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Merge pull request #360 from jodyphelan/dev
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Dev
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@jodyphelan
jodyphelan authored May 10, 2024
2 parents 152d603 + 8151bc8 commit 5da1ce4
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Showing 3 changed files with 47 additions and 37 deletions.
74 changes: 39 additions & 35 deletions tb-profiler
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Original file line number Diff line number Diff line change
Expand Up @@ -187,6 +187,10 @@ def main_profile(args):
pp.logging.info("[green]Profiling finished sucessfully![/]",extra={"markup": True})

def main_update_tbdb(args):

if args.match_ref:
args.match_ref = os.path.abspath(args.match_ref)

if pp.nofolder("tbdb"):
pp.run_cmd(f"git clone {args.repo}")
os.chdir("tbdb")
Expand Down Expand Up @@ -379,7 +383,7 @@ algorithm.add_argument('--snp_diff_db','--snp-diff_db',type=str,help=argparse.SU
algorithm.add_argument('--snp_diff_no_store','--snp-diff-no-store',action='store_true',help=argparse.SUPPRESS)
algorithm.add_argument('--no_trim','--no-trim',action="store_true",help="Don't trim files using trimmomatic")
algorithm.add_argument('--no_coverage_qc','--no-coverage-qc',action="store_true",help="Don't collect flagstats")
algorithm.add_argument('--no_samclip','--no-samclip',action="store_false",help="Don't remove clipped reads from variant calling")
algorithm.add_argument('--no_samclip','--no-samclip',action="store_true",help="Don't remove clipped reads from variant calling")
algorithm.add_argument('--no_delly','--no-delly',action="store_true",help="Don't run delly")
algorithm.add_argument('--no_lineage','--no-lineage',action="store_true",help=argparse.SUPPRESS)
algorithm.add_argument('--add_variant_annotations','--add-variant-annotations',action="store_true",help=argparse.SUPPRESS)
Expand All @@ -400,17 +404,17 @@ parser_sub.set_defaults(func=main_profile)
parser_sub = subparsers.add_parser('lineage', help='Profile only lineage', formatter_class=ArgumentDefaultsRichHelpFormatter)
parser_sub.add_argument('--bam','-a',required=True, help='BAM file. Make sure it has been generated using the H37Rv genome (GCA_000195955.2)')
parser_sub.add_argument('--prefix','-p',default="tbprofiler",help='Sample prefix')
parser_sub.add_argument('--snps',action="store_true",help='Sample prefix')
parser_sub.add_argument('--barcode_snps','--barcode-snps',help='Dump barcoding mutations to a file')
parser_sub.add_argument('--caller',default='freebayes',choices=["bcftools","freebayes","gatk"],type=str,help="Variant caller")
parser_sub.add_argument('--kmer_counter',default='kmc',choices=["kmc","dsk"],type=str,help="Kmer counter")
parser_sub.add_argument('--kmer_counter','--kmer-counter',default='kmc',choices=["kmc","dsk"],type=str,help="Kmer counter")
parser_sub.add_argument('--platform','-m',choices=["illumina","nanopore","pacbio"],default="illumina",help='NGS Platform used to generate data')
parser_sub.add_argument('--db',default='tbdb',help='Mutation panel name')
parser_sub.add_argument('--spoligotype',action="store_true",help="Perform in-silico spoligotyping")
parser_sub.add_argument('--external_db',type=str,help='Path to db files prefix (overrides "--db" parameter)')
parser_sub.add_argument('--text_template',type=str,help='Jinja2 formatted template for output')
parser_sub.add_argument('--external_db','--external-db',type=str,help='Path to db files prefix (overrides "--db" parameter)')
parser_sub.add_argument('--text_template','--text-template',type=str,help='Jinja2 formatted template for output')
parser_sub.add_argument('--threads','-t',default=1,help='Threads to use',type=int)
parser_sub.add_argument('--dir','-d',default=".",help='Storage directory')
parser_sub.add_argument('--no_clean', action='store_true',help=argparse.SUPPRESS)
parser_sub.add_argument('--no_clean','--no-clean', action='store_true',help=argparse.SUPPRESS)
parser_sub.add_argument('--temp',help="Temp firectory to process all files",type=str,default=".")
