# HG changeset patch
# User ieguinoa
# Date 1539164676 14400
# Node ID a4d4da89aae1b88e2618880aef66403267c0d5ac
Uploaded
diff -r 000000000000 -r a4d4da89aae1 README.md
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md Wed Oct 10 05:44:36 2018 -0400
@@ -0,0 +1,2 @@
+# data_manager_fetch_tx2gene
+Load entries in tx2gene table with transcript to gene tables or GTF/GFF file.
diff -r 000000000000 -r a4d4da89aae1 data_manager/data_manager_fetch_tx2gene.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_fetch_tx2gene.py Wed Oct 10 05:44:36 2018 -0400
@@ -0,0 +1,307 @@
+#!/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 = 'tx2gene'
+
+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 convert_tx2gene( fasta_filename, file_type, params ):
+ if file_type is 'tx2gene':
+ return #no need to extract tx2gene table
+ #If the file is actually a GFF/GTF file then extract the tx2gene
+ gff_temp_filename = tempfile.NamedTemporaryFile().name
+ shutil.move(fasta_filename, gff_temp_filename)
+ args= ['Rscript']
+ args.append(RSCRIPT_GFF_TO_TX2GENE)
+ args.append(gff_temp_filename)
+ args.append(fasta_filename)
+
+ #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 _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 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_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_tx2gene.tab" % 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()
+
+ convert_to_tx2gene( fasta_filename, params['param_dict']['file_type'], 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( 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' )
+ 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
+ global RSCRIPT_GFF_TO_TX2GENE= os.path.join( options.base_dir, 'tximport.r')
+
+
+ if options.file_type == 'gff_gtf':
+ #DATA_TABLE_NAME= 'representative_gff'
+ else: #file_type='tx2gene'
+
+ 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 input file
+ 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()
diff -r 000000000000 -r a4d4da89aae1 data_manager/data_manager_fetch_tx2gene.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_fetch_tx2gene.xml Wed Oct 10 05:44:36 2018 -0400
@@ -0,0 +1,68 @@
+
+ fetching
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+**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.
+
+
+
diff -r 000000000000 -r a4d4da89aae1 data_manager_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml Wed Oct 10 05:44:36 2018 -0400
@@ -0,0 +1,20 @@
+
+
+
+
+
+
+
+
diff -r 000000000000 -r a4d4da89aae1 tool-data/all_gff.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/all_gff.loc.sample Wed Oct 10 05:44:36 2018 -0400
@@ -0,0 +1,3 @@
+#The all_gff.loc file has this format:
+#
+#
diff -r 000000000000 -r a4d4da89aae1 tool-data/representative_gff.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/representative_gff.loc.sample Wed Oct 10 05:44:36 2018 -0400
@@ -0,0 +1,3 @@
+#The representative_gff.loc file has this format:
+#
+#
diff -r 000000000000 -r a4d4da89aae1 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Wed Oct 10 05:44:36 2018 -0400
@@ -0,0 +1,4 @@
+
+
+
+