Mercurial > repos > public-health-bioinformatics > screen_abricate_report
changeset 0:2c6153023368 draft
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report"
| author | public-health-bioinformatics |
|---|---|
| date | Wed, 30 Oct 2019 23:01:01 -0400 |
| parents | |
| children | 45542cd244ad |
| files | abricate_report_screening_files.loc.sample screen_abricate_report.py screen_abricate_report.xml test-data/abricate_report.tsv test-data/gene_detection_status.tsv test-data/screen.tsv test-data/screen.yaml test-data/screened_report.tsv test-data/screening_file.tsv tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
| diffstat | 11 files changed, 201 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/abricate_report_screening_files.loc.sample Wed Oct 30 23:01:01 2019 -0400 @@ -0,0 +1,7 @@ +# Expect three columns, tab separated, as follows: +# - value (Galaxy records this in the Galaxy DB) +# - name (Galaxy shows this in the UI) +# - path (Path to the abricate report screening file (tsv format)) +# +# e.g. +# 76cc857a-7747-4d69-b2a3-a8fbddbf64c2<tab>Carbapenemase Genes<tab>/path/to/screening_file.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/screen_abricate_report.py Wed Oct 30 23:01:01 2019 -0400 @@ -0,0 +1,58 @@ +#!/usr/bin/env python + +from __future__ import print_function + +import argparse +import os +import re +import sys +import csv +from pprint import pprint + +def parse_screen_file(screen_file): + screen = [] + with open(screen_file) as f: + reader = csv.DictReader(f, delimiter="\t", quotechar='"') + for row in reader: + screen.append(row) + return screen + +def get_fieldnames(input_file): + with open(input_file) as f: + reader = csv.DictReader(f, delimiter="\t", quotechar='"') + row = next(reader) + fieldnames = row.keys() + return fieldnames + +def main(args): + screen = parse_screen_file(args.screening_file) + abricate_report_fieldnames = get_fieldnames(args.abricate_report) + gene_detection_status_fieldnames = ['gene_name', 'detected'] + with open(args.abricate_report, 'r') as f1, open(args.screened_report, 'w') as f2, open(args.gene_detection_status, 'w') as f3: + abricate_report_reader = csv.DictReader(f1, delimiter="\t", quotechar='"') + screened_report_writer = csv.DictWriter(f2, delimiter="\t", quotechar='"', fieldnames=abricate_report_fieldnames) + gene_detection_status_writer = csv.DictWriter(f3, delimiter="\t", quotechar='"', fieldnames=gene_detection_status_fieldnames) + screened_report_writer.writeheader() + gene_detection_status_writer.writeheader() + + for gene in screen: + gene_detection_status = { + 'gene_name': gene['gene_name'], + 'detected': False + } + for abricate_report_row in abricate_report_reader: + if re.search(gene['regex'], abricate_report_row['GENE']): + gene_detection_status['detected'] = True + screened_report_writer.writerow(abricate_report_row) + gene_detection_status_writer.writerow(gene_detection_status) + f1.seek(0) # return file pointer to start of abricate report + + +if __name__ == '__main__': + parser = argparse.ArgumentParser() + parser.add_argument("abricate_report", help="Input: Abricate report to screen (tsv)") + parser.add_argument("--screening_file", help="Input: List of genes to screen for (tsv)") + parser.add_argument("--screened_report", help="Output: Screened abricate report including only genes of interest (tsv)") + parser.add_argument("--gene_detection_status", help="Output: detection status for all genes listed in the screening file (tsv)") + args = parser.parse_args() + main(args)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/screen_abricate_report.xml Wed Oct 30 23:01:01 2019 -0400 @@ -0,0 +1,34 @@ +<tool id="screen_abricate_report" name="Screen Abricate Report" version="0.1.0"> + <description>Screens an abricate report for genes of interest</description> + <requirements> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + '${__tool_directory__}/screen_abricate_report.py' + '${abricate_report}' + --screening_file '${screening_file.fields.path}' + --screened_report '${screened_report}' + --gene_detection_status '${gene_detection_status}' + ]]></command> + <inputs> + <param name="abricate_report" type="data" format="tabular" /> + <param name="screening_file" type="select" format="tabular"> + <options from_data_table="abricate_report_screening_files"> + <validator type="no_options" message="No abricate report screening files are available" /> + </options> + </param> + </inputs> + <outputs> + <data name="screened_report" type="data" format="tabular" label="Screened Abricate Report" /> + <data name="gene_detection_status" type="data" format="tabular" label="Gene Detection Status" /> + </outputs> + <tests> + <test> + <param name="abricate_report" value="abricate_report.tsv"/> + <param name="screen" value="screen.tsv"/> + </test> + </tests> + <help><![CDATA[ + ]]></help> + <citations> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abricate_report.tsv Wed Oct 30 23:01:01 2019 -0400 @@ -0,0 +1,65 @@ +#FILE SEQUENCE START END STRAND GENE COVERAGE COVERAGE_MAP GAPS %COVERAGE %IDENTITY DATABASE ACCESSION PRODUCT RESISTANCE +Shovill_on_data_31_and_data_32__Contigs contig00001 125167 126915 - msbA 1-1749/1749 =============== 0/0 100.00 100.00 card U00096.3:966621-968370 MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability. peptide/rifamycin/pleuromutilin/nitroimidazole/tetracycline/acridine_dye/cephalosporin/macrolide/penam/fluoroquinolone +Shovill_on_data_31_and_data_32__Contigs contig00001 208622 209854 - Escherichia_coli_mdfA 1-1233/1233 =============== 0/0 100.00 98.38 card JQ394987:1-1234 Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter. antibacterial_free_fatty_acids/bicyclomycin/diaminopyrimidine/isoniazid/lincosamide/benzalkonium_chloride/rifamycin/nitroimidazole/nucleoside/macrolide/penam/rhodamine/peptide/fosfomycin/glycylcycline/phenicol/cephalosporin/fluoroquinolone/tetracycline/acridine_dye/oxazolidinone +Shovill_on_data_31_and_data_32__Contigs contig00002 94909 95877 - pmrF 1-969/969 =============== 0/0 100.00 100.00 card U00096:2367071-2368040 PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58. peptide +Shovill_on_data_31_and_data_32__Contigs contig00002 154214 155857 + yojI 1-1644/1644 =============== 0/0 100.00 97.51 card U00096.3:2306972-2308616 YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI. peptide/nitroimidazole/rifamycin/pleuromutilin/penam/fluoroquinolone/cephalosporin/macrolide/tetracycline/acridine_dye +Shovill_on_data_31_and_data_32__Contigs contig00002 298738 299460 - baeR 1-723/723 =============== 0/0 100.00 99.45 card AP009048.1:2166413-2167136 BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes. phenicol/monobactam/glycylcycline/tetracycline/triclosan/acridine_dye/penam/fluoroquinolone/macrolide/aminoglycoside/carbapenem/diaminopyrimidine/antibacterial_free_fatty_acids/aminocoumarin +Shovill_on_data_31_and_data_32__Contigs contig00002 299457 300860 - baeS 1-1404/1404 =============== 0/0 100.00 99.93 card AP009048:2165013-2166417 BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance. aminocoumarin/carbapenem/diaminopyrimidine/aminoglycoside/antibacterial_free_fatty_acids/tetracycline/triclosan/acridine_dye/macrolide/fluoroquinolone/penam/monobactam/glycylcycline/phenicol +Shovill_on_data_31_and_data_32__Contigs contig00002 302273 305350 - mdtC 1-3078/3078 =============== 0/0 100.00 99.84 card U00096:2158386-2161464 MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58. diaminopyrimidine/carbapenem/aminoglycoside/antibacterial_free_fatty_acids/aminocoumarin/glycylcycline/monobactam/phenicol/acridine_dye/triclosan/tetracycline/macrolide/fluoroquinolone/penam +Shovill_on_data_31_and_data_32__Contigs contig00002 305351 308473 - mdtB 1-3123/3123 =============== 0/0 100.00 99.84 card U00096:2155263-2158386 MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. aminocoumarin/aminoglycoside/diaminopyrimidine/carbapenem/antibacterial_free_fatty_acids/acridine_dye/tetracycline/triclosan/penam/fluoroquinolone/macrolide/phenicol/glycylcycline/monobactam +Shovill_on_data_31_and_data_32__Contigs contig00002 308473 309720 - mdtA 1-1248/1248 =============== 0/0 100.00 98.00 card U00096:2154016-2155264 MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC. antibacterial_free_fatty_acids/aminoglycoside/diaminopyrimidine/carbapenem/aminocoumarin/phenicol/glycylcycline/monobactam/penam/fluoroquinolone/macrolide/acridine_dye/triclosan/tetracycline +Shovill_on_data_31_and_data_32__Contigs contig00003 97936 99402 - mdtP 1-1467/1467 =============== 0/0 100.00 100.00 card AP009048.1:4303043-4304510 Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride benzalkonium_chloride/isoniazid/lincosamide/antibacterial_free_fatty_acids/bicyclomycin/diaminopyrimidine/penam/macrolide/nitroimidazole/rifamycin/nucleoside/rhodamine/peptide/fluoroquinolone/cephalosporin/tetracycline/acridine_dye/oxazolidinone/fosfomycin/phenicol/glycylcycline +Shovill_on_data_31_and_data_32__Contigs contig00003 99399 101450 - mdtO 1-2052/2052 =============== 0/0 100.00 99.95 card AP009048.1:4304506-4306558 Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride nucleoside/rifamycin/nitroimidazole/macrolide/penam/diaminopyrimidine/bicyclomycin/antibacterial_free_fatty_acids/isoniazid/lincosamide/benzalkonium_chloride/glycylcycline/phenicol/fosfomycin/oxazolidinone/acridine_dye/tetracycline/cephalosporin/fluoroquinolone/peptide/rhodamine +Shovill_on_data_31_and_data_32__Contigs contig00003 101450 102481 - mdtN 1-1032/1032 =============== 0/0 100.00 100.00 card AP009048.1:4306557-4307589 Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride. tetracycline/oxazolidinone/acridine_dye/cephalosporin/fluoroquinolone/glycylcycline/phenicol/fosfomycin/peptide/rhodamine/macrolide/penam/nucleoside/rifamycin/nitroimidazole/isoniazid/lincosamide/benzalkonium_chloride/diaminopyrimidine/antibacterial_free_fatty_acids/bicyclomycin +Shovill_on_data_31_and_data_32__Contigs contig00003 131919 133562 - eptA 1-1644/1644 =============== 0/0 100.00 99.94 card AP009048:4338625-4340269 PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B. peptide +Shovill_on_data_31_and_data_32__Contigs contig00003 175790 176923 - Escherichia_coli_ampC 1-1134/1134 =============== 0/0 100.00 97.27 card NC_000913.3:4377811-4378945 A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics. cephalosporin/penam +Shovill_on_data_31_and_data_32__Contigs contig00004 47739 48122 + marA 1-384/384 =============== 0/0 100.00 100.00 card AP009048.1:1621288-1621672 In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF. antibacterial_free_fatty_acids/penem/diaminopyrimidine/macrolide/penam/rifamycin/cephamycin/aminocoumarin/carbapenem/aminoglycoside/cephalosporin/fluoroquinolone/tetracycline/triclosan/acridine_dye/monobactam/glycylcycline/phenicol +Shovill_on_data_31_and_data_32__Contigs contig00004 80515 80839 - Klebsiella_pneumoniae_KpnF 6-330/330 =============== 0/0 98.48 75.39 card AP006725.1:2484239-2484569 KpnF subunit of KpnEF resembles EbrAB from E. coli. Mutation in KpnEF resulted in increased susceptibility to cefepime ceftriaxon colistin erythromycin rifampin tetracycline and streptomycin as well as enhanced sensitivity toward sodium dodecyl sulfate deoxycholate dyes benzalkonium chloride chlorhexidine and triclosan. fosfomycin/glycylcycline/phenicol/cephalosporin/fluoroquinolone/acridine_dye/oxazolidinone/tetracycline/aminoglycoside/rhodamine/peptide/rifamycin/nitroimidazole/nucleoside/macrolide/penam/bicyclomycin/antibacterial_free_fatty_acids/diaminopyrimidine/isoniazid/lincosamide/benzalkonium_chloride +Shovill_on_data_31_and_data_32__Contigs contig00004 80831 81189 - Klebsiella_pneumoniae_KpnE 5-363/363 ========/====== 2/2 98.62 75.83 card AP006725.1:2483890-2484253 KpnE subunit of KpnEF resembles EbrAB from E. coli. Mutation in KpnEF resulted in increased susceptibility to cefepime ceftriaxon colistin erythromycin rifampin tetracycline and streptomycin