# HG changeset patch # User public-health-bioinformatics # Date 1572550995 14400 # Node ID b2d56a44a872eb253d099ec67dea7d85bc9934aa "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 1d569fc27b052d1982d82ca19455caaff6386f46" diff -r 000000000000 -r b2d56a44a872 abricate_report_screening_files.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/abricate_report_screening_files.loc.sample Thu Oct 31 15:43:15 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-a8fbddbf64c2Carbapenemase Genes/path/to/screening_file.tsv diff -r 000000000000 -r b2d56a44a872 screen_abricate_report.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/screen_abricate_report.py Thu Oct 31 15:43:15 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_reader.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) diff -r 000000000000 -r b2d56a44a872 screen_abricate_report.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/screen_abricate_report.xml Thu Oct 31 15:43:15 2019 -0400 @@ -0,0 +1,36 @@ + + Screens an abricate report for genes of interest + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r 000000000000 -r b2d56a44a872 test-data/SAMN13042171_abricate_report.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SAMN13042171_abricate_report.tsv Thu Oct 31 15:43:15 2019 -0400 @@ -0,0 +1,47 @@ +#FILE SEQUENCE START END STRAND GENE COVERAGE COVERAGE_MAP GAPS %COVERAGE %IDENTITY DATABASE ACCESSION PRODUCT RESISTANCE +SAMN13042171.fasta contig00001 181303 181975 + kdpE 1-673/678 =============== 0/0 99.26 76.08 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 +SAMN13042171.fasta contig00001 362878 363231 - ramA 21-375/375 ========/====== 1/1 94.40 80.56 card JQ727668:1-376 RamA (resistance antibiotic multiple) is a positive regulator of AcrAB-TolC and leads to high level multidrug resistance in Klebsiella pneumoniae Salmonella enterica and Enterobacter aerugenes increasing the expression of both the mar operon as well as AcrAB. RamA also decreases OmpF expression. cephamycin/aminocoumarin/aminoglycoside/carbapenem/fluoroquinolone/cephalosporin/triclosan/tetracycline/acridine_dye/phenicol/monobactam/glycylcycline/antibacterial_free_fatty_acids/penem/diaminopyrimidine/penam/macrolide/rifamycin +SAMN13042171.fasta contig00001 568102 569295 + Klebsiella_pneumoniae_acrA 1-1197/1197 ========/====== 2/3 99.75 95.07 card AJ318073.1:794-1991 AcrA is a subunit of the AcrAB multidrug efflux system that in K. pneumoniae which is encoded by the acrRAB operon. aminocoumarin/carbapenem/aminoglycoside/triclosan/tetracycline/acridine_dye/cephalosporin/fluoroquinolone/monobactam/glycylcycline/phenicol/diaminopyrimidine/antibacterial_free_fatty_acids/macrolide/penam/rifamycin +SAMN13042171.fasta contig00001 569318 572462 + acrB 1-3148/3150 ========/====== 1/3 99.84 83.74 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 +SAMN13042171.fasta contig00001 698224 699350 + Escherichia_coli_ampH 1-1127/1158 =============== 0/0 97.32 77.46 card AP012030.1:395554-396712 AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli. cephalosporin/penam +SAMN13042171.fasta contig00002 345289 346827 - Klebsiella_pneumoniae_KpnH 1-1539/1539 =============== 0/0 100.00 84.41 card ASTU01000063.1:61249-62788 KpnH consists of ~511 residues resembles EmrB of E. coli and is probably a translocase in the KpnGH-TolC efflux protein in K. pneumoniae. Disruption of the pump components KpnG-KpnH signficantly decrease resistance to azithromycin ceftazidime ciprofloxacin ertapenem erythromycin gentamicin imipenem ticarcillin norfloxacin polymyxin-B piperacillin spectinomycin tobramycin and streptomycin. isoniazid/lincosamide/benzalkonium_chloride/diaminopyrimidine/penem/bicyclomycin/antibacterial_free_fatty_acids/macrolide/penam/nucleoside/nitroimidazole/peptide/rhodamine/acridine_dye/oxazolidinone/cephalosporin/fluoroquinolone/phenicol/fosfomycin/rifamycin/carbapenem/aminoglycoside/tetracycline/glycylcycline +SAMN13042171.fasta contig00002 346843 348015 - Klebsiella_pneumoniae_KpnG 1-1173/1173 =============== 0/0 100.00 94.54 card ACWO01000051.1:22093-23266 KpnG consists of ~390 residues and resembles EmrA of E. coli. Disruption of the pump components KpnG-KpnH signficantly decrease resistance to azithromycin ceftazidime ciprofloxacin ertapenem erythromycin gentamicin imipenem ticarcillin norfloxacin polymyxin-B piperacillin spectinomycin tobramycin and streptomycin penam/macrolide/nitroimidazole/nucleoside/benzalkonium_chloride/lincosamide/isoniazid/bicyclomycin/antibacterial_free_fatty_acids/diaminopyrimidine/penem/fluoroquinolone/cephalosporin/acridine_dye/oxazolidinone/fosfomycin/phenicol/rhodamine/peptide/rifamycin/tetracycline/glycylcycline/aminoglycoside/carbapenem +SAMN13042171.fasta contig00002 348162 348671 - emrR 1-510/531 =============== 0/0 96.05 83.33 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 +SAMN13042171.fasta contig00002 389327 392479 - oqxB 1-3153/3153 =============== 0/0 100.00 95.53 card EU370913.1:47851-51004 RND efflux pump conferring resistance to fluoroquinolone tetracycline/triclosan/acridine_dye/fluoroquinolone/penam/nitrofuran/macrolide/phenicol/monobactam/glycylcycline/aminocoumarin/aminoglycoside/carbapenem/diaminopyrimidine/antibacterial_free_fatty_acids +SAMN13042171.fasta contig00002 392503 393678 - oqxA 1-1176/1176 =============== 0/0 100.00 93.71 card EU370913.1:46652-47828 RND efflux pump conferring resistance to fluoroquinolone phenicol/monobactam/glycylcycline/penam/fluoroquinolone/nitrofuran/macrolide/tetracycline/triclosan/acridine_dye/antibacterial_free_fatty_acids/aminoglycoside/carbapenem/diaminopyrimidine/aminocoumarin +SAMN13042171.fasta contig00003 27739 29154 - mdtK 1-1416/1425 ========/====== 2/2 99.30 76.71 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 +SAMN13042171.fasta contig00003 144300 145294 + mdtA 178-1172/1248 .=======/====== 2/2 79.65 78.51 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 +SAMN13042171.fasta contig00003 145364 148486 + mdtB 1-3123/3123 ========/====== 2/4 99.94 80.90 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 +SAMN13042171.fasta contig00003 148487 151564 + mdtC 1-3078/3078 =============== 0/0 100.00 82.00 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 +SAMN13042171.fasta contig00003 152979 153244 + baeS 2-267/1404 ===............ 0/0 18.95 80.45 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 +SAMN13042171.fasta contig00003 154462 155174 + baeR 1-713/723 =============== 0/0 98.62 82.61 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 +SAMN13042171.fasta contig00003 277916 279555 - yojI 1-1640/1644 ========/====== 6/6 99.57 75.65 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 +SAMN13042171.fasta contig00004 25617 26032 + FosA5 1-416/420 =============== 0/0 99.05 93.51 card KP143090.1:1200-1620 fosA5 is a fosfomycin resistance gene isolated from clinical strain of Escherichia coli E265. It is susceptible to amikacin tetracycline and imipenem and resistant to sulphonamide cephalosporins gentamicin ciprofloxacin chloramphenicol and streptomycin fosfomycin +SAMN13042171.fasta contig00006 173 577 - H-NS 1-405/414 =============== 0/0 97.83 87.16 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 +SAMN13042171.fasta contig00007 21771 22687 - pmrF 16-932/969 =============== 0/0 94.63 76.77 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 +SAMN13042171.fasta contig00008 29896 31020 - Klebsiella_pneumoniae_OmpK37 1-1125/1125 =============== 0/0 100.00 92.71 card AJ011502.1:301-1426 Klebsiella pneumoniae outer membrane porin protein. Is preferentially detected in porin-deficient strains. Functional characterization of this new porin revealed a narrower pore than those of porins OmpK35 and OmpK36 which did not allow penetration by certain ##-lactams. Also when a resistant