Mercurial > repos > ieguinoa > data_manager_salmon_index_builder
changeset 0:6cd60ba8a842 draft
Uploaded
| author | ieguinoa |
|---|---|
| date | Tue, 14 Aug 2018 11:14:52 -0400 |
| parents | |
| children | c5dea2080109 |
| files | README.md data_manager/data_manager_fetch_gff.py data_manager/data_manager_fetch_gff.xml data_manager_conf.xml tool-data/all_gff.loc.sample tool-data/representative_gff.loc.sample tool_data_table_conf.xml.sample |
| diffstat | 7 files changed, 559 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Tue Aug 14 11:14:52 2018 -0400 @@ -0,0 +1,2 @@ +# data_manager_fetch_gff +Galaxy Data Manager to fetch gene annotation files
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/data_manager_fetch_gff.py Tue Aug 14 11:14:52 2018 -0400 @@ -0,0 +1,445 @@ +#!/usr/bin/env python +#Dan Blankenberg + +import sys +import os +import tempfile +import shutil +import optparse +from ftplib import FTP +import tarfile +import zipfile +import gzip +import bz2 +try: + # For Python 3.0 and later + from urllib.request import urlopen + from io import BytesIO as StringIO + from io import UnsupportedOperation +except ImportError: + # Fall back to Python 2's urllib2 + from urllib2 import urlopen + from StringIO import StringIO + UnsupportedOperation = AttributeError +from json import loads, dumps + + +CHUNK_SIZE = 2**20 # 1mb + +DATA_TABLE_NAME = 'all_gff' + +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 + sequence_id = params['param_dict']['sequence_id'] + if not sequence_id: + sequence_id = dbkey #uuid.uuid4() generate and use an uuid instead? + +# if params['param_dict']['dbkey_source']['dbkey_source_selector'] == 'new': +# dbkey_name = params['param_dict']['dbkey_source']['dbkey_name'] +# if not dbkey_name: +# dbkey_name = dbkey +# else: +# dbkey_name = None + dbkey = params['param_dict']['dbkey'] + dbkey_name = dbkey_description + sequence_name = params['param_dict']['sequence_name'] + if not sequence_name: + sequence_name = dbkey_description + if not sequence_name: + 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, tmp_dir ): + fasta_tar = tarfile.open( fileobj=fh, mode='r:*' ) + return [x for x in [fasta_tar.extractfile(member) for member in fasta_tar.getmembers()] if x] + + +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(): + fasta_zip.extract( member, tmp_dir ) + rval.append( open( os.path.join( tmp_dir, member ), 'rb' ) ) + return rval + + +def _get_stream_readers_for_gzip( fh, tmp_dir ): + return [ gzip.GzipFile( fileobj=fh, mode='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: + 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_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_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 = { + b"\x1f\x8b\x08": _get_stream_readers_for_gzip, + b"\x42\x5a\x68": _get_stream_readers_for_bz2, + b"\x50\x4b\x03\x04": _get_stream_readers_for_zip, + } + start_of_file = fh.read(CHUNK_SIZE) + try: + fh.seek(0) + except UnsupportedOperation: # This is if fh has been created by urlopen + fh = _download_file(start_of_file, fh) + for k,v in magic_dict.items(): + if start_of_file.startswith(k): + 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 + """ + UCSC_FTP_SERVER = 'hgdownload.cse.ucsc.edu' + UCSC_DOWNLOAD_PATH = '/goldenPath/%s/bigZips/' + COMPRESSED_EXTENSIONS = ['.tar.gz', '.tgz', '.tar.bz2', '.zip', '.fa.gz', '.fa.bz2'] + + email = params['param_dict']['__user_email__'] + if not email: + email = 'anonymous@example.com' + + ucsc_dbkey = params['param_dict']['reference_source']['requested_dbkey'] or dbkey + UCSC_CHROM_FA_FILENAMES = ['%s.chromFa' % ucsc_dbkey, 'chromFa', ucsc_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) + ftp.quit() + + 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%s" % (UCSC_FTP_SERVER, ucsc_file_name) + + raise Exception('Unable to determine filename for UCSC Genome for %s: %s' % (ucsc_dbkey, path_contents)) + +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_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(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(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, tmp_dir ): + urls = filter( bool, map( lambda x: x.strip(), params['param_dict']['reference_source']['user_url'].split( '\n' ) ) ) + fasta_readers = [ get_stream_reader(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, 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'), tmp_dir) for filename in input_filename ] + else: + 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, 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'), tmp_dir) for filename in input_filename ] + else: + 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( DATA_TABLE_NAME, [] ) + 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.gff" % sequence_id + fasta_filename = os.path.join( target_directory, fasta_base_filename ) + 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 ): + last_char = None + for fh in fasta_stream: + if last_char not in [ None, '\n', '\r', b'\n', b'\r' ]: + fasta_writer.write( b'\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() + + #sort_fasta( fasta_filename, params['param_dict']['sorting']['sort_selector'], params ) + + + return [ ( DATA_TABLE_NAME, 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 + out = open( out_file, 'w') + + fasta_title = '' + seq_len = 0 + + first_entry = True + + for line in open( infile ): + line = line.strip() + if not line or line.startswith( '#' ): + continue + if line[0] == '>': + if first_entry == False: + if keep_first_word: + fasta_title = fasta_title.split()[0] + out.write( "%s\t%d\n" % ( fasta_title[ 1: ], seq_len ) ) + else: + first_entry = False + fasta_title = line + seq_len = 0 + else: + seq_len += len(line) + + # last