parser_sub.add_argument('--version', action='version', version="tb-profiler version %s" % tbp.__version__)
parser_sub.add_argument('--logging',type=str.upper,default="INFO",choices=["DEBUG","INFO","WARNING","ERROR","CRITICAL"],help='Logging level')
Expand All @@ -427,12 +431,12 @@ parser_sub.add_argument('--txt',action="store_true",help="Add text output")
parser_sub.add_argument('--csv',action="store_true",help="Add CSV output")
parser_sub.add_argument('--docx',action="store_true",help="Add docx output. This requires docxtpl to be installed")
parser_sub.add_argument('--text_template',type=str,help='Jinja2 formatted template for output')
parser_sub.add_argument('--kmer_counter',default='kmc',choices=["kmc","dsk"],type=str,help="Kmer counter")
parser_sub.add_argument('--kmer_counter','--kmer-counter',default='kmc',choices=["kmc","dsk"],type=str,help="Kmer counter")
parser_sub.add_argument('--platform','-m',choices=["illumina","nanopore","pacbio"],default="illumina",help='NGS Platform used to generate data')
parser_sub.add_argument('--db',default='tbdb',help='Mutation panel name')
parser_sub.add_argument('--external_db',type=str,help='Path to db files prefix (overrides "--db" parameter)')
parser_sub.add_argument('--external_db','--external-db',type=str,help='Path to db files prefix (overrides "--db" parameter)')
parser_sub.add_argument('--dir','-d',default=".",help='Storage directory')
parser_sub.add_argument('--no_clean', action='store_true',help=argparse.SUPPRESS)
parser_sub.add_argument('--no_clean','--no-clean', action='store_true',help=argparse.SUPPRESS)
parser_sub.add_argument('--threads','-t',default=1,help='Threads to use',type=int)
parser_sub.add_argument('--ram',default=2,type=int_2_or_more,help='Maximum memory to use in Gb')
parser_sub.add_argument('--temp',help="Temp firectory to process all files",type=str,default=".")
Expand All @@ -445,13 +449,13 @@ parser_sub.add_argument('--prefix','-p',default="tbprofiler",help='Sample prefix
parser_sub.add_argument('--samples',help='File with samples (one per line)')
parser_sub.add_argument('--itol',action="store_true",help='Generate itol config files')
parser_sub.add_argument('--full',action="store_true",help='Output mutations in main result file')
parser_sub.add_argument('--all_variants',action="store_true",help='Output all variants in variant matrix')
parser_sub.add_argument('--mark_missing',action="store_true",help='An asteriks will be use to mark predictions which are affected by missing data at a drug resistance position')
parser_sub.add_argument('--all_variants','--all-variants',action="store_true",help='Output all variants in variant matrix')
parser_sub.add_argument('--mark_missing','--mark-missing',action="store_true",help='An asteriks will be use to mark predictions which are affected by missing data at a drug resistance position')
parser_sub.add_argument('--db',default='tbdb',help='Full path to mutation database json file to use')
parser_sub.add_argument('--format',default='txt',choices=['txt','csv'],help='Format of the output')
parser_sub.add_argument('--external_db',type=str,help='Path to db files prefix (overrides "--db" parameter)')
parser_sub.add_argument('--external_db','--external-db',type=str,help='Path to db files prefix (overrides "--db" parameter)')
parser_sub.add_argument('--dir','-d',nargs="+",default=["results"],help='Storage directory')
parser_sub.add_argument('--no_clean', action='store_true',help=argparse.SUPPRESS)
parser_sub.add_argument('--no_clean','--no-clean', action='store_true',help=argparse.SUPPRESS)
parser_sub.add_argument('--temp',help="Temp firectory to process all files",type=str,default=".")
