annotate hubArchiveCreator.py @ 6:816956489fe9 draft

planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 20817d2bd61639d88226c9cd0392cea420ded222

#!/usr/bin/python
# -*- coding: utf8 -*-

"""
This Galaxy tool permits to prepare your files to be ready for
Assembly Hub visualization.
Program test arguments:
hubArchiveCreator.py -g test-data/augustusDbia3.gff3 -f test-data/dbia3.fa -d . -u ./tools -o output.html
"""

import argparse
import collections
import json
import sys

# Internal dependencies
from TrackHub import TrackHub
from Gff3 import Gff3
from Bam import Bam
from BedSimpleRepeats import BedSimpleRepeats
from Bed import Bed
from BigWig import BigWig
from Gtf import Gtf


# TODO: Verify each subprocessed dependency is accessible [gff3ToGenePred, genePredToBed, twoBitInfo, faToTwoBit, bedToBigBed, sort


def main(argv):
    # Command Line parsing init
    parser = argparse.ArgumentParser(description='Create a foo.txt inside the given folder.')

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

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

    # GTF Management
    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')

    # Bam Management
    parser.add_argument('--bam', action='append', help='Bam format')

    # TODO: Check if the running directory can have issues if we run the tool outside
    parser.add_argument('-d', '--directory',
                        help='Running tool directory, where to find the templates. Default is running directory')
    parser.add_argument('-u', '--ucsc_tools_path',
                        help='Directory where to find the executables needed to run this tool')
    parser.add_argument('-e', '--extra_files_path',
                        help='Name, in galaxy, of the output folder. Where you would want to build the Track Hub Archive')
    parser.add_argument('-o', '--output', help='Name of the HTML summarizing the content of the Track Hub Archive')

    parser.add_argument('-j', '--data_json', help='Json containing the metadata of the inputs')

    ucsc_tools_path = ''

    toolDirectory = '.'
    extra_files_path = '.'

    # Get the args passed in parameter
    args = parser.parse_args()

    input_fasta_file = args.fasta

    # TODO: Add array for each input because we can add multiple -b for example + filter the data associated


    array_inputs_gff3 = args.gff3
    array_inputs_bed_simple_repeats = args.bedSimpleRepeats
    array_inputs_bed_generic = args.bed
    array_inputs_gtf = args.gtf
    array_inputs_bam = args.bam
    array_inputs_bigwig = args.bigwig

    outputFile = args.output
    json_inputs_data = args.data_json

    json_inputs_data = args.data_json

    inputs_data = json.loads(json_inputs_data)
    # We remove the spaces in ["name"] of inputs_data
    sanitize_name_inputs(inputs_data)

    if args.directory:
        toolDirectory = args.directory
    if args.extra_files_path:
        extra_files_path = args.extra_files_path

    # TODO: Check here all the binaries / tools we need. Exception is missing

    # Create the Track Hub folder
    trackHub = TrackHub(input_fasta_file, outputFile, extra_files_path, toolDirectory)

    all_datatype_dictionary = {}

    # Process Augustus
    if array_inputs_gff3:
        create_ordered_datatype_objects(Gff3, array_inputs_gff3, inputs_data, input_fasta_file,
                                        extra_files_path, all_datatype_dictionary, toolDirectory)

    # Process Bed simple repeats => From Tandem Repeats Finder / TrfBig
    if array_inputs_bed_simple_repeats:
        create_ordered_datatype_objects(BedSimpleRepeats, array_inputs_bed_simple_repeats, inputs_data, input_fasta_file,
                                        extra_files_path, all_datatype_dictionary, toolDirectory)

    # Process a Bed => tBlastN or TopHat
    if array_inputs_bed_generic:
        create_ordered_datatype_objects(Bed, array_inputs_bed_generic, inputs_data, input_fasta_file,
                                        extra_files_path, all_datatype_dictionary, toolDirectory)

    # Process a GTF => Tophat
    if array_inputs_gtf:
        create_ordered_datatype_objects(Gtf, array_inputs_gtf, inputs_data, input_fasta_file,
                                        extra_files_path, all_datatype_dictionary, toolDirectory)

    # Process a Bam => Tophat
    if array_inputs_bam:
        create_ordered_datatype_objects(Bam, array_inputs_bam, inputs_data, input_fasta_file,
                                        extra_files_path, all_datatype_dictionary, toolDirectory)

    # Process a BigWig => From Bam
    if array_inputs_bigwig:
        create_ordered_datatype_objects(BigWig, array_inputs_bigwig, inputs_data, input_fasta_file,
                                        extra_files_path, all_datatype_dictionary, toolDirectory)

    # Create Ordered Dictionary to add the tracks in the tool form order
    all_datatype_ordered_dictionary = collections.OrderedDict(all_datatype_dictionary)

    for index, datatypeObject in all_datatype_ordered_dictionary.iteritems():
        trackHub.addTrack(datatypeObject.track.trackDb)

    # We process all the modifications to create the zip file
    trackHub.createZip()

    # We terminate le process and so create a HTML file summarizing all the files
    trackHub.terminate()

    sys.exit(0)


def sanitize_name_inputs(inputs_data):
    """
    Sometimes output from Galaxy, or even just file name from user have spaces
    Also, it can contain '/' character and could break the use of os.path function
    :param inputs_data: dict[string, dict[string, string]]
    :return:
    """
    for key in inputs_data:
        inputs_data[key]["name"] = inputs_data[key]["name"]\
            .replace("/", "_")\
            .replace(" ", "_")


def create_ordered_datatype_objects(ExtensionClass, array_inputs, inputs_data, input_fasta_file,
                                    extra_files_path, all_datatype_dictionary, tool_directory):
    """
    Function which executes the creation all the necessary files / folders for a special Datatype, for TrackHub
    and update the dictionary of datatype
    :param ExtensionClass: T <= Datatype
    :param array_inputs: list[string]
    :param inputs_data:
    :param input_fasta_file: string
    :param extra_files_path: string
    :param tool_directory; string
    """

    datatype_dictionary = {}

    # TODO: Optimize this double loop
    for input_false_path in array_inputs:
        for key, data_value in inputs_data.items():
            if key == input_false_path:
                extensionObject = ExtensionClass(input_false_path, data_value,
                                                 input_fasta_file, extra_files_path, tool_directory)
                datatype_dictionary.update({data_value["order_index"]: extensionObject})
    all_datatype_dictionary.update(datatype_dictionary)

if __name__ == "__main__":
    main(sys.argv)