fasta-entry + if keep_first_word: + fasta_title = fasta_title.split()[0] + 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 ) + os.symlink( input_filename, fasta_filename ) + return [ ( DATA_TABLE_NAME, 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' ) + parser.add_option( '-t', '--type', dest='file_type', action='store', type='string', default=None, help='file_type') + (options, args) = parser.parse_args() + + filename = args[0] + global DATA_TABLE_NAME + if options.file_type == 'representative': + DATA_TABLE_NAME= 'representative_gff' + params = loads( open( filename ).read() ) + target_directory = params[ 'output_data' ][0]['extra_files_path'] + os.mkdir( target_directory ) + data_manager_dict = {} + + dbkey, dbkey_name, sequence_id, sequence_name = get_dbkey_dbname_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 ) ) + + # Create a tmp_dir, in case a zip file needs to be uncompressed + tmp_dir = tempfile.mkdtemp() + #Fetch the FASTA + 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 ).encode() ) + +if __name__ == "__main__": + main()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/data_manager_fetch_gff.xml Tue Aug 14 11:14:52 2018 -0400 @@ -0,0 +1,66 @@ +<tool id="data_manager_fetch_gff" name="Create entries in gff data table" version="0.0.1" tool_type="manage_data"> + <description>fetching</description> + <command><![CDATA[ + python "$__tool_directory__"/data_manager_fetch_gff.py "${out_file}" + --type $file_type + --dbkey_description ${ dbkey.get_display_text() } + + ]]></command> + <inputs> + <param name="file_type" type="select" label="GFF file with only one representative transcript per gene (for htseq-count use) or full features file"> + <option value="representative">Representative GFF</option> + <option value="full">GFF with complete features</option> + </param> + + <param name="dbkey" type="genomebuild" label="DBKEY to assign to data" /> + <param type="text" name="sequence_name" value="" label="Name of sequence" /> + <param type="text" name="sequence_id" value="" label="ID for sequence" /> + <conditional name="reference_source"> + <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"> + <option value="url">URL</option> + <option value="history">History</option> + <option value="directory">Directory on Server</option> + </param> + <when value="url"> + <param type="text" area="True" name="user_url" value="http://" label="URLs" optional="False" /> + </when> + <when value="history"> + <param name="input_fasta" type="data" format="fasta" label="FASTA File" multiple="False" optional="False" /> + </when> + <when value="directory"> + <param type="text" name="fasta_filename" value="" label="Full path to FASTA File on disk" optional="False" /> + <param type="boolean" name="create_symlink" truevalue="create_symlink" falsevalue="copy_file" label="Create symlink to original data instead of copying" checked="False" /> + </when> + </conditional> + </inputs> + <outputs> + <data name="out_file" format="data_manager_json"/> + </outputs> + <tests> + <!-- TODO: need some way to test that new entry was added to data table --> + <test> + <param name="dbkey" value="anoGam1"/> + <param name="sequence_name" value=""/> + <param name="sequence_desc" value=""/> + <param name="sequence_id" value=""/> + <param name="reference_source_selector" value="history"/> + <param name="input_fasta" value="phiX174.fasta"/> + <param name="sort_selector" value="as_is"/> + <output name="out_file" file="phiX174.data_manager_json"/> + </test> + </tests> + <help> +**What it does** + +Fetches a gff file from various sources (URL, Galaxy History, or a server directory) and populates the "all_gff" data table. + +------ + + + +.. 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 Aug 14 11:14:52 2018 -0400 @@ -0,0 +1,35 @@ +<?xml version="1.0"?> +<data_managers> +<data_manager tool_file="data_manager/data_manager_fetch_gff.xml" id="data_manager_fetch_gff"> + <data_table name="all_gff"> + <output> + <column name="value" /> + <column name="dbkey" /> + <column name="name" /> + <column name="path" output_ref="out_file"> + <move type="file"> + <source>${path}</source> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${dbkey}/gff/${path}</target> + </move> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/gff/${path}</value_translation> + <value_translation type="function">abspath</value_translation> + </column> + </output> + </data_table> + <data_table name="representative_gff"> + <output> + <column name="value" /> + <column name="dbkey" /> + <column name="name" /> + <column name="path" output_ref="out_file"> + <move type="file"> + <source>${path}</source> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${dbkey}/representative_gff/${path}</target> + </move> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/representative_gff/${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_gff.loc.sample Tue Aug 14 11:14:52 2018 -0400 @@ -0,0 +1,3 @@ +#The all_gff.loc file has this format: +# +#<unique_build_id> <dbkey> <display_name> <path_to_gff_file>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/representative_gff.loc.sample Tue Aug 14 11:14:52 2018 -0400 @@ -0,0 +1,3 @@ +#The representative_gff.loc file has this format: +# +#<unique_build_id> <dbkey> <display_name> <path_to_gff_file>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Tue Aug 14 11:14:52 2018 -0400 @@ -0,0 +1,5 @@ +<?xml version="1.0"?> +<tables> + <table name="all_gff" comment_char="#"> <columns>value, dbkey, name, path</columns> <file path="tool-data/all_gff.loc" /> </table> + <table name="representative_gff" comment_char="#"> <columns>value, dbkey, name, path</columns> <file path="tool-data/representative_gff.loc" /> </table> +</tables>