as well as enhanced sensitivity toward sodium dodecyl sulfate deoxycholate dyes benzalkonium chloride chlorhexidine and triclosan diaminopyrimidine/bicyclomycin/antibacterial_free_fatty_acids/benzalkonium_chloride/isoniazid/lincosamide/nucleoside/nitroimidazole/rifamycin/penam/macrolide/aminoglycoside/peptide/rhodamine/phenicol/glycylcycline/fosfomycin/oxazolidinone/acridine_dye/tetracycline/fluoroquinolone/cephalosporin +Shovill_on_data_31_and_data_32__Contigs contig00006 257 1665 + mdtK 1-1409/1425 ========/====== 2/4 98.74 75.34 card CP014358.1:2161326-2162751 A multidrug and toxic compound extrusions (MATE) transporter conferring resistance to norfloxacin doxorubicin and acriflavine. glycylcycline/fluoroquinolone/tetracycline/acridine_dye +Shovill_on_data_31_and_data_32__Contigs contig00007 114166 114642 - mphB 1-477/477 =============== 0/0 100.00 98.32 card AE005174.2:3397371-3397848 The mphB gene encodes for MPH(2')-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2'-OH hydroxyl of desosamine sugar of macrolides. macrolide +Shovill_on_data_31_and_data_32__Contigs contig00007 135328 138441 - acrD 1-3114/3114 =============== 0/0 100.00 100.00 card AP009048.1:2586251-2589365 AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR. aminocoumarin/aminoglycoside/carbapenem/diaminopyrimidine/antibacterial_free_fatty_acids/tetracycline/triclosan/acridine_dye/fluoroquinolone/penam/macrolide/phenicol/monobactam/glycylcycline +Shovill_on_data_31_and_data_32__Contigs contig00007 169840 171144 - Escherichia_coli_ampC1_beta-lactamase 1-1305/1305 =============== 0/0 100.00 100.00 card FN649414.1:2765051-2766356 An ampC-like beta-lactamase identified from Escherichia coli. cephalosporin/penam +Shovill_on_data_31_and_data_32__Contigs contig00010 14993 15625 + CRP 1-633/633 =============== 0/0 100.00 99.68 card AP009048.1:4153664-4154297 CRP is a global regulator that represses MdtEF multidrug efflux pump expression. tetracycline/triclosan/acridine_dye/fluoroquinolone/penam/macrolide/phenicol/monobactam/glycylcycline/aminocoumarin/aminoglycoside/carbapenem/diaminopyrimidine/antibacterial_free_fatty_acids +Shovill_on_data_31_and_data_32__Contigs contig00011 37607 38800 + Escherichia_coli_acrA 1-1194/1194 =============== 0/0 100.00 100.00 card U00096.3:484426-485620 AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli. rifamycin/macrolide/penam/diaminopyrimidine/antibacterial_free_fatty_acids/glycylcycline/monobactam/phenicol/acridine_dye/tetracycline/triclosan/cephalosporin/fluoroquinolone/carbapenem/aminoglycoside/aminocoumarin +Shovill_on_data_31_and_data_32__Contigs contig00011 38823 41972 + acrB 1-3150/3150 =============== 0/0 100.00 100.00 card U00096.3:481254-484404 Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter. antibacterial_free_fatty_acids/diaminopyrimidine/rifamycin/penam/macrolide/aminoglycoside/carbapenem/aminocoumarin/phenicol/monobactam/glycylcycline/fluoroquinolone/cephalosporin/tetracycline/triclosan/acridine_dye +Shovill_on_data_31_and_data_32__Contigs contig00011 126851 128008 + Escherichia_coli_ampH 1-1158/1158 =============== 0/0 100.00 100.00 card AP012030.1:395554-396712 AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli. cephalosporin/penam +Shovill_on_data_31_and_data_32__Contigs contig00013 15251 16072 - bacA 1-822/822 =============== 0/0 100.00 100.00 card U00096.3:3203310-3204132 The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin. peptide +Shovill_on_data_31_and_data_32__Contigs contig00014 85736 87223 + tolC 1-1488/1488 =============== 0/0 100.00 100.00 card FJ768952:1-1489 TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex. rifamycin/triclosan/tetracycline/glycylcycline/cephamycin/carbapenem/aminoglycoside/macrolide/penam/pleuromutilin/nitroimidazole/nucleoside/isoniazid/lincosamide/benzalkonium_chloride/antibacterial_free_fatty_acids/bicyclomycin/penem/diaminopyrimidine/cephalosporin/fluoroquinolone/oxazolidinone/acridine_dye/fosfomycin/monobactam/phenicol/rhodamine/peptide/aminocoumarin +Shovill_on_data_31_and_data_32__Contigs contig00019 43436 44974 - emrY 1-1539/1539 =============== 0/0 100.00 98.83 card D78168:1592-3131 emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB. oxazolidinone/acridine_dye/tetracycline/cephalosporin/fluoroquinolone/glycylcycline/phenicol/fosfomycin/peptide/rhodamine/macrolide/penam/nucleoside/rifamycin/nitroimidazole/lincosamide/isoniazid/benzalkonium_chloride/diaminopyrimidine/bicyclomycin/antibacterial_free_fatty_acids +Shovill_on_data_31_and_data_32__Contigs contig00019 44974 46029 - emrK 1-1056/1056 =============== 0/0 100.00 99.72 card D78168:537-1593 emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux. macrolide/penam/rifamycin/nitroimidazole/nucleoside/isoniazid/lincosamide/benzalkonium_chloride/bicyclomycin/antibacterial_free_fatty_acids/diaminopyrimidine/cephalosporin/fluoroquinolone/acridine_dye/oxazolidinone/tetracycline/fosfomycin/glycylcycline/phenicol/rhodamine/peptide +Shovill_on_data_31_and_data_32__Contigs contig00019 46553 47167 + evgA 1-615/615 =============== 0/0 100.00 99.02 card BA000007.3:3212026-3212641 EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed. diaminopyrimidine/antibacterial_free_fatty_acids/bicyclomycin/benzalkonium_chloride/isoniazid/lincosamide/nucleoside/nitroimidazole/rifamycin/penam/macrolide/aminoglycoside/carbapenem/aminocoumarin/peptide/rhodamine/phenicol/monobactam/glycylcycline/fosfomycin/triclosan/tetracycline/oxazolidinone/acridine_dye/fluoroquinolone/cephalosporin +Shovill_on_data_31_and_data_32__Contigs contig00019 47172 50765 + evgS 1-3594/3594 =============== 0/0 100.00 99.11 card U00096:2484374-2487968 EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58. triclosan/tetracycline/acridine_dye/oxazolidinone/fluoroquinolone/cephalosporin/phenicol/monobactam/glycylcycline/fosfomycin/aminocoumarin/peptide/rhodamine/aminoglycoside/carbapenem/penam/macrolide/nucleoside/nitroimidazole/rifamycin/benzalkonium_chloride/isoniazid/lincosamide/diaminopyrimidine/antibacterial_free_fatty_acids/bicyclomycin +Shovill_on_data_31_and_data_32__Contigs contig00021 6389 7762 + cpxA 1-1374/1374 =============== 0/0 100.00 98.98 card BA000007.3:4903689-4905063 CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression. acridine_dye/tetracycline/triclosan/macrolide/fluoroquinolone/penam/glycylcycline/monobactam/phenicol/aminocoumarin/diaminopyrimidine/carbapenem/aminoglycoside/antibacterial_free_fatty_acids +Shovill_on_data_31_and_data_32__Contigs contig00023 3691 5229 - emrB 1-1539/1539 =============== 0/0 100.00 100.00 card U00096:2812616-2814155 emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin. rhodamine/peptide/fosfomycin/glycylcycline/phenicol/cephalosporin/fluoroquinolone/tetracycline/acridine_dye/oxazolidinone/antibacterial_free_fatty_acids/bicyclomycin/diaminopyrimidine/lincosamide/isoniazid/benzalkonium_chloride/rifamycin/nitroimidazole/nucleoside/macrolide/penam +Shovill_on_data_31_and_data_32__Contigs contig00023 5246 6418 - emrA 1-1173/1173 =============== 0/0 100.00 100.00 card AP009048:2810083-2811256 EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium. benzalkonium_chloride/isoniazid/lincosamide/diaminopyrimidine/bicyclomycin/antibacterial_free_fatty_acids/penam/macrolide/nucleoside/nitroimidazole/rifamycin/peptide/rhodamine/acridine_dye/oxazolidinone/tetracycline/fluoroquinolone/cephalosporin/phenicol/glycylcycline/fosfomycin +Shovill_on_data_31_and_data_32__Contigs contig00023 6545 7075 - emrR 1-531/531 =============== 0/0 100.00 99.81 card U00096.3:2810770-2811301 EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression. rifamycin/nitroimidazole/nucleoside/macrolide/penam/bicyclomycin/antibacterial_free_fatty_acids/diaminopyrimidine/lincosamide/isoniazid/benzalkonium_chloride/fosfomycin/glycylcycline/phenicol/cephalosporin/fluoroquinolone/oxazolidinone/acridine_dye/tetracycline/rhodamine/peptide +Shovill_on_data_31_and_data_32__Contigs