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| Original file line number | Diff line number | Diff line change |
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| @@ -1,23 +1,34 @@ | ||
| {% set name = "MentaLiST" %} | ||
| {% set version = "0.1.3" %} | ||
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| package: | ||
| name: mentalist | ||
| version: 0.1.3 | ||
| name: {{ name|lower }} | ||
| version: {{ version }} | ||
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| source: | ||
| git_url: https://github.com/WGS-TB/MentaLiST.git | ||
| git_rev: v0.1.3 | ||
| folder: MentaLiST | ||
| fn: {{ name|lower }}-{{ version }}.tar.gz | ||
| url: https://github.com/WGS-TB/MentaLiST/archive/v{{ version }}.tar.gz | ||
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| build: | ||
| number: 0 | ||
| skip: True # [osx] | ||
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| requirements: | ||
| build: | ||
| - julia 0.5.2 | ||
| - hdf5 | ||
| - mpfr | ||
| run: | ||
| - julia 0.5.2 | ||
| - hdf5 | ||
| - mpfr | ||
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| build: | ||
| number: 0 | ||
| test: | ||
| commands: | ||
| - mentalist -h | ||
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| about: | ||
| home: https://github.com/WGS-TB/MentaLiST | ||
| summary: The MLST pipeline developed by the PathOGiST research group. | ||
| license: MIT | ||
| license_file: LICENSE |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,210 @@ | ||
| #!/usr/bin/env julia | ||
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| using Suppressor | ||
| @suppress_err begin | ||
| using Lumberjack | ||
| using ArgParse | ||
| end | ||
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| function parse_commandline() | ||
| s = ArgParseSettings() | ||
| @add_arg_table s begin | ||
| "call" | ||
| help = "MLST caller, given a sample and a k-mer database." | ||
| action = :command | ||
| "build_db" | ||
| help = "Build a MLST k-mer database, given a list of FASTA files." | ||
| action = :command | ||
| "list_pubmlst" | ||
| help = "List all available MLST schemes from www.pubmlst.org. " | ||
| action = :command | ||
| "download_pubmlst" | ||
| help = "Dowload a MLST scheme from pubmlst and build a MLST k-mer database." | ||
| action = :command | ||
| "list_cgmlst" | ||
| help = "List all available cgMLST schemes from www.cgmlst.org." | ||
| action = :command | ||
| "download_cgmlst" | ||
| help = "Dowload a MLST scheme from cgmlst.org and build a MLST k-mer database." | ||
| action = :command | ||
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| end | ||
| # Calling MLST options: | ||
| @add_arg_table s["call"] begin | ||
| "-o" | ||
| help = "Output file with MLST call" | ||
| arg_type = String | ||
| required = true | ||
| "-s" | ||
| help = "Sample name" | ||
| arg_type = String | ||
| required = true | ||
| "--db" | ||
| help = "Kmer database" | ||
| required = true | ||
| arg_type = String | ||
| "files" | ||
| nargs = '*' | ||
| help = "FastQ input files" | ||
| required = true | ||
| arg_type = String | ||
| end | ||
| # Build DB from FASTA, options: | ||
| @add_arg_table s["build_db"] begin | ||
| "--db" | ||
| help = "Output file (kmer database)" | ||
| arg_type = String | ||
| required = true | ||
| "-k" | ||
| help = "Kmer size" | ||
| required = true | ||
| arg_type = Int8 | ||
| "-f", "--fasta_files" | ||
| nargs = '+' | ||
| arg_type = String | ||
| help = "Fasta files with the MLST scheme" | ||
| required = true | ||
| "-p", "--profile" | ||
| arg_type = String | ||
| help = "Profile file for known genotypes." | ||
| "-c", "--disable_compression" | ||
| help = "Disables the default compression of the database, that stores only the most informative kmers. Not recommended unless for debugging." | ||
| action = :store_true | ||
| end | ||
| @add_arg_table s["list_pubmlst"] begin | ||
| "-p", "--prefix" | ||
| help = "Only list schemes that starts with this prefix." | ||
| arg_type = String | ||
| end | ||
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| @add_arg_table s["list_cgmlst"] begin | ||
| "-p", "--prefix" | ||
| help = "Only list schemes that start with this prefix." | ||
| arg_type = String | ||
| end | ||
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| @add_arg_table s["download_pubmlst"] begin | ||
| "-o", "--output" | ||
| help = "Output folder for the scheme files." | ||
| arg_type = String | ||
| required = true | ||
| "-s", "--scheme" | ||
| help = "Species name or ID of the scheme." | ||
| arg_type = String | ||
| required = true | ||
| "-k" | ||
