view galaxy/tools/config_builder/config_builder @ 9:728c6b81b45e draft default tip

New Concatenator

#!/usr/bin/env python

import sys
import yaml
import argparse as ap
import urllib.request as urllib

# Version of PathOGiST
MAJOR_VERSION = 0
MINOR_VERSION = 3

parser = ap.ArgumentParser(prog='config_builder', conflict_handler='resolve',
                           description="Builds the config file for PathOGiST")

parser.add_argument('forward', help="File to list of forward reads")
parser.add_argument('reverse', help="File to list of reverse reads")
parser.add_argument('output', help="Output prefix for final consensus clustering and visualization")

tools = parser.add_argument_group('Tools')
tools.add_argument('--snippy', action='store_true', help="Run Snippy")
tools.add_argument('--kwip', action='store_true', help="Run Kwip")
tools.add_argument('--prince', action='store_true', help="Run Prince")
tools.add_argument('--spotyping', action='store_true', help="Run Spotyping")
tools.add_argument('--mentalist', action='store_true', help="Run Mentalist")

mentalist = parser.add_argument_group('Mentalist')
mentalist.add_argument('--local_file', action='store_true', help="Use local database")
mentalist.add_argument('--build_db', action='store_true', help="Build a database")
mentalist.add_argument('--download_pubmlst', action='store_true', help="Download pubMLST scheme")
mentalist.add_argument('--download_cgmlst', action='store_true', help="Download cgMLST scheme")
mentalist.add_argument('--download_enterobase', action='store_true', help="Download Enterobase scheme")

mentalist.add_argument('--local_db', metavar="STRING", help="Location of database")
mentalist.add_argument('--kmer', metavar="INT", help="Kmer size")
mentalist.add_argument('--fasta_files', metavar="STRING", help="Location of FASTA files for MLST scheme")
mentalist.add_argument('--profile', metavar="STRING", help="Profile file for known genotypes")
mentalist.add_argument('--scheme', metavar="STRING", help="Species name or scheme ID")
mentalist.add_argument('--entero_scheme', metavar="STRING", help="(S)almonella, (Y)ersinia, or (E)scherichia/Shigella")
mentalist.add_argument('--entero_type', metavar="STRING", help="'cg' or 'wg' for cgMLST or wgMLST, respectively.")
mentalist.add_argument('--mutation_threshold', metavar="INT", help="Maximum number of mutations when looking for novel "
                                                                   "alleles")
mentalist.add_argument('--kt', metavar="INT", help="Minimum number of times a kmer is seen to be considered present "
                                                   "in the sample")

kwip = parser.add_argument_group('Kwip')
kwip.add_argument('--N', metavar="INT", help="Number of tables")
kwip.add_argument('--x', metavar="INT", help="Maximum table size")
kwip.add_argument('--ksize', metavar="INT", help="kmer size to use")
kwip.add_argument('--unique_kmers', metavar="INT", help="Approximate number of unique kmers in the input set")

snippy = parser.add_argument_group('Snippy')
snippy.add_argument('--reference', metavar="STRING", help="Reference genome. Supports FASTA, GenBank, EMBL (not GFF)")
snippy.add_argument('--mapqual', metavar="INT", help="Minimum read mapping quality to consider")
snippy.add_argument('--basequal', metavar="INT", help="Minimum base quality to consider")
snippy.add_argument('--mincov', metavar="INT", help="Minimum coverage of variant site")
snippy.add_argument('--minfrac', metavar="FLOAT", help="Minimum proportion for variant evidence")

clustering = parser.add_argument_group('Clustering')
clustering.add_argument('--fine_snp', action='store_true', help="Use SNP as a fine datatype")
clustering.add_argument('--fine_mlst', action='store_true', help="Use MLST as a fine datatype")
clustering.add_argument('--fine_kwip', action='store_true', help="Use Kwip as a fine datatype")
clustering.add_argument('--fine_spoligo', action='store_true', help="Use Spoligotyping as a fine datatype")
clustering.add_argument('--fine_cnv', action='store_true', help="Use CNV as a fine datatype")
clustering.add_argument('--snp_thresh', metavar="INT", help="Threshold value for SNP")
clustering.add_argument('--mlst_thresh', metavar="INT", help="Threshold value for MLST")
clustering.add_argument('--kwip_thresh', metavar="INT", help="Threshold value for Kwip")
clustering.add_argument('--spoligo_thresh', metavar="INT", help="Threshold value for Spoligotyping")
clustering.add_argument('--cnv_thresh', metavar="INT", help="Threshold value for CNV")
clustering.add_argument('--less_constraints', action='store_true', help="Use less constraints when clustering")
clustering.add_argument('--method', metavar="STRING", help="Use `C4` or `ILP` as clustering method")
clustering.add_argument('--no_presolve', action='store_true', help="Do not perform presolving")
clustering.add_argument('--visualize', action='store_true', help="Visualize clusters")

