view data_manager/rnastar_index_builder.py @ 7:0ff626afce84 draft

planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit ad4ee919a27115e2cb5d999b6e4f0b876b3b6bfc

#!/usr/bin/env python

from __future__ import print_function
import argparse
from subprocess import check_call, CalledProcessError
from json import load, dump, dumps
from os import environ, mkdir, makedirs
from os.path import isdir, exists
import shlex
import sys

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

    sequence_name = params['param_dict']['sequence_name']
    if not sequence_name:
        sequence_name = fasta_description
        if not sequence_name:
            sequence_name = dbkey
    return sequence_id, sequence_name

def make_rnastar_index(output_directory, fasta_filename):
    #STAR
    #    --runMode genomeGenerate
    #    --genomeDir tempstargenomedir
    #    --genomeFastaFiles $input1
    #    --runThreadsN \${GALAXY_SLOTS:-1}
    #    --genomeChrBinNbits $advanced_options.chr_bin_nbits

    if exists(output_directory) and not isdir(output_directory):
        print("Output directory path already exists but is not a directory: {}".format(output_directory), file=sys.stderr)
    elif not exists(output_directory):
        mkdir(output_directory)

    if 'GALAXY_SLOTS' in environ:
        nslots = environ['GALAXY_SLOTS']
    else:
        nslots = 1

    # cmdline_str = 'STAR --runMode genomeGenerate --genomeDir {} --genomeFastaFiles {} --runThreadsN {}'.format(output_directory,
    #                                                                                                            fasta_filename,
    #                                                                                                            nslots)
    # cmdline = shlex.split(cmdline_str)
    cmdline = ('touch', '{}/foo'.format(output_directory))
    try:
        check_call(cmdline)
    except CalledProcessError:
        print("Error building RNA STAR index", file=sys.stderr)
    return(output_directory)

parser = argparse.ArgumentParser(description="Generate RNA STAR genome index and JSON describing this")
parser.add_argument('output_filename')
parser.add_argument('--fasta_filename')
parser.add_argument('--fasta_dbkey')
parser.add_argument('--fasta_description', default=None)
parser.add_argument('--data_table_name', default='rnastar_indexes')
args = parser.parse_args()

filename = args.output_filename

params = load(open(filename, 'rb'))
output_directory = params[ 'output_data' ][0]['extra_files_path']
makedirs( output_directory )
data_manager_dict = {}

make_rnastar_index(output_directory, args.fasta_filename)
(sequence_id, sequence_name) = get_id_name(params, args.fasta_dbkey, args.fasta_description)
data_table_entry = dict(value=sequence_id, dbkey=args.fasta_dbkey, name=sequence_name, path=output_directory)

#dt_tables = {args.data_table_name : [data_table_entry]}
output_datatable_dict = dict(data_tables={args.data_table_name : [data_table_entry]})
open( filename, 'wb' ).write( dumps( output_datatable_dict ) )