| help = "K-mer size" | ||
| required = true | ||
| arg_type = Int8 | ||
| "--db" | ||
| help = "Output file for the kmer database." | ||
| arg_type = String | ||
| required = true | ||
| "-c", "--disable_compression" | ||
| help = "Disables the default compression of the database, that stores only the most informative kmers. Not recommended unless for debugging." | ||
| action = :store_true | ||
| end | ||
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| @add_arg_table s["download_cgmlst"] begin | ||
| "-o", "--output" | ||
| help = "Output folder for the scheme files." | ||
| arg_type = String | ||
| required = true | ||
| "-s", "--scheme" | ||
| help = "Species name or ID of the scheme" | ||
| arg_type = String | ||
| required = true | ||
| "-k" | ||
| help = "K-mer size" | ||
| required = true | ||
| arg_type = Int8 | ||
| "--db" | ||
| help = "Output file for the kmer database." | ||
| arg_type = String | ||
| required = true | ||
| "-c", "--disable_compression" | ||
| help = "Disables the default compression of the database, that stores only the most informative kmers. Not recommended unless for debugging." | ||
| action = :store_true | ||
| end | ||
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| return parse_args(s) | ||
| end | ||
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| #### Main COMMAND functions: | ||
| function call_mlst(args) | ||
| include("build_db_functions.jl") | ||
| # check if the files exist: | ||
| check_files([args["db"];args["files"]]) | ||
| info("Opening kmer database ... ") | ||
| kmer_db, loci, loci2alleles, k, profile = open_db(args["db"]) | ||
| info("Opening fastq file(s) ... ") | ||
| votes, loci_votes = count_kmers_and_vote(DNAKmer{k}, args["files"], kmer_db, loci2alleles) | ||
| info("Writing output ...") | ||
| write_calls(votes, loci_votes, loci, loci2alleles, args["s"], args["o"], profile) | ||
| info("Done.") | ||
| end | ||
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| function list_pubmlst(args) | ||
| include("mlst_download_functions.jl") | ||
| list_pubmlst_schema(args["prefix"]) | ||
| end | ||
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| function download_pubmlst(args) | ||
| include("mlst_download_functions.jl") | ||
| loci_files, profile_file = download_pubmlst_scheme(args["scheme"], args["output"]) | ||
| info("Building the k-mer database ...") | ||
| args["fasta_files"] = loci_files | ||
| args["profile"] = profile_file | ||
| build_db(args) | ||
| end | ||
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| function list_cgmlst(args) | ||
| include("mlst_download_functions.jl") | ||
| list_cgmlst_schema(args["prefix"]) | ||
| end | ||
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| function download_cgmlst(args) | ||
| include("mlst_download_functions.jl") | ||
| loci_files = download_cgmlst_scheme(args["scheme"], args["output"]) | ||
| info("Building the k-mer database ...") | ||
| args["fasta_files"] = loci_files | ||
| args["profile"] = nothing | ||
| build_db(args) | ||
| end | ||
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| function build_db(args) | ||
| include("build_db_functions.jl") | ||
| check_files(args["fasta_files"]) | ||
| k::Int8 = args["k"] | ||
| info("Opening FASTA files ... ") | ||
| results, loci = kmer_class_for_each_locus(k, args["fasta_files"], !args["disable_compression"]) | ||
| # Combine results: | ||
| info("Combining results for each locus ...") | ||
| kmer_classification = combine_loci_classification(k, results, loci) | ||
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| info("Saving DB ...") | ||
| save_db(k, kmer_classification, loci, args["db"], args["profile"]) | ||
| info("Done!") | ||
| end | ||
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| ##### Main function: just calls the appropriate commands, with arguments: | ||
| function main() | ||
| args = parse_commandline() | ||
| # determine command: | ||
| if args["%COMMAND%"] == "call" | ||
| call_mlst(args["call"]) | ||
| elseif args["%COMMAND%"] == "build_db" | ||
| build_db(args["build_db"]) | ||
| elseif args["%COMMAND%"] == "list_pubmlst" | ||
| list_pubmlst(args["list_pubmlst"]) | ||
| elseif args["%COMMAND%"] == "download_pubmlst" | ||
| download_pubmlst(args["download_pubmlst"]) | ||
| elseif args["%COMMAND%"] == "list_cgmlst" | ||
| list_cgmlst(args["list_cgmlst"]) | ||
| elseif args["%COMMAND%"] == "download_cgmlst" | ||
| download_cgmlst(args["download_cgmlst"]) | ||
| end | ||
| end | ||
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| main() |
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