comparison data_manager/novoalign_index_builder.py @ 2:e51fb8188ed9 draft

planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit 7c74dfc33ffac5de44aae81def9c374f5f5e2a20

1:4d67344bdea7

#!/usr/bin/env python
# Z. Mashologu (SANBI-UWC)
#import dict as dict
import os
import shutil
import optparse
import urllib2
import logging
log = logging.getLogger( __name__ )

from json import loads, dumps

def cleanup_before_exit( tmp_dir ):
    if tmp_dir and os.path.exists( tmp_dir ):
        shutil.rmtree( tmp_dir )

def _stream_fasta_to_file( fasta_stream, target_directory, 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+' )

    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' )
            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()

    fasta_writer.close()

    return dict( path=fasta_base_filename )

def download_from_url( data_manager_dict, params, target_directory, dbkey, sequence_id, sequence_name ):
    #TODO: we should automatically do decompression here
    urls = filter( bool, map( lambda x: x.strip(), params['param_dict']['reference_source']['user_url'].split( '\n' ) ) )
    fasta_reader = [ urllib2.urlopen( url ) for url in urls ]

    data_table_entry = _stream_fasta_to_file( fasta_reader, target_directory, params )
    _add_data_table_entry( data_manager_dict, data_table_entry )

def download_from_history( data_manager_dict, params, target_directory):
    #TODO: allow multiple FASTA input files
    input_filename = params['param_dict']['reference_source']['input_fasta']
    if isinstance( input_filename, list ):
        fasta_reader = [ open( filename, 'rb' ) for filename in input_filename ]
    else:
        fasta_reader = open( input_filename )

    data_table_entry = _stream_fasta_to_file( fasta_reader, target_directory, params )
    _add_data_table_entry( data_manager_dict, data_table_entry )

def copy_from_directory( data_manager_dict, params, target_directory ):
    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_entry = _create_symlink( input_filename, target_directory )
    else:
        if isinstance( input_filename, list ):
            fasta_reader = [ open( filename, 'rb' ) for filename in input_filename ]
        else:
            fasta_reader = open( input_filename )
        data_table_entry = _stream_fasta_to_file( fasta_reader, target_directory, params )
    _add_data_table_entry( data_manager_dict, data_table_entry )

def _create_symlink( input_filename, target_directory ):
    fasta_base_filename = "%s.fa" % sequence_id
    fasta_filename = os.path.join( target_directory, fasta_base_filename )
    os.symlink( input_filename, fasta_filename )
    return dict( 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', '--data_table_name' )
    (options, args) = parser.parse_args()

    filename = args[0]

    params = loads( open( filename ).read() )
    target_directory = params[ 'output_data' ][0]['extra_files_path']
    os.mkdir( target_directory )
    data_manager_dict = {}

    #Fetch the FASTA
    REFERENCE_SOURCE_TO_DOWNLOAD[ params['param_dict']['reference_source']['reference_source_selector'] ]( data_manager_dict, params, target_directory )

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

if __name__ == "__main__": main()

2:e51fb8188ed9

#!/usr/bin/env python
# Z. Mashologu (SANBI-UWC)
# import dict as dict
import os
import sys
import urllib2
import logging
import argparse
import shlex
from subprocess import check_call, CalledProcessError
from __future__ import print_function

log = logging.getLogger(__name__)

from json import loads, dumps

def get_dbkey_id_name(params, dbkey_description=None):
    dbkey = params['param_dict']['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?

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


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

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

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


def download_from_url(params, target_directory):
    # TODO: we should automatically do decompression here
    urls = filter(bool, map(lambda x: x.strip(), params['param_dict']['reference_source']['user_url'].split('\n')))
    fasta_reader = [urllib2.urlopen(url) for url in urls]

    _make_novocraft_index(fasta_reader, target_directory)


def download_from_history( params, target_directory):
    # TODO: allow multiple FASTA input files
    input_filename = params['param_dict']['reference_source']['input_fasta']

    _make_novocraft_index(input_filename, target_directory)

REFERENCE_SOURCE_TO_DOWNLOAD = dict(url=download_from_url, history=download_from_history)

def main():
    parser = argparse.ArgumentParser(description="Generate Novo-align genome index and JSON describing this")
    parser.add_argument('output_filename')
    parser.add_argument('--data_table_name', default='novocraft_index')
    (options, args) = parser.parse_args()

    filename = args.output_filename

    params = loads(open(filename).read())
    target_directory = params['output_data'][0]['extra_files_path']
    os.mkdir(target_directory)

    dbkey, sequence_id, sequence_name = get_dbkey_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))

    # Fetch the FASTA
    REFERENCE_SOURCE_TO_DOWNLOAD[params['param_dict']['reference_source']['reference_source_selector']]\
        (params, target_directory, dbkey, sequence_id, sequence_name)

    data_table_entry = dict(value=sequence_id, dbkey=dbkey, name=sequence_name, path=target_directory)

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

if __name__ == "__main__": main()