parser_sub.add_argument('--version', action='version', version="tb-profiler version %s" % tbp.__version__)
parser_sub.add_argument('--logging',type=str.upper,default="INFO",choices=["DEBUG","INFO","WARNING","ERROR","CRITICAL"],help='Logging level')
Expand All @@ -463,39 +467,39 @@ parser_sub.add_argument('json',default="tbprofiler",help='Sample prefix')
parser_sub.add_argument('--txt',action="store_true",help="Add text output")
parser_sub.add_argument('--csv',action="store_true",help="Add CSV output")
parser_sub.add_argument('--docx',action="store_true",help="Add docx output. This requires docxtpl to be installed")
parser_sub.add_argument('--docx_template',help="Supply custom template for --docx output")
parser_sub.add_argument('--text_template',type=str,help='Jinja2 formatted template for output')
parser_sub.add_argument('--docx_template','--docx-template',help="Supply custom template for --docx output")
parser_sub.add_argument('--text_template','--text-template',type=str,help='Jinja2 formatted template for output')
parser_sub.add_argument('--db',default='tbdb',help='Mutation panel name')
parser_sub.add_argument('--external_db',type=str,help='Path to db files prefix (overrides "--db" parameter)')
parser_sub.add_argument('--external_db','--external-db',type=str,help='Path to db files prefix (overrides "--db" parameter)')
parser_sub.add_argument('--dir','-d',default=".",help='Storage directory')
parser_sub.add_argument('--no_clean', action='store_true',help=argparse.SUPPRESS)
parser_sub.add_argument('--no_clean','--no-clean', action='store_true',help=argparse.SUPPRESS)
parser_sub.add_argument('--suspect',action="store_true",help=argparse.SUPPRESS)
parser_sub.add_argument('--temp',help="Temp firectory to process all files",type=str,default=".")
parser_sub.add_argument('--version', action='version', version="tb-profiler version %s" % tbp.__version__)
parser_sub.add_argument('--logging',type=str.upper,default="INFO",choices=["DEBUG","INFO","WARNING","ERROR","CRITICAL"],help='Logging level')
parser_sub.set_defaults(func=main_reformat)

parser_sub = subparsers.add_parser('create_db', help='Generate the files required to run tb-profiler', formatter_class=ArgumentDefaultsRichHelpFormatter)
parser_sub.add_argument('--prefix','-p',type=str,help='The input CSV file containing the mutations',required=True)
parser_sub.add_argument('--csv','-c',nargs="+",default=["mutations.csv"],type=str,help='The prefix for all output files')
parser_sub.add_argument('--prefix','-p',type=str,help='The prefix for all output files',required=True)
parser_sub.add_argument('--csv','-c',nargs="+",default=["mutations.csv"],type=str,help='The input CSV file containing the mutations')
parser_sub.add_argument('--watchlist','-w',default="watchlist.csv",type=str,help='A csv file containing genes to profile but without any specific associated mutations')
parser_sub.add_argument('--spoligotypes',default="spoligotype_spacers.txt",type=str,help='A file containing a list of spoligotype spacers')
parser_sub.add_argument('--spoligotype_annotations',default="spoligotype_list.csv")
parser_sub.add_argument('--spoligotype_annotations','--spoligotype-annotations',default="spoligotype_list.csv")
parser_sub.add_argument('--barcode',default="barcode.bed",type=str,help='A bed file containing lineage barcode SNPs')
parser_sub.add_argument('--bedmask',default="mask.bed",type=str,help='A bed file containing a list of low-complexity regions')
parser_sub.add_argument('--rules',type=str,default="rules.txt",help='A file containing python rules')
parser_sub.add_argument('--amplicon_primers',type=str,help='A file containing a list of amplicon primers')
parser_sub.add_argument('--match_ref',type=str,help='The prefix for all output files')
parser_sub.add_argument('--amplicon_primers','--amplicon-primers',type=str,help='A file containing a list of amplicon primers')
parser_sub.add_argument('--match_ref','--match-ref',type=str,help='Match the chromosome name to the given fasta file')