contig00030 19630 20838 + mdtH 1-1209/1209 =============== 0/0 100.00 99.92 card U00096:1124118-1125327 Multidrug resistance protein MdtH nitroimidazole/rifamycin/nucleoside/penam/macrolide/antibacterial_free_fatty_acids/bicyclomycin/diaminopyrimidine/benzalkonium_chloride/isoniazid/lincosamide/fosfomycin/phenicol/glycylcycline/fluoroquinolone/cephalosporin/tetracycline/acridine_dye/oxazolidinone/rhodamine/peptide +Shovill_on_data_31_and_data_32__Contigs contig00030 29467 30693 + mdtG 1-1227/1227 =============== 0/0 100.00 99.43 card CP000800.1:1191728-1192955 The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon. macrolide/penam/rifamycin/nitroimidazole/nucleoside/isoniazid/lincosamide/benzalkonium_chloride/bicyclomycin/antibacterial_free_fatty_acids/diaminopyrimidine/cephalosporin/fluoroquinolone/acridine_dye/oxazolidinone/tetracycline/fosfomycin/glycylcycline/phenicol/rhodamine/peptide +Shovill_on_data_31_and_data_32__Contigs contig00031 41010 41423 + H-NS 1-414/414 =============== 0/0 100.00 99.28 card BA000007.3:1737691-1738105 H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters. bicyclomycin/antibacterial_free_fatty_acids/diaminopyrimidine/benzalkonium_chloride/isoniazid/lincosamide/nitroimidazole/rifamycin/nucleoside/penam/macrolide/aminoglycoside/carbapenem/rhodamine/cephamycin/aminocoumarin/peptide/fosfomycin/phenicol/glycylcycline/monobactam/fluoroquinolone/cephalosporin/acridine_dye/oxazolidinone/triclosan/tetracycline +Shovill_on_data_31_and_data_32__Contigs contig00036 35264 36421 + mdtE 1-1158/1158 =============== 0/0 100.00 100.00 card AP009048.1:3980026-3981184 MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA. glycylcycline/monobactam/phenicol/acridine_dye/tetracycline/triclosan/macrolide/fluoroquinolone/penam/diaminopyrimidine/carbapenem/aminoglycoside/antibacterial_free_fatty_acids/aminocoumarin +Shovill_on_data_31_and_data_32__Contigs contig00036 36446 39559 + mdtF 1-3114/3114 =============== 0/0 100.00 99.97 card U00096:3660414-3663528 MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex. triclosan/tetracycline/acridine_dye/macrolide/fluoroquinolone/penam/monobactam/glycylcycline/phenicol/aminocoumarin/carbapenem/diaminopyrimidine/aminoglycoside/antibacterial_free_fatty_acids +Shovill_on_data_31_and_data_32__Contigs contig00036 39922 40650 - gadW 1-729/729 =============== 0/0 100.00 94.65 card CP015085.1:2551712-2552441 GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC. phenicol/monobactam/glycylcycline/penam/fluoroquinolone/macrolide/triclosan/tetracycline/acridine_dye/antibacterial_free_fatty_acids/aminoglycoside/carbapenem/diaminopyrimidine/aminocoumarin +Shovill_on_data_31_and_data_32__Contigs contig00036 41018 41842 - gadX 1-825/825 =============== 0/0 100.00 100.00 card AP009048.1:3974605-3975430 GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. aminoglycoside/diaminopyrimidine/carbapenem/antibacterial_free_fatty_acids/aminocoumarin/phenicol/glycylcycline/monobactam/acridine_dye/tetracycline/triclosan/penam/fluoroquinolone/macrolide +Shovill_on_data_31_and_data_32__Contigs contig00044 20047 20190 - kdpE 535-678/678 ...........==== 0/0 21.24 90.28 card U00096.3:721056-721734 kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding. aminoglycoside +Shovill_on_data_31_and_data_32__Contigs contig00044 24152 24829 - kdpE 1-678/678 =============== 0/0 100.00 100.00 card U00096.3:721056-721734 kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding. aminoglycoside +Shovill_on_data_31_and_data_32__Contigs contig00045 7836 8188 + Nocardia_rifampin_resistant_beta-subunit_of_RNA_polymerase_(rpoB2) 2980-3332/3489 ......../...