry( data_manager_dict, data_table_entry )
+
+
+def copy_from_directory( data_manager_dict, params, target_directory, database_id, database_name ):
+ input_filename = params['param_dict']['reference_source']['fasta_filename']
+ create_symlink = params['param_dict']['reference_source']['create_symlink'] == 'create_symlink'
+ if create_symlink:
+ data_table_entry = _create_symlink( input_filename, target_directory, database_id, database_name )
+ else:
+ if isinstance( input_filename, list ):
+ fasta_reader = [ open( filename, 'rb' ) for filename in input_filename ]
+ else:
+ fasta_reader = open( input_filename )
+ data_table_entry = _stream_fasta_to_file( fasta_reader, target_directory, database_id, database_name, 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']['diamond_database'] = data_manager_dict['data_tables'].get( 'diamond_database', [] )
+ data_manager_dict['data_tables']['diamond_database'].append( data_table_entry )
+ return data_manager_dict
+
+
+def _stream_fasta_to_file( fasta_stream, target_directory, database_id, database_name, params, close_stream=True ):
+ fasta_base_filename = "%s.fa" % database_id
+ fasta_filename = os.path.join( target_directory, fasta_base_filename )
+
+ temp_fasta = tempfile.NamedTemporaryFile( delete=False, suffix=".fasta" )
+ temp_fasta.close()
+ fasta_writer = open( temp_fasta.name, 'wb+' )
+
+ if isinstance( fasta_stream, list ) and len( fasta_stream ) == 1:
+ fasta_stream = fasta_stream[0]
+
+ if isinstance( fasta_stream, list ):
+ last_char = None
+ for fh in fasta_stream:
+ if last_char not in [ None, '\n', '\r' ]:
+ fasta_writer.write( '\n' )
+ while True:
+ data = fh.read( CHUNK_SIZE )
+ if data:
+ fasta_writer.write( data )
+ last_char = data[-1]
+ else:
+ break
+ if close_stream:
+ fh.close()
+ else:
+ while True:
+ data = fasta_stream.read( CHUNK_SIZE )
+ if data:
+ fasta_writer.write( data )
+ else:
+ break
+ if close_stream:
+ fasta_stream.close()
+
+ fasta_writer.close()
+
+ args = [ 'diamond', 'makedb', '--in', temp_fasta.name, '--db', fasta_filename]
+
+ tmp_stderr = tempfile.NamedTemporaryFile( prefix = "tmp-data-manager-diamond-database-builder-stderr" )
+ proc = subprocess.Popen( args=args, shell=False, cwd=target_directory, stderr=tmp_stderr.fileno() )
+ return_code = proc.wait()
+ if return_code:
+ tmp_stderr.flush()
+ tmp_stderr.seek(0)
+ print >> sys.stderr, "Error building diamond database:"
+ while True:
+ chunk = tmp_stderr.read( CHUNK_SIZE )
+ if not chunk:
+ break
+ sys.stderr.write( chunk )
+ sys.exit( return_code )
+ tmp_stderr.close()
+ os.remove( temp_fasta.name )
+ return dict( value=database_id, name=database_name, db_path="%s.dmnd" % fasta_base_filename )
+
+
+def _create_symlink( input_filename, target_directory, database_id, database_name ):
+ fasta_base_filename = "%s.fa" % database_id
+ fasta_filename = os.path.join( target_directory, fasta_base_filename )
+ os.symlink( input_filename, fasta_filename )
+ return dict( value=database_id, name=database_name, db_path=fasta_base_filename )
+
+
+REFERENCE_SOURCE_TO_DOWNLOAD = dict( ncbi=download_from_ncbi, url=download_from_url, history=download_from_history, directory=copy_from_directory )
+
+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]
+
+ params = from_json_string( open( filename ).read() )
+ target_directory = params[ 'output_data' ][0]['extra_files_path']
+ os.mkdir( target_directory )
+ data_manager_dict = {}
+
+ database_id = params['param_dict']['database_id']
+ database_name = params['param_dict']['database_name']
+
+ #Fetch the FASTA
+ REFERENCE_SOURCE_TO_DOWNLOAD[ params['param_dict']['reference_source']['reference_source_selector'] ]( data_manager_dict, params, target_directory, database_id, database_name )
+
+ #save info to json file
+ open( filename, 'wb' ).write( to_json_string( data_manager_dict ) )
+
+if __name__ == "__main__":
+ main()
diff -r 000000000000 -r ce62d0912b10 data_manager/data_manager_diamond_database_builder.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_diamond_database_builder.xml Sun Feb 08 10:05:20 2015 -0500
@@ -0,0 +1,46 @@
+
+ Database builder
+
+ diamond
+
+
+ data_manager_diamond_database_builder.py "${out_file}"
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+.. class:: infomark
+
+NCBI databases can be downded from ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/
+For example the NR database can be downloaded from ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nr.gz
+
+
+
diff -r 000000000000 -r ce62d0912b10 data_manager_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml Sun Feb 08 10:05:20 2015 -0500
@@ -0,0 +1,19 @@
+
+
+
+
+
+
+
+
diff -r 000000000000 -r ce62d0912b10 tool-data/diamond_database.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/diamond_database.loc.sample Sun Feb 08 10:05:20 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):
+#
+#
+#
+#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.
+#
diff -r 000000000000 -r ce62d0912b10 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Sun Feb 08 10:05:20 2015 -0500
@@ -0,0 +1,7 @@
+
+
+
+ value, name, db_path
+
+
+
diff -r 000000000000 -r ce62d0912b10 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Sun Feb 08 10:05:20 2015 -0500
@@ -0,0 +1,6 @@
+
+
+
+
+
+