parser_sub.add_argument('--custom',action="store_true",help='Tells the script this is a custom database, this is used to alter the generation of the version definition')
parser_sub.add_argument('--db_name',help='Overrides the name of the database in the version file')
parser_sub.add_argument('--db_commit',help='Overrides the commit string of the database in the version file')
parser_sub.add_argument('--db_author',help='Overrides the author of the database in the version file')
parser_sub.add_argument('--db_date',help='Overrides the date of the database in the version file')
parser_sub.add_argument('--include_original_mutation',action="store_true", help='Include the original mutation (before reformatting) as part of the variant annotaion')
parser_sub.add_argument('--db_commit','--db-commit',help='Overrides the commit string of the database in the version file')
parser_sub.add_argument('--db_author','--db-author',help='Overrides the author of the database in the version file')
parser_sub.add_argument('--db_date','--db-date',help='Overrides the date of the database in the version file')
parser_sub.add_argument('--include_original_mutation','--include-original-mutation',action="store_true", help='Include the original mutation (before reformatting) as part of the variant annotaion')
parser_sub.add_argument('--load',action="store_true", help='Automaticaly load database')
parser_sub.add_argument('--no_overwrite',action="store_true", help="Don't load if existing database with prefix exists")
parser_sub.add_argument('--no_overwrite','--no-overwrite',action="store_true", help="Don't load if existing database with prefix exists")
parser_sub.add_argument('--dir','-d',default=".",help='Storage directory')
parser_sub.add_argument('--no_clean', action='store_true',help=argparse.SUPPRESS)
parser_sub.add_argument('--no_clean','--no-clean', action='store_true',help=argparse.SUPPRESS)
parser_sub.add_argument('--temp',help="Temp firectory to process all files",type=str,default=".")
parser_sub.add_argument('--version', action='version', version="tb-profiler version %s" % tbp.__version__)
parser_sub.add_argument('--logging',type=str.upper,default="INFO",choices=["DEBUG","INFO","WARNING","ERROR","CRITICAL"],help='Logging level')
Expand All @@ -504,7 +508,7 @@ parser_sub.set_defaults(func=main_create_db)
parser_sub = subparsers.add_parser('load_library', help='Load new library', formatter_class=ArgumentDefaultsRichHelpFormatter)
parser_sub.add_argument('prefix',type=str,help='Prefix to the library files')
parser_sub.add_argument('--dir','-d',default=".",help='Storage directory')
parser_sub.add_argument('--no_clean', action='store_true',help=argparse.SUPPRESS)
parser_sub.add_argument('--no_clean','--no-clean', action='store_true',help=argparse.SUPPRESS)
parser_sub.add_argument('--temp',help="Temp firectory to process all files",type=str,default=".")
parser_sub.add_argument('--version', action='version', version="tb-profiler version %s" % tbp.__version__)
parser_sub.add_argument('--logging',type=str.upper,default="INFO",choices=["DEBUG","INFO","WARNING","ERROR","CRITICAL"],help='Logging level')
Expand All @@ -515,9 +519,9 @@ parser_sub.add_argument('--prefix','-p',help='Database name')
parser_sub.add_argument('--repo','-r',default="https://github.com/jodyphelan/tbdb.git",help='Repository to pull from')
parser_sub.add_argument('--branch','-b',default="tbdb",help='Branch to pull from')
parser_sub.add_argument('--commit','-c',help='Git commit hash to checkout (default: latest)')
parser_sub.add_argument('--match_ref',type=str,help='The prefix for all output files')
parser_sub.add_argument('--match_ref','--match-ref',type=str,help='The prefix for all output files')
parser_sub.add_argument('--dir','-d',default=".",help='Storage directory')
parser_sub.add_argument('--no_clean', action='store_true',help=argparse.SUPPRESS)
parser_sub.add_argument('--no_clean','--no-clean', action='store_true',help=argparse.SUPPRESS)
parser_sub.add_argument('--temp',help="Temp firectory to process all files",type=str,default=".")
