diff data_manager/data_manager_fetch_genome_all_fasta.py @ 0:2ebc856bce29 draft

Uploaded data manager definition.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_fetch_genome_all_fasta.py	Fri Mar 28 14:14:24 2014 -0400
@@ -0,0 +1,350 @@
+#!/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 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_dbkey_id_name( params, dbkey_description=None ):
+    dbkey = params['param_dict']['dbkey']
+    #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 #uuid.uuid4() generate and use an uuid instead?
+    
+    sequence_name = params['param_dict']['sequence_name']
+    if not sequence_name:
+        sequence_name = dbkey_description
+        if not sequence_name:
+            sequence_name = dbkey
+    return dbkey, sequence_id, sequence_name
+
+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 sort_fasta( fasta_filename, sort_method, params ):
+    if sort_method is None:
+        return
+    assert sort_method in SORTING_METHODS, ValueError( "%s is not a valid sorting option." % sort_method )
+    return SORTING_METHODS[ sort_method ]( fasta_filename, params )
+
+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 _sort_fasta_as_is( fasta_filename, params ):
+    return
+
+def _sort_fasta_lexicographical( fasta_filename, params ):
+    ( unsorted_filename, fasta_offsets, current_order ) = _move_and_index_fasta_for_sorting( fasta_filename )
+    sorted_names = sorted( fasta_offsets.keys() )
+    if sorted_names == current_order:
+        shutil.move( unsorted_filename, fasta_filename )
+    else:
+        _write_sorted_fasta( sorted_names, fasta_offsets, fasta_filename, unsorted_filename )    
+
+def _sort_fasta_gatk( fasta_filename, params ):
+    #This method was added by reviewer request.
+    ( unsorted_filename, fasta_offsets, current_order ) = _move_and_index_fasta_for_sorting( fasta_filename )
+    sorted_names = map( str, range( 1, 23 ) ) + [ 'X', 'Y' ]
+    #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)
+        sorted_names.insert( 0, "chrM" )
+    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:
+        if name in current_order:
+            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 _sort_fasta_custom( fasta_filename, params ):
+    ( unsorted_filename, fasta_offsets, current_order ) = _move_and_index_fasta_for_sorting( fasta_filename )
+    sorted_names = []
+    for id_repeat in params['param_dict']['sorting']['sequence_identifiers']:
+        sorted_names.append( id_repeat[ 'identifier' ] )
+    handle_not_listed = params['param_dict']['sorting']['handle_not_listed']['handle_not_listed_selector']
+    if handle_not_listed.startswith( 'keep' ):
+        add_list = []
+        for name in current_order:
+            if name not in sorted_names:
+                add_list.append( name )
+        if add_list:
+            if handle_not_listed == 'keep_append':
+                sorted_names.extend( add_list )
+            else:
+                add_list.extend( sorted_names )
+                sorted_names = add_list
+    if sorted_names == current_order:
+        shutil.move( unsorted_filename, fasta_filename )
+    else:
+        _write_sorted_fasta( sorted_names, fasta_offsets, fasta_filename, unsorted_filename )
+
+def download_from_ucsc( data_manager_dict, params, target_directory, dbkey, sequence_id, sequence_name ):
+    UCSC_FTP_SERVER = 'hgdownload.cse.ucsc.edu'
+    UCSC_CHROM_FA_FILENAME = 'chromFa'
+    UCSC_DOWNLOAD_PATH = '/goldenPath/%s/bigZips/'
+    COMPRESSED_EXTENSIONS = [ ( '.tar.gz', _get_stream_readers_for_tar ), ( '.tar.bz2', _get_stream_readers_for_tar ), ( '.zip', _get_stream_readers_for_zip ), ( '.fa.gz', _get_stream_readers_for_gzip ), ( '.fa.bz2', _get_stream_readers_for_bz2 ) ]
+    
+    email = params['param_dict']['__user_email__']
+    if not email:
+        email = '[e-mail]'
+
+    ucsc_dbkey = params['param_dict']['reference_source']['requested_dbkey'] or dbkey
+    ftp = FTP( UCSC_FTP_SERVER )
+    ftp.login( 'anonymous', email )
+    
+    ucsc_path = UCSC_DOWNLOAD_PATH % ucsc_dbkey
+    path_contents = _get_files_in_ftp_path( ftp, ucsc_path )
+    
+    ucsc_file_name = None
+    get_stream_reader = None
+    ext = None
