view jbrowse_hub.py @ 30:daf6a1122200 draft

planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit e81fecac281f299db00cfc88a068e056b031ae9d-dirty

#!/usr/bin/env python

import os
import sys
import argparse
import subprocess
from bedToGff3 import bedToGff3
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 structure: gene->transcription->CDS
    parser.add_argument('--gff3_transcript', action='append', help='GFF3 format, structure: gene->transcription->CDS')

    # GFF3 structure: gene->mRNA->CDS
    parser.add_argument('--gff3_mrna', action='append', help='GFF3 format, structure: gene->mRNA->CDS')

    # trfBig simple repeats (BED 4+12)
    parser.add_argument('--bedSimpleRepeats', action='append', help='BED 4+12 format, using simpleRepeats.as')

    # regtools (BED 12+1)
    parser.add_argument('--bedSpliceJunctions', action='append', help='BED 12+1 format, using spliceJunctions.as')

    # tblastn alignment (blastxml)
    parser.add_argument('--blastxml', action='append', help='blastxml format from tblastn')

    # BAM format
    parser.add_argument('--bam', action='append', help='BAM format from HISAT')

    # BIGWIG format
    parser.add_argument('--bigwig', action='append', help='BIGWIG format to show rnaseq coverage')

    # 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_transcript = args.gff3_transcript
    array_inputs_gff3_mrna = args.gff3_mrna
    array_inputs_gtf = args.gtf
    array_inputs_blastxml = args.blastxml
    if array_inputs_bam:
        all_datatype_dictionary['bam'] = array_inputs_bam
    if array_inputs_bed_simple_repeats:
        all_datatype_dictionary['bedSimpleRepeats'] = array_inputs_bed_simple_repeats
    if array_inputs_bed_splice_junctions:
        all_datatype_dictionary['bedSpliceJunctions'] = array_inputs_bed_splice_junctions
    if array_inputs_bigwig:
        all_datatype_dictionary['bigwig'] = array_inputs_bigwig
    if array_inputs_gff3_transcript:
        all_datatype_dictionary['gff3_transcript'] = array_inputs_gff3_transcript
    if array_inputs_gff3_mrna:
        all_datatype_dictionary['gff3_mrna'] = array_inputs_gff3_mrna
    if array_inputs_gtf:
        all_datatype_dictionary['gtf'] = array_inputs_gtf
    if array_inputs_blastxml:
        all_datatype_dictionary['blastxml'] = array_inputs_blastxml
    
    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 __name__ == "__main__":
    main(sys.argv)