=== 4/6 10.03 75.56 card AP006618.1:4835200-4838689 Due to gene duplication the genomes of Nocardia species include both rifampin-sensitive beta-subunit of RNA polymerase (rpoB) and rifampin-resistant beta-subunit of RNA polymerase (rpoB2) genes with ~88% similarity between the two gene products. Expression of the rpoB2 variant results in replacement of rifampin sensitivity with rifampin resistance. rifamycin +Shovill_on_data_31_and_data_32__Contigs contig00049 17804 19036 - mdtM 1-1233/1233 =============== 0/0 100.00 96.27 card U00096.3:4567287-4568520 Multidrug resistance protein MdtM nitroimidazole/rifamycin/nucleoside/penam/macrolide/bicyclomycin/antibacterial_free_fatty_acids/diaminopyrimidine/benzalkonium_chloride/lincosamide/isoniazid/fosfomycin/phenicol/glycylcycline/fluoroquinolone/cephalosporin/oxazolidinone/acridine_dye/tetracycline/rhodamine/peptide +Shovill_on_data_31_and_data_32__Contigs contig00050 14464 15710 - tet(A) 1-1247/1275 =============== 0/0 97.80 100.00 card AF534183.1:2971-4246 TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria. phenicol/glycylcycline/fosfomycin/tetracycline/oxazolidinone/acridine_dye/fluoroquinolone/cephalosporin/peptide/rhodamine/nucleoside/nitroimidazole/rifamycin/penam/macrolide/diaminopyrimidine/antibacterial_free_fatty_acids/bicyclomycin/benzalkonium_chloride/isoniazid/lincosamide +Shovill_on_data_31_and_data_32__Contigs contig00064 832 1080 + AAC(6')-Ib7 1-249/980 ====........... 0/0 25.41 98.80 card Y11946.1:1-981 AAC(6')-Ib7 is a plasmid-encoded aminoglycoside acetyltransferase in E. cloacae and C. freundii aminoglycoside +Shovill_on_data_31_and_data_32__Contigs contig00064 1081 1578 + dfrA12 1-498/498 =============== 0/0 100.00 100.00 card GU585907.1:21606-22104 dfrA12 is an integron-encoded dihydrofolate reductase found in Vibrio cholerae diaminopyrimidine +Shovill_on_data_31_and_data_32__Contigs contig00064 1998 2777 + aadA2 1-780/780 =============== 0/0 100.00 99.87 card AF156486:5013-5793 aadA2 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids and integrons in K. pneumoniae Salmonella spp. Corynebacterium glutamicum C. freundii and Aeromonas spp. aminoglycoside +Shovill_on_data_31_and_data_32__Contigs contig00064 3282 4121 + sul1 1-840/840 =============== 0/0 100.00 100.00 card JF969163:1054-1894 Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons. sulfonamide +Shovill_on_data_31_and_data_32__Contigs contig00064 8065 8430 - determinant_of_bleomycin_resistance 1-366/366 =============== 0/0 100.00 100.00 card KC503911.1:9884-10250 A novel bleomycin resistance protein encoded by a metallo-beta-lactamase-associated ble gene. Expression of BRP(MBL) confers resistance to bleomycin and bleomycin-like antibiotics in Enterobacteriaceae and Acinetobacter where it is co-expressed with an MBL and controlled by the same promoter region. glycopeptide +Shovill_on_data_31_and_data_32__Contigs contig00064 8434 9246 - NDM-5 1-813/813 =============== 0/0 100.00 100.00 card JN104597:115-928 New Delhi beta-lactamase NDM-5. cephamycin/penam/cephalosporin/carbapenem +Shovill_on_data_31_and_data_32__Contigs contig00066 63 1029 + acrE 192-1158/1158 ..============= 0/0 83.51 99.90 card U00096:3413864-3415022 AcrE is a membrane fusion protein similar to AcrA. aminocoumarin/cephamycin/carbapenem/diaminopyrimidine/aminoglycoside/antibacterial_free_fatty_acids/triclosan/tetracycline/acridine_dye/cephalosporin/macrolide/penam/fluoroquinolone/monobactam/glycylcycline/phenicol +Shovill_on_data_31_and_data_32__Contigs contig00066 1041 4145 + acrF 1-3105/3105 =============== 0/0 100.00 99.97 card U00096:3415033-3418138 AcrF is a inner membrane transporter similar to AcrB. aminoglycoside/carbapenem/diaminopyrimidine/antibacterial_free_fatty_acids/aminocoumarin/cephamycin/phenicol/monobactam/glycylcycline/tetracycline/triclosan/acridine_dye/fluoroquinolone/penam/cephalosporin/macrolide +Shovill_on_data_31_and_data_32__Contigs contig00070 1686 2546 + TEM-1 1-861/861 =============== 0/0 100.00 99.88 card AL513383:161911-162772 TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins. penam/cephalosporin/penem/monobactam +Shovill_on_data_31_and_data_32__Contigs contig00070 2716 3471 + rmtB 1-756/756 =============== 0/0 100.00 100.00 card AM886293.1:116480-117236 RmtB is a 16S rRNA methyltransferase that targets