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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,102 @@ | ||
| #!/usr/bin/env python3 | ||
| from sys import argv, exit, stderr | ||
| from collections import defaultdict | ||
| import argparse | ||
|
|
||
| """Identify top ranked genus in output report from Kraken2. | ||
| Script was developed for internal use in the Nextflow pipeline BACTpipe. | ||
| """ | ||
|
|
||
| def parse_args(): | ||
| """Parse command line arguments. | ||
| """ | ||
| parser = argparse.ArgumentParser(description=__doc__) | ||
| parser.add_argument("-r", "--kreport", | ||
| required=True, | ||
| help="Path to Kraken2 report output file (txt/kreport)") | ||
| parser.add_argument("-m", "--min-proportion", | ||
| type=float, | ||
| default=50.00, | ||
| help="Minimum proportion on species level [%(default)s].") | ||
| parser.add_argument("-g", "--gramstains", | ||
| help="Path to text file containing gram staining classifications in " | ||
| "two-column tab separated format (Genus<TAB>Stain)") | ||
|
|
||
| if len(argv) < 2: | ||
| parser.print_help() | ||
| exit(1) | ||
|
|
||
| args = parser.parse_args() | ||
|
|
||
| return args | ||
|
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|
|
||
| def parse_gramstains(gramstains): | ||
| gramstain_db = defaultdict(lambda: "Unknown") | ||
| try: | ||
| with open(gramstains) as f: | ||
| for line in f: | ||
| genus, gramstain = line.rstrip().split("\t") | ||
| gramstain_db[genus] = gramstain | ||
| except TypeError as e: | ||
| print("WARNING: No gramstain database specified, gramstain set to Unknown", file=stderr) | ||
| return gramstain_db | ||
|
|
||
|
|
||
| def parse_kreport(kreport_file): | ||
| with open(kreport_file) as f: | ||
| for line_no, line in enumerate(f, start=1): | ||
| try: | ||
| (clade_fraction, clade_fragments, | ||
| taxon_fragments, rank, taxid, name) = line.strip().split("\t") | ||
| except ValueError as e: | ||
| print(f"WARNING: Could not parse line {line_no}, ignoring...", file=stderr) | ||
| continue | ||
|
|
||
| try: | ||
| clade_fraction = float(clade_fraction) | ||
| except ValueError as e: | ||
| print(f"WARNING: Could not interpret {clade_fraction} on row {line_no} as float, ignoring...", file=stderr) | ||
| continue | ||
|
|
||
| if rank == "S": | ||
| clean_name = name.strip().split()[:2] | ||
| yield clade_fraction, clean_name | ||
|
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|
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| def classify(detected_species, min_proportion, gramstain_db): | ||
| taxon_names = [ | ||
| species for proportion, species in | ||
| filter(lambda x: x[0] > min_proportion, detected_species) | ||
| ] | ||
|
|
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| output_genus = "Unknown" | ||
| output_species = "unknown" | ||
|
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| genera = set(genus for genus, species in taxon_names) | ||
| if len(genera) > 1: | ||
| output_genus = "Mixed" | ||
| elif len(genera) == 1: | ||
| output_genus = genera.pop() | ||
|
|
||
| species = set(species for genus, species in taxon_names) | ||
| if (len(species) > 1) and output_genus: | ||
| output_species = "spp." | ||
| elif len(species) == 1: | ||
| output_species = species.pop() | ||
|
|
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| output_gramstain = gramstain_db.get(output_genus, "Unknown") | ||
|
|
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| return output_genus, output_species, output_gramstain | ||
|
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|
|
||
| if __name__ == "__main__": | ||
| args = parse_args() | ||
|
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| gramstain_db = parse_gramstains(args.gramstains) | ||
| detected_species = list(parse_kreport(args.kreport)) | ||
| genus, species, gramstain = classify(detected_species, args.min_proportion, gramstain_db) | ||
|
|
||
| print(genus, species, gramstain, sep="\t") | ||
|
|
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,60 @@ | ||
| // vim: syntax=groovy expandtab | ||
| // BACTpipe Nextflow configuration file for use on CTMR Gandalf | ||
|
|
||
| params { | ||
| project = 'bio' | ||
| partition = 'ctmr' | ||
| } | ||
|
|
||
| process { | ||
| errorStrategy = 'terminate' | ||
| executor = 'slurm' | ||
| clusterOptions = { | ||
| " --partition ${params.partition} -A ${params.project}" + (params.clusterOptions ?: '') | ||
| } | ||
| scratch = false | ||
| stageInMode = 'copy' | ||
| stageOutMode = 'copy' | ||
|
|
||
| withName: | ||
| FASTP { | ||
| cpus = 4 | ||
| time = 20.m | ||
| conda = 'bioconda::fastp' | ||
| } | ||
|
|
||
| withName: | ||
| SHOVILL { | ||
| cpus = 10 | ||
| time = 2.h | ||
| conda = 'bioconda::shovill bioconda::bwa=0.7.16 python=3' | ||
| } | ||
|
|
||
| withName: | ||
| CLASSIFY_TAXONOMY { | ||
| cpus = 10 | ||
| time = 30.m | ||
| conda = 'bioconda::kraken2' | ||
| } | ||
|
|
||
| withName: | ||
| ASSEMBLY_STATS { | ||
| cpus = 1 | ||
| time = 20.m | ||
| conda = 'bioconda::bbmap' | ||
| } | ||
|
|
||
| withName: | ||
| PROKKA { | ||
| cpus = 4 | ||
| time = 2.h | ||
| conda = 'bioconda::prokka' | ||
| } | ||
|
|
||
| withName: | ||
| MULTIQC { | ||
| cpus = 1 | ||
| time = 10.m | ||
| conda = 'bioconda::multiqc' | ||
| } | ||
| } |
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