Mercurial > repos > mvdbeek > data_manager_fetch_genome_dbkeys_all_fasta_compressed
changeset 1:29209aa4c829 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 592acc3119624e0f213483d952b4cbd3b7e827bd-dirty
| author | mvdbeek |
|---|---|
| date | Thu, 18 Aug 2016 06:09:29 -0400 |
| parents | 39fc40852a3b |
| children | 0738889ff4d2 |
| files | data_manager/data_manager_fetch_genome_all_fasta_dbkeys.py data_manager/data_manager_fetch_genome_all_fasta_dbkeys.xml test-data/test.tar test-data/test.tar.bz2 test-data/test.tar.gz test-data/test.zip |
| diffstat | 6 files changed, 120 insertions(+), 86 deletions(-) [+] |
line wrap: on
line diff
--- a/data_manager/data_manager_fetch_genome_all_fasta_dbkeys.py Wed Aug 17 07:36:44 2016 -0400 +++ b/data_manager/data_manager_fetch_genome_all_fasta_dbkeys.py Thu Aug 18 06:09:29 2016 -0400 @@ -7,26 +7,29 @@ import shutil import optparse import urllib2 -#import uuid from ftplib import FTP import tarfile import zipfile import gzip import bz2 +from StringIO import StringIO from json import loads, dumps -CHUNK_SIZE = 2**20 #1mb +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_dbname_id_name( params, dbkey_description=None ): dbkey = params['param_dict']['dbkey_source']['dbkey'] #TODO: ensure sequence_id is unique and does not already appear in location file @@ -48,16 +51,23 @@ sequence_name = dbkey return dbkey, dbkey_name, 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( fh ): + +def _get_stream_readers_for_tar( fh, tmp_dir ): fasta_tar = tarfile.open( fileobj=fh, mode='r:*' ) return filter( lambda x: x is not None, [ fasta_tar.extractfile( member ) for member in fasta_tar.getmembers() ] ) + def _get_stream_readers_for_zip( fh, tmp_dir ): + """ + Unpacks all archived files in a zip file. + Individual files will be concatenated (in _stream_fasta_to_file) + """ fasta_zip = zipfile.ZipFile( fh, 'r' ) rval = [] for member in fasta_zip.namelist(): @@ -65,11 +75,14 @@ rval.append( open( os.path.join( tmp_dir, member ), 'rb' ) ) return rval -def _get_stream_readers_for_gzip( fh ): - return [ gzip.GzipFile( fileobj=fh, mode='rb' ) ] + +def _get_stream_readers_for_gzip( fh, tmp_dir ): + return [ gzip.GzipFile( fileobj=fh, mode='rb') ] -def _get_stream_readers_for_bz2( fh ): - return [ bz2.BZ2Decompressor( fh.name, 'rb' ) ] + +def _get_stream_readers_for_bz2( fh, tmp_dir ): + return [ bz2.BZ2File( fh.name, 'rb') ] + def sort_fasta( fasta_filename, sort_method, params ): if sort_method is None: @@ -77,6 +90,7 @@ 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 ) @@ -94,6 +108,7 @@ 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+' ) @@ -110,6 +125,7 @@ unsorted_fh.close() sorted_fh.close() + def _sort_fasta_as_is( fasta_filename, params ): return @@ -121,6 +137,7 @@ 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 ) @@ -153,6 +170,7 @@ 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 = [] @@ -175,24 +193,42 @@ else: _write_sorted_fasta( sorted_names, fasta_offsets, fasta_filename, unsorted_filename ) -def get_stream_reader(fh): + +def _download_file(start, fh): + tmp = tempfile.NamedTemporaryFile() + tmp.write(start) + tmp.write(fh.read()) + tmp.flush() + tmp.seek(0) + return tmp + + +def get_stream_reader(fh, tmp_dir): + """ + Check if file is compressed and return correct stream reader. + If file has to be downloaded, do it now. + """ magic_dict = { "\x1f\x8b\x08": _get_stream_readers_for_gzip, "\x42\x5a\x68": _get_stream_readers_for_bz2, "\x50\x4b\x03\x04": _get_stream_readers_for_zip, - "\x76\x2f\x31\x01": _get_stream_readers_for_tar } start_of_file = fh.read(CHUNK_SIZE) try: fh.seek(0) except AttributeError: # This is if fh has been created by urllib2.urlopen - url = fh.url - fh = urllib2.urlopen(url) - for k,v in magic_dict: + fh = _download_file(start_of_file, fh) + for k,v in magic_dict.items(): if start_of_file.startswith(k): - return v(fh) + return v(fh, tmp_dir) + try: # Check if file is tar file + if tarfile.open(fileobj=StringIO(start_of_file)): + return _get_stream_readers_for_tar(fh, tmp_dir) + except tarfile.ReadError: + pass return fh + def _get_ucsc_download_address(params, dbkey): """ Check if we can find the correct file for the supplied dbkey on UCSC's FTP server @@ -213,115 +249,107 @@ ucsc_path = UCSC_DOWNLOAD_PATH % ucsc_dbkey path_contents = _get_files_in_ftp_path(ftp, ucsc_path) + ftp.close() for ucsc_chrom_fa_filename in UCSC_CHROM_FA_FILENAMES: for ext 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) - return "ftp://%s" % ucsc_file_name + return "ftp://%s%s" % (UCSC_FTP_SERVER, ucsc_file_name) raise Exception('Unable to determine filename for UCSC Genome for %s: %s' % (ucsc_dbkey, path_contents)) - -def download_from_ucsc( data_manager_dict, params, target_directory, dbkey, dbkey_name, sequence_id, sequence_name ): - - # TODO: may need to think of a good way to merge multiple fasta files if necessary - url = _get_ucsc_download_address(params, dbkey) - fasta_readers = get_stream_reader( urllib2.urlopen(url) ) - +def add_fasta_to_table(data_manager_dict, fasta_readers, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params): for data_table_name, data_table_entry in _stream_fasta_to_file( fasta_readers, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params ): if data_table_entry: _add_data_table_entry( data_manager_dict, data_table_entry, data_table_name ) -def download_from_ncbi( data_manager_dict, params, target_directory, dbkey, dbkey_name, sequence_id, sequence_name ): + +def download_from_ucsc( data_manager_dict, params, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, tmp_dir ): + url = _get_ucsc_download_address(params, dbkey) + fasta_readers = get_stream_reader(urllib2.urlopen(url), tmp_dir) + add_fasta_to_table(data_manager_dict, fasta_readers, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params) + + +def download_from_ncbi( data_manager_dict, params, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, tmp_dir ): 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_readers = get_stream_reader(urllib2.urlopen( url )) - - for data_table_name, data_table_entry in _stream_fasta_to_file( fasta_readers, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params ): - if data_table_entry: - _add_data_table_entry( data_manager_dict, data_table_entry, data_table_name ) + fasta_readers = get_stream_reader(urllib2.urlopen(url), tmp_dir) + add_fasta_to_table(data_manager_dict, fasta_readers, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params) + -def download_from_url( data_manager_dict, params, target_directory, dbkey, dbkey_name, sequence_id, sequence_name ): - #TODO: we should automatically do decompression here +def download_from_url( data_manager_dict, params, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, tmp_dir ): urls = filter( bool, map( lambda x: x.strip(), params['param_dict']['reference_source']['user_url'].split( '\n' ) ) ) - fasta_readers = [ get_stream_reader(urllib2.urlopen( url )) for url in urls ] - - for data_table_name, data_table_entry in _stream_fasta_to_file( fasta_readers, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params ): - if data_table_entry: - _add_data_table_entry( data_manager_dict, data_table_entry, data_table_name ) + fasta_readers = [ get_stream_reader(urllib2.urlopen( url ), tmp_dir) for url in urls ] + add_fasta_to_table(data_manager_dict, fasta_readers, target_directory, dbkey, dbkey_name, sequence_id,sequence_name, params) -def download_from_history( data_manager_dict, params, target_directory, dbkey, dbkey_name, sequence_id, sequence_name ): + +def download_from_history( data_manager_dict, params, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, tmp_dir ): #TODO: allow multiple FASTA input files input_filename = params['param_dict']['reference_source']['input_fasta'] if isinstance( input_filename, list ): - fasta_readers = [ get_stream_reader(open( filename, 'rb' )) for filename in input_filename ] + fasta_readers = [ get_stream_reader(open(filename, 'rb'), tmp_dir) for filename in input_filename ] else: - fasta_readers = get_stream_reader(open( input_filename )) - - for data_table_name, data_table_entry in _stream_fasta_to_file( fasta_readers, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params ): - if data_table_entry: - _add_data_table_entry( data_manager_dict, data_table_entry, data_table_name ) + fasta_readers = get_stream_reader(open(input_filename), tmp_dir) + add_fasta_to_table(data_manager_dict, fasta_readers, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params) -def copy_from_directory( data_manager_dict, params, target_directory, dbkey, dbkey_name, sequence_id, sequence_name ): + +def copy_from_directory( data_manager_dict, params, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, tmp_dir ): 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_entries = _create_symlink( input_filename, target_directory, dbkey, dbkey_name, sequence_id, sequence_name ) else: if isinstance( input_filename, list ): - fasta_readers = [ get_stream_reader(open( filename, 'rb' )) for filename in input_filename ] + fasta_readers = [ get_stream_reader(open(filename, 'rb'), tmp_dir) for filename in input_filename ] else: - fasta_readers = get_stream_reader(open( input_filename )) + fasta_readers = get_stream_reader(open(input_filename), tmp_dir) data_table_entries = _stream_fasta_to_file( fasta_readers, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params ) for data_table_name, data_table_entry in data_table_entries: if data_table_entry: _add_data_table_entry( data_manager_dict, data_table_entry, data_table_name ) + def _add_data_table_entry( data_manager_dict, data_table_entry, data_table_name ): 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( 'all_fasta', [] ) data_manager_dict['data_tables'][data_table_name].append( data_table_entry ) return data_manager_dict + def _stream_fasta_to_file( fasta_stream, target_directory, dbkey, dbkey_name, 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+' ) + with open( fasta_filename, 'wb+' ) as fasta_writer: - if isinstance( fasta_stream, list ) and len( fasta_stream ) == 1: - fasta_stream = fasta_stream[0] + 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' ) + 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 = fh.read( CHUNK_SIZE ) + data = fasta_stream.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_stream.close() - fasta_writer.close() - - - sort_fasta( fasta_filename, params['param_dict']['sorting']['sort_selector'], params ) dbkey_dict = None @@ -333,6 +361,7 @@ return [ ( '__dbkeys__', dbkey_dict ), ( 'all_fasta', dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_filename ) ) ] + def compute_fasta_length( fasta_file, out_file, keep_first_word=False ): infile = fasta_file @@ -365,6 +394,7 @@ out.write( "%s\t%d\n" % ( fasta_title[ 1: ], seq_len ) ) out.close() + def _create_symlink( input_filename, target_directory, dbkey, dbkey_name, sequence_id, sequence_name ): fasta_base_filename = "%s.fa" % sequence_id fasta_filename = os.path.join( target_directory, fasta_base_filename ) @@ -380,12 +410,11 @@ return [ ( '__dbkeys__', dbkey_dict ), ( 'all_fasta', 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() @@ -403,11 +432,16 @@ if dbkey in [ None, '', '?' ]: raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( dbkey ) ) - + + # Create a tmp_dir, in case a zip file needs to be uncompressed + tmp_dir = tempfile.mkdtemp() #Fetch the FASTA - REFERENCE_SOURCE_TO_DOWNLOAD[ params['param_dict']['reference_source']['reference_source_selector'] ]( data_manager_dict, params, target_directory, dbkey, dbkey_name, sequence_id, sequence_name ) - + try: + REFERENCE_SOURCE_TO_DOWNLOAD[ params['param_dict']['reference_source']['reference_source_selector'] ]( data_manager_dict, params, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, tmp_dir ) + finally: + cleanup_before_exit(tmp_dir) #save info to json file open( filename, 'wb' ).write( dumps( data_manager_dict ) ) -if __name__ == "__main__": main() +if __name__ == "__main__": + main()
--- a/data_manager/data_manager_fetch_genome_all_fasta_dbkeys.xml Wed Aug 17 07:36:44 2016 -0400 +++ b/data_manager/data_manager_fetch_genome_all_fasta_dbkeys.xml Thu Aug 18 06:09:29 2016 -0400 @@ -1,13 +1,13 @@ -<tool id="data_manager_fetch_genome_all_fasta_dbkey" name="Create DBKey and Reference Genome" version="0.0.1" tool_type="manage_data"> +<tool id="data_manager_fetch_genome_all_fasta_dbkey" name="Create DBKey and Reference Genome" version="0.0.2" tool_type="manage_data"> <description>fetching</description> - <command interpreter="python">data_manager_fetch_genome_all_fasta_dbkeys.py "${out_file}" - #if str( $dbkey_source.dbkey_source_selector ) == 'existing': - --dbkey_description ${ dbkey_source.dbkey.get_display_text() } - #else - --dbkey_description "${ dbkey_source.dbkey_name or $dbkey_source.dbkey }" - #end if - - </command> + <command><![CDATA[ + python "$__tool_directory__"/data_manager_fetch_genome_all_fasta_dbkeys.py "${out_file}" + #if str( $dbkey_source.dbkey_source_selector ) == 'existing': + --dbkey_description ${ dbkey_source.dbkey.get_display_text() } + #else + --dbkey_description "${ dbkey_source.dbkey_name or $dbkey_source.dbkey }" + #end if + ]]></command> <inputs> <conditional name="dbkey_source"> <param name="dbkey_source_selector" type="select" label="Use existing dbkey or create a new one."> @@ -37,7 +37,7 @@ <param type="text" name="requested_dbkey" value="" label="UCSC's DBKEY for source FASTA" optional="False" /> </when> <when value="ncbi"> - <param type="text" name="requested_identifier" value="" label="NCBI identifier" optional="False" /> + <param type="text" name="requested_identifier" value="" label="NCBI identifier/accession" help="Identifiers (e.g 667699573) or accessions (e.g AC020606.7) may be used" optional="False" /> </when> <when value="url"> <param type="text" area="True" name="user_url" value="http://" label="URLs" optional="False" />