mature or nearly mature 30S subunits. It transfers a methyl group from S-adenosyl-L-methionine to N7-G1405 of the 16S rRNA an aminoglycoside binding site. aminoglycoside +Shovill_on_data_31_and_data_32__Contigs contig00070 5220 5975 - rmtB 1-756/756 =============== 0/0 100.00 100.00 card AM886293.1:116480-117236 RmtB is a 16S rRNA methyltransferase that targets mature or nearly mature 30S subunits. It transfers a methyl group from S-adenosyl-L-methionine to N7-G1405 of the 16S rRNA an aminoglycoside binding site. aminoglycoside +Shovill_on_data_31_and_data_32__Contigs contig00070 6145 7005 - TEM-1 1-861/861 =============== 0/0 100.00 99.88 card AL513383:161911-162772 TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins. penam/cephalosporin/penem/monobactam +Shovill_on_data_31_and_data_32__Contigs contig00083 2703 3578 - CTX-M-15 1-876/876 =============== 0/0 100.00 100.00 card AY044436:1436-2312 CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family cephalosporin +Shovill_on_data_31_and_data_32__Contigs contig00086 2455 3357 - mphA 1-903/906 =============== 0/0 99.67 100.00 card D16251.1:1626-2532 The mphA gene encodes for resistance enzyme MPH(2')-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2'-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner. macrolide +Shovill_on_data_31_and_data_32__Contigs contig00093 130 779 + OXA-368 2072-2721/2721 ...........==== 0/0 23.89 99.08 card KT736121.1:1-2722 OXA-368 is a beta-lactamase found in Aeromonas sobria. From the Lahey list of OXA beta-lactamases. cephalosporin/penam +Shovill_on_data_31_and_data_32__Contigs contig00093 844 1674 + OXA-1 1-831/831 =============== 0/0 100.00 100.00 card JN420336.1:1400-2231 OXA-1 is a beta-lactamase found in E. coli penam/cephalosporin +Shovill_on_data_31_and_data_32__Contigs contig00093 1812 2256 + catB3 1-445/633 ===========.... 0/0 70.30 99.78 card JX101693.1:58201-58834 catB3 is a plasmid or chromosome-encoded variant of the cat gene found in Salmonella typhimurium Acinetobacter baumannii and Escherichia coli phenicol
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gene_detection_status.tsv Wed Oct 30 23:01:01 2019 -0400 @@ -0,0 +1,4 @@ +gene_name detected +KPC False +NDM True +OXA-48 False
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/screen.tsv Wed Oct 30 23:01:01 2019 -0400 @@ -0,0 +1,4 @@ +gene_name regex +KPC KPC +NDM NDM +OXA OXA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/screen.yaml Wed Oct 30 23:01:01 2019 -0400 @@ -0,0 +1,7 @@ +--- +- gene: KPC + regex: KPC +- gene: OXA + regex: OXA +- gene: NDM + regex: NDM
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/screened_report.tsv Wed Oct 30 23:01:01 2019 -0400 @@ -0,0 +1,2 @@ +#FILE SEQUENCE START END STRAND GENE COVERAGE COVERAGE_MAP GAPS %COVERAGE %IDENTITY DATABASE ACCESSION PRODUCT RESISTANCE +Shovill_on_data_31_and_data_32__Contigs contig00064 8434 9246 - NDM-5 1-813/813 =============== 0/0 100.00 100.00 card JN104597:115-928 New Delhi beta-lactamase NDM-5. cephamycin/penam/cephalosporin/carbapenem
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/screening_file.tsv Wed Oct 30 23:01:01 2019 -0400 @@ -0,0 +1,4 @@ +gene_name regex +KPC KPC +NDM NDM +OXA-48 OXA\-48
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Wed Oct 30 23:01:01 2019 -0400 @@ -0,0 +1,8 @@ +<?xml version="1.0"?> +<tables> + <!-- Locations of abricate report screening files in the required format --> + <table name="abricate_report_screening_files" comment_char="#"> + <columns>value, name, path</columns> + <file path="tool-data/abricate_report_screening_files.loc" /> + </table> +</tables>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Wed Oct 30 23:01:01 2019 -0400 @@ -0,0 +1,8 @@ +<?xml version="1.0"?> +<tables> + <!-- Locations of Kraken2 database in the required format --> + <table name="kraken2_databases" comment_char="#"> + <columns>value, name, path</columns> + <file path="${__HERE__}/test-data/test_database.loc" /> + </table> +</tables>