parser_sub.add_argument('--version', action='version', version="tb-profiler version %s" % tbp.__version__)
parser_sub.add_argument('--logging',type=str.upper,default="INFO",choices=["DEBUG","INFO","WARNING","ERROR","CRITICAL"],help='Logging level')
Expand All @@ -527,25 +531,25 @@ parser_sub = subparsers.add_parser('batch', help='Run tb-profiler for several sa
parser_sub.add_argument('--csv',help='CSV with samples and files',required=True)
parser_sub.add_argument('--args',type=str, help='Arguments to use with tb-profiler')
parser_sub.add_argument('--jobs','-j',default=1,help='Threads to use',type=int)
parser_sub.add_argument('--threads_per_job','-t',default=1,help='Threads to use',type=int)
parser_sub.add_argument('--threads_per_job','--threads-per-job','-t',default=1,help='Threads to use',type=int)
parser_sub.add_argument('--dir','-d',default=".",help='Storage directory')
parser_sub.add_argument('--no_clean', action='store_true',help=argparse.SUPPRESS)
parser_sub.add_argument('--no_clean','--no-clean', action='store_true',help=argparse.SUPPRESS)
parser_sub.add_argument('--temp',help="Temp firectory to process all files",type=str,default=".")
parser_sub.add_argument('--version', action='version', version="tb-profiler version %s" % tbp.__version__)
parser_sub.add_argument('--logging',type=str.upper,default="INFO",choices=["DEBUG","INFO","WARNING","ERROR","CRITICAL"],help='Logging level')
parser_sub.set_defaults(func=main_batch)

parser_sub = subparsers.add_parser('list_db', help='List loaded databases', formatter_class=ArgumentDefaultsRichHelpFormatter)
parser_sub.add_argument('--dir','-d',default=".",help='Storage directory')
parser_sub.add_argument('--no_clean', action='store_true',help=argparse.SUPPRESS)
parser_sub.add_argument('--no_clean','--no-clean', action='store_true',help=argparse.SUPPRESS)
parser_sub.add_argument('--temp',help="Temp firectory to process all files",type=str,default=".")
parser_sub.add_argument('--version', action='version', version="tb-profiler version %s" % tbp.__version__)
parser_sub.add_argument('--logging',type=str.upper,default="INFO",choices=["DEBUG","INFO","WARNING","ERROR","CRITICAL"],help='Logging level')
parser_sub.set_defaults(func=main_list_db)

parser_sub = subparsers.add_parser('version', help='Output program version and exit', formatter_class=ArgumentDefaultsRichHelpFormatter)
parser_sub.add_argument('--dir','-d',default=".",help='Storage directory')
parser_sub.add_argument('--no_clean', action='store_true',help=argparse.SUPPRESS)
parser_sub.add_argument('--no_clean','--no-clean', action='store_true',help=argparse.SUPPRESS)
parser_sub.add_argument('--temp',help="Temp firectory to process all files",type=str,default=".")
parser_sub.add_argument('--version', action='version', version="tb-profiler version %s" % tbp.__version__)
parser_sub.add_argument('--logging',type=str.upper,default="INFO",choices=["DEBUG","INFO","WARNING","ERROR","CRITICAL"],help='Logging level')
Expand Down
6 changes: 6 additions & 0 deletions tbprofiler/reformat.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -203,13 +203,19 @@ def create_lineage_result(
lineage: List[Lineage]
):
main_lineage, sub_lineage = get_main_lineage(lineage)
pipeline = Pipeline(
software_version=args.version,
db_version=args.conf['version'],
software=[{'process':k,'software':v} for k,v in shared_dict.items()]
)
data = {
'id':args.prefix,
'lineage':lineage,
'sub_lineage':sub_lineage,
'main_lineage':main_lineage,
'tbprofiler_version':args.version,
'db_version':args.conf['version'],
'pipeline':pipeline
}
return LineageResult(**data)

Expand Down
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