comparison jbrowse_hub.py @ 5:e7c80e9b70ae draft

planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty

4:c7c1474a6b7d

import blastxmlToGff3
import utils
import tempfile
import trackObject
import TrackHub

def main(argv):
    parser = argparse.ArgumentParser(description='Create a hub to display in jbrowse.')

    # Reference genome mandatory
    parser.add_argument('-f', '--fasta', help='Fasta file of the reference genome')

    # Output folder
    parser.add_argument('-o', '--out', help='Name of the HTML summarizing the content of the JBrowse Hub')

    # GFF3
    parser.add_argument('--gff3', action='append', help='GFF3 format')

    # trfBig simple repeats (BED 4+12)

    # GTF format
    parser.add_argument('--gtf', action='append', help='GTF format from StringTie')

    args = parser.parse_args()
    all_datatype_dictionary = dict()
    all_tracks = []

    reference = args.fasta
    out_path = args.out
    tool_directory = 'JBrowse-1.12.1/bin'
    chrom_size = utils.getChromSizes(reference, '../ucsc_tools_340_for_HAC')
    array_inputs_bam = args.bam
    array_inputs_bed_simple_repeats = args.bedSimpleRepeats
    array_inputs_bed_splice_junctions = args.bedSpliceJunctions
    array_inputs_bigwig = args.bigwig
    array_inputs_gff3 = args.gff3

    
    print all_datatype_dictionary

    for datatype, inputfiles in all_datatype_dictionary.items():
        try:
            user_input = inputfiles
            if not user_input:
                raise ValueError('empty input, must provide track files!\n')
        except IOError:
            print 'Cannot open', datatype
        else:
            for f in inputfiles:
                track = trackObject.trackObject(f, datatype, chrom_size.name)
                track.addToRaw()
                all_tracks.append(track)

    jbrowseHub = TrackHub.TrackHub(all_tracks, reference, out_path, tool_directory)
    jbrowseHub.createHub()
            
            
'''
    if reference:
        p = subprocess.Popen(['JBrowse-1.12.1/bin/prepare-refseqs.pl', '--fasta', reference, '--out', out_path])
        # Wait for process to terminate.
        p.communicate()

5:e7c80e9b70ae

import blastxmlToGff3
import utils
import tempfile
import trackObject
import TrackHub
import shutil

def main(argv):
    parser = argparse.ArgumentParser(description='Create a hub to display in jbrowse.')

    # Reference genome mandatory
    parser.add_argument('-f', '--fasta', help='Fasta file of the reference genome')

    # Genome name
    parser.add_argument('-g', '--genome_name', help='Name of reference genome')

    # Output folder
    parser.add_argument('-o', '--out', help='output html')

    # Output folder
    parser.add_argument('-e', '--extra_files_path', help="Directory of JBrowse Hub folder")

    # GFF3
    parser.add_argument('--gff3', action='append', help='GFF3 format')

    # trfBig simple repeats (BED 4+12)

    # GTF format
    parser.add_argument('--gtf', action='append', help='GTF format from StringTie')

    args = parser.parse_args()
    all_datatype_dictionary = dict()
    

    reference = args.fasta
    genome = 'unknown'
    out_path = '.'
    extra_files_path = '.'
    if args.genome_name:
        genome = utils.sanitize_name_path(args.genome_name)
    if args.out:
        out_path = args.out
    if args.extra_files_path:
        extra_files_path = utils.sanitize_name_path(args.extra_files_path)
    cwd = os.getcwd()
    #tool_directory not work for Galaxy tool, all tools need to exist in the current PATH, deal with it with tool dependencies
    tool_directory = os.path.join(cwd, 'JBrowse-1.12.1/bin')
    chrom_size = utils.getChromSizes(reference, tool_directory)
    all_tracks = trackObject.trackObject(chrom_size.name, genome, extra_files_path) #store converted files in the array: all_tracks.tracks
    array_inputs_bam = args.bam
    array_inputs_bed_simple_repeats = args.bedSimpleRepeats
    array_inputs_bed_splice_junctions = args.bedSpliceJunctions
    array_inputs_bigwig = args.bigwig
    array_inputs_gff3 = args.gff3

    
    print all_datatype_dictionary

    for datatype, inputfiles in all_datatype_dictionary.items():
        try:
            if not inputfiles:
                raise ValueError('empty input, must provide track files!\n')
        except IOError:
            print 'Cannot open', datatype
        else:
            for f in inputfiles:
                all_tracks.addToRaw(f, datatype)

    jbrowseHub = TrackHub.TrackHub(all_tracks, reference, out_path, tool_directory, genome, extra_files_path)
    jbrowseHub.createHub()
         
    

'''
    if reference:
        p = subprocess.Popen(['JBrowse-1.12.1/bin/prepare-refseqs.pl', '--fasta', reference, '--out', out_path])
        # Wait for process to terminate.
        p.communicate()