comparison data_manager/hisat2_index_builder.py @ 4:d210e1f185bd draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f

3:98a60a4cfb9a

#!/usr/bin/env python
# Based heavily on the Bowtie 2 data manager wrapper script by Dan Blankenberg

import shlex
import sys
import os
import argparse
import subprocess

from json import loads, dumps


DEFAULT_DATA_TABLE_NAME = "hisat2_indexes"


def get_id_name( params, dbkey, fasta_description=None):

    args.extend( shlex.split( options.indexer_options ) )
    args.extend( [ sym_linked_fasta_filename, sequence_id ] )
    proc = subprocess.Popen( args=args, shell=False, cwd=target_directory )
    return_code = proc.wait()
    if return_code:
        print >> sys.stderr, "Error building index."
        sys.exit( return_code )
    data_table_entry = dict( value=sequence_id, dbkey=options.fasta_dbkey, name=sequence_name, path=sequence_id )
    _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry )

    params = loads( open( filename ).read() )
    data_manager_dict = {}

    if options.fasta_dbkey in [ None, '', '?' ]:
        raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( dbkey ) )

    sequence_id, sequence_name = get_id_name( params, dbkey=options.fasta_dbkey, fasta_description=options.fasta_description )

    # build the index
    build_hisat_index( data_manager_dict, options, params, sequence_id, sequence_name )

    # save info to json file
    open( filename, 'wb' ).write( dumps( data_manager_dict ) )

if __name__ == "__main__":
    main()

4:d210e1f185bd

#!/usr/bin/env python
# Based heavily on the Bowtie 2 data manager wrapper script by Dan Blankenberg
from __future__ import print_function

import argparse
import os
import shlex
import subprocess
import sys
from json import dumps, loads

DEFAULT_DATA_TABLE_NAME = "hisat2_indexes"


def get_id_name( params, dbkey, fasta_description=None):

    args.extend( shlex.split( options.indexer_options ) )
    args.extend( [ sym_linked_fasta_filename, sequence_id ] )
    proc = subprocess.Popen( args=args, shell=False, cwd=target_directory )
    return_code = proc.wait()
    if return_code:
        print("Error building index.", file=sys.stderr)
        sys.exit( return_code )
    data_table_entry = dict( value=sequence_id, dbkey=options.fasta_dbkey, name=sequence_name, path=sequence_id )
    _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry )

    params = loads( open( filename ).read() )
    data_manager_dict = {}

    if options.fasta_dbkey in [ None, '', '?' ]:
        raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( options.fasta_dbkey ) )

    sequence_id, sequence_name = get_id_name( params, dbkey=options.fasta_dbkey, fasta_description=options.fasta_description )

    # build the index
    build_hisat_index( data_manager_dict, options, params, sequence_id, sequence_name )

    # save info to json file
    open( filename, 'w' ).write( dumps( data_manager_dict ) )


if __name__ == "__main__":
    main()