comparison hubArchiveCreator.py @ 5:7b0d359de7ee draft

planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit e2db8aa3672f1222b415716054bfb3c5ccd132a1-dirty

4:9018229c0969

import sys

# Internal dependencies
from Bam import Bam
from BedSimpleRepeats import BedSimpleRepeats
from BedSpliceJunctions import BedSpliceJunctions
from Bed import Bed
from BigWig import BigWig
from util.Fasta import Fasta
from util.Filters import TraceBackFormatter
from Gff3 import Gff3

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

    # Bed4+12 (TrfBig)
    parser.add_argument('--bedSimpleRepeats', action='append', help='Bed4+12 format, using simpleRepeats.as')

    # Bed12+1 (regtools)
    parser.add_argument('--bedSpliceJunctions', action='append', help='Bed12+1 format, using spliceJunctions.as')

    # Generic Bed (Blastx transformed to bed)
    parser.add_argument('--bed', action='append', help='Bed generic format')

    # BigWig Management
    parser.add_argument('--bigwig', action='append', help='BigWig format')

    # ARRAY[DICT{FILE_PATH: DICT{NAME: NAME_VALUE, EXTRA_DATA: EXTRA_DATA_VALUE}}]
    # EXTRA_DATA could be anything, for example the index of a BAM => {"index", FILE_PATH}
    array_inputs_bam = args.bam
    array_inputs_bed_generic = args.bed
    array_inputs_bed_simple_repeats = args.bedSimpleRepeats
    array_inputs_bed_splice_junctions = args.bedSpliceJunctions
    array_inputs_bigwig = args.bigwig
    array_inputs_gff3 = args.gff3
    array_inputs_gtf = args.gtf
    array_inputs_psl = args.psl

    for (inputs, datatype_class) in [
                        (array_inputs_bam, Bam),
                        (array_inputs_bed_generic, Bed),
                        (array_inputs_bigwig, BigWig),
                        (array_inputs_bed_simple_repeats, BedSimpleRepeats),
                        (array_inputs_bed_splice_junctions, BedSpliceJunctions),
                        (array_inputs_gff3, Gff3),
                        (array_inputs_gtf, Gtf),
                        (array_inputs_psl, Psl)]:
        if inputs:
            all_datatype_dictionary.update(create_ordered_datatype_objects(datatype_class, inputs, inputs_data))

5:7b0d359de7ee

import sys

# Internal dependencies
from Bam import Bam
from BedSimpleRepeats import BedSimpleRepeats
from Bed import Bed
from BigWig import BigWig
from util.Fasta import Fasta
from util.Filters import TraceBackFormatter
from Gff3 import Gff3

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

    # Bed4+12 (TrfBig)
    parser.add_argument('--bedSimpleRepeats', action='append', help='Bed4+12 format, using simpleRepeats.as')

    # Generic Bed (Blastx transformed to bed)
    parser.add_argument('--bed', action='append', help='Bed generic format')

    # BigWig Management
    parser.add_argument('--bigwig', action='append', help='BigWig format')

    # ARRAY[DICT{FILE_PATH: DICT{NAME: NAME_VALUE, EXTRA_DATA: EXTRA_DATA_VALUE}}]
    # EXTRA_DATA could be anything, for example the index of a BAM => {"index", FILE_PATH}
    array_inputs_bam = args.bam
    array_inputs_bed_generic = args.bed
    array_inputs_bed_simple_repeats = args.bedSimpleRepeats
    array_inputs_bigwig = args.bigwig
    array_inputs_gff3 = args.gff3
    array_inputs_gtf = args.gtf
    array_inputs_psl = args.psl

    for (inputs, datatype_class) in [
                        (array_inputs_bam, Bam),
                        (array_inputs_bed_generic, Bed),
                        (array_inputs_bigwig, BigWig),
                        (array_inputs_bed_simple_repeats, BedSimpleRepeats),
                        (array_inputs_gff3, Gff3),
                        (array_inputs_gtf, Gtf),
                        (array_inputs_psl, Psl)]:
        if inputs:
            all_datatype_dictionary.update(create_ordered_datatype_objects(datatype_class, inputs, inputs_data))