if len(sys.argv) == 1:
    parser.print_usage()
    sys.exit(1)

args = parser.parse_args()

urllib.urlretrieve("https://github.com/WGS-TB/PathOGiST/releases/download/v{0}.{1}/blank_config.yaml"
                   .format(MAJOR_VERSION, MINOR_VERSION), 'blank_config.yaml')

with open('blank_config.yaml') as f:
    list_doc = yaml.load(f)

for line in list_doc:
    if line == 'temp':
        list_doc[line] = 'tmp_dir'

    if line == 'threads':
        pass

    if line == 'run':
        if args.snippy:
            list_doc[line]['snippy'] = 1
        if args.kwip:
            list_doc[line]['kwip'] = 1
        if args.prince:
            list_doc[line]['prince'] = 1
        if args.spotyping:
            list_doc[line]['spotyping'] = 1
        if args.mentalist:
            list_doc[line]['mentalist'] = 1

    if line == 'genotyping':
        # Forward and reverse reads
        list_doc[line]['input_reads']['forward_reads'] = args.forward
        list_doc[line]['input_reads']['reverse_reads'] = args.reverse

        if args.mentalist:
            if args.local_file:
                list_doc[line]['mentalist']['local_file']['database'] = args.local_db
            elif args.build_db:
                list_doc[line]['mentalist']['build_db']['options']['k'] = args.kmer
                list_doc[line]['mentalist']['build_db']['options']['fasta_files'] = args.fasta_files
                list_doc[line]['mentalist']['build_db']['options']['profile'] = args.profile
            elif args.download_pubmlst:
                list_doc[line]['mentalist']['download_pubmlst']['options']['k'] = args.kmer
                list_doc[line]['mentalist']['download_pubmlst']['options']['scheme'] = args.scheme
            elif args.download_cgmlst:
                list_doc[line]['mentalist']['download_cgmlst']['options']['k'] = args.kmer
                list_doc[line]['mentalist']['download_cgmlst']['options']['scheme'] = args.scheme
            elif args.download_enterobase:
                list_doc[line]['mentalist']['download_enterobase']['options']['k'] = args.kmer
                list_doc[line]['mentalist']['download_enterobase']['options']['scheme'] = args.entero_scheme
                list_doc[line]['mentalist']['download_enterobase']['options']['type'] = args.entero_type

            if args.mutation_threshold:
                list_doc[line]['mentalist']['call']['options']['mutation_threshold'] = args.mutation_threshold
            if args.kt:
                list_doc[line]['mentalist']['call']['options']['kt'] = args.kt

        if args.kwip:
            if args.N:
                list_doc[line]['kwip']['khmer_options']['N'] = args.N
            if args.x:
                list_doc[line]['kwip']['khmer_options']['x'] = args.x
            if args.ksize:
                list_doc[line]['kwip']['khmer_options']['ksize'] = args.ksize
            if args.unique_kmers:
                list_doc[line]['kwip']['khmer_options']['unique-kmers'] = args.unique_kmers

        if args.snippy:
            list_doc[line]['snippy']['options']['reference'] = args.reference
            if args.mapqual:
                list_doc[line]['snippy']['options']['mapqual'] = args.mapqual
            if args.basequal:
                list_doc[line]['snippy']['options']['basequal'] = args.basequal
            if args.mincov:
                list_doc[line]['snippy']['options']['mincov'] = args.mincov
            if args.minfrac:
                list_doc[line]['snippy']['options']['minfrac'] = args.minfrac

    if line == 'clustering':
        list_doc[line]['output_prefix'] = args.output

        fine = []
        if args.fine_snp:
            fine.append('SNP')
        if args.fine_mlst:
            fine.append('MLST')
        if args.fine_kwip:
            fine.append('kWIP')
        if args.fine_spoligo:
            fine.append('spoligotyping')
        if args.fine_cnv:
            fine.append('CNV')
        list_doc[line]['fine_clusterings'] = fine

        if args.snp_thresh:
            list_doc[line]['thresholds']['SNP'] = args.snp_thresh
        if args.mlst_thresh:
            list_doc[line]['thresholds']['MLST'] = args.snp_thresh
        if args.kwip_thresh:
            list_doc[line]['thresholds']['kWIP'] = args.snp_thresh
        if args.spoligo_thresh:
            list_doc[line]['thresholds']['spoligotyping'] = args.snp_thresh
        if args.cnv_thresh:
            list_doc[line]['thresholds']['CNV'] = args.snp_thresh

        if args.less_constraints:
            list_doc[line]['all_constraints'] = False
        if args.method:
            list_doc[line]['method'] = args.method
        if args.no_presolve:
            list_doc[line]['presolve'] = False
        if args.visualize:
            list_doc[line]['visualize'] = True

with open("config.yaml", 'w') as f:
    yaml.dump(list_doc, f)