+    for ext, get_stream_reader in COMPRESSED_EXTENSIONS:
+        if "%s%s" % ( UCSC_CHROM_FA_FILENAME, ext ) in path_contents:
+            ucsc_file_name = "%s%s%s" % ( ucsc_path, UCSC_CHROM_FA_FILENAME, ext )
+            break
+    
+    if not ucsc_file_name:
+        raise Exception( 'Unable to determine filename for UCSC Genome for %s: %s' % ( ucsc_dbkey, path_contents ) )
+    
+    
+    tmp_dir = tempfile.mkdtemp( prefix='tmp-data-manager-ucsc-' )
+    ucsc_fasta_filename = os.path.join( tmp_dir, "%s%s" % ( UCSC_CHROM_FA_FILENAME, ext ) )
+    
+    fasta_base_filename = "%s.fa" % sequence_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( ucsc_fasta_filename, 'wb+' )
+    
+    ftp.retrbinary( 'RETR %s' % ucsc_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, dbkey, sequence_id, sequence_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_ncbi( data_manager_dict, params, target_directory, dbkey, sequence_id, sequence_name ):
+    NCBI_DOWNLOAD_URL = 'http://togows.dbcls.jp/entry/ncbi-nucleotide/%s.fasta' #FIXME: taken from dave's genome manager...why some japan site?
+    
+    requested_identifier = params['param_dict']['reference_source']['requested_identifier']
+    url = NCBI_DOWNLOAD_URL % requested_identifier
+    fasta_reader = urllib2.urlopen( url )
+    
+    data_table_entry = _stream_fasta_to_file( fasta_reader, target_directory, dbkey, sequence_id, sequence_name, params )
+    _add_data_table_entry( data_manager_dict, data_table_entry )
+
+def download_from_url( data_manager_dict, params, target_directory, dbkey, sequence_id, sequence_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, dbkey, sequence_id, sequence_name, params )
+    _add_data_table_entry( data_manager_dict, data_table_entry )
+
+def download_from_history( data_manager_dict, params, target_directory, dbkey, sequence_id, sequence_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, dbkey, sequence_id, sequence_name, params )
+    _add_data_table_entry( data_manager_dict, data_table_entry )
+
+def copy_from_directory( data_manager_dict, params, target_directory, dbkey, sequence_id, sequence_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, dbkey, sequence_id, sequence_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, dbkey, sequence_id, sequence_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']['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, dbkey, sequence_id, sequence_name, params, close_stream=True ):
+    fasta_base_filename = "%s.fa" % sequence_id
+    fasta_filename = os.path.join( target_directory, fasta_base_filename )
+    fasta_writer = open( fasta_filename, '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()
+    
+    sort_fasta( fasta_filename, params['param_dict']['sorting']['sort_selector'], params )
+    
+    return dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_filename )
+
+def _create_symlink( input_filename, target_directory, dbkey, sequence_id, sequence_name ):
+    fasta_base_filename = "%s.fa" % sequence_id
+    fasta_filename = os.path.join( target_directory, fasta_base_filename )
+    os.symlink( input_filename, fasta_filename )
+    return dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_filename )
+
+
+
+
+REFERENCE_SOURCE_TO_DOWNLOAD = dict( ucsc=download_from_ucsc, ncbi=download_from_ncbi, url=download_from_url, history=download_from_history, directory=copy_from_directory )
+
+SORTING_METHODS = dict( as_is=_sort_fasta_as_is, lexicographical=_sort_fasta_lexicographical, gatk=_sort_fasta_gatk, custom=_sort_fasta_custom )
+
+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 = {}
+    
+    dbkey, sequence_id, sequence_name = get_dbkey_id_name( params, dbkey_description=options.dbkey_description ) 
+    
+    if dbkey in [ None, '', '?' ]:
+        raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( dbkey ) )
+    
+    #Fetch the FASTA
+    REFERENCE_SOURCE_TO_DOWNLOAD[ params['param_dict']['reference_source']['reference_source_selector'] ]( data_manager_dict, params, target_directory, dbkey, sequence_id, sequence_name )
+    
+    #save info to json file
+    open( filename, 'wb' ).write( to_json_string( data_manager_dict ) )
+        
+if __name__ == "__main__": main()