strain expresses porin OmpK37 is less susceptible to cefotaxime and cefoxitin than when it is expressing either OmpK36 or OmpK35. cephalosporin/penam/cephamycin/monobactam/carbapenem/penem +SAMN13042171.fasta contig00008 175297 175659 + Klebsiella_pneumoniae_KpnE 1-363/363 =============== 0/0 100.00 88.43 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 +SAMN13042171.fasta contig00008 175646 175975 + Klebsiella_pneumoniae_KpnF 1-330/330 =============== 0/0 100.00 92.42 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 +SAMN13042171.fasta contig00008 217869 218728 - OKP-B-18 1-860/861 =============== 0/0 99.88 99.53 card AM850920:41-902 OKP-B-18 is a beta-lactamase found in Klebsiella pneumoniae cephalosporin/penam +SAMN13042171.fasta contig00009 93196 94580 + tolC 1-1403/1488 ========/====== 2/18 93.08 78.40 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 +SAMN13042171.fasta contig00009 108077 108898 - bacA 1-822/822 =============== 0/0 100.00 80.53 card U00096.3:3203310-3204132 The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin. peptide +SAMN13042171.fasta contig00012 114632 116380 - msbA 1-1749/1749 =============== 0/0 100.00 80.96 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 +SAMN13042171.fasta contig00012 155728 155882 - macB 1586-1740/1935 ............==. 0/0 8.01 76.13 card AY768532:1-1936 MacB is an ATP-binding cassette (ABC) transporter that exports macrolides with 14- or 15- membered lactones. It forms an antibiotic efflux complex with MacA and TolC. macB corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58. macrolide/cephalosporin/fluoroquinolone/penam/acridine_dye/tetracycline/pleuromutilin/rifamycin/nitroimidazole/peptide +SAMN13042171.fasta contig00015 140084 143160 + acrF 1-3080/3105 ========/====== 7/9 99.00 76.74 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 +SAMN13042171.fasta contig00016 114383 115015 - CRP 1-633/633 =============== 0/0 100.00 87.36 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 +SAMN13042171.fasta contig00018 59247 60613 - cpxA 1-1367/1374 =============== 0/0 99.49 81.71 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 +SAMN13042171.fasta contig00019 55611 58724 + acrD 1-3114/3114 ========/====== 2/2 99.97 80.58 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 +SAMN13042171.fasta contig00024 52994 54169 + mdtH 1-1176/1209 =============== 0/0 97.27 77.04 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 +SAMN13042171.fasta contig00024 60718 61881 + mdtG 18-1181/1227 ========/====== 3/8 94.54 76.03 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 +SAMN13042171.fasta contig00025 3007 3375 - marA 1-369/384 =============== 0/0 96.09 81.57 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 +SAMN13042171.fasta contig00028 4483 5688 + Escherichia_coli_mdfA 1-1206/1233 ========/====== 2/2 97.73 78.21 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 +SAMN13042171.fasta contig00030 26098 26477 - Nocardia_rifampin_resistant_beta-subunit_of_RNA_polymerase_(rpoB2) 2980-3359/3489 ......../...=== 2/2 10.86 76.11 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 +SAMN13042171.fasta contig00030 26758 26924 - Nocardia_rifampin_resistant_beta-subunit_of_RNA_polymerase_(rpoB2) 2605-2771/3489 ...........=... 0/0 4.79 75.45 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 +SAMN13042171.fasta contig00035 7853 8713 - TEM-150 1-861/861 =============== 0/0 100.00 99.88 card AM183304:209-1070 TEM-150 is a beta-lactamase found in Enterobacter spp. E. coli and Klebsiella pneumoniae. penem/monobactam/cephalosporin/penam +SAMN13042171.fasta contig00035 9413 10237 - OXA-9 1-825/825 =============== 0/0 100.00 100.00 card M55547:1-826 OXA-9 is a beta-lactamase found in Klebsiella pneumoniae. cephalosporin/penam +SAMN13042171.fasta contig00035 10297 11098 - ANT(3'')-IIa 168-972/972 ..======/====== 1/3 82.51 99.25 card X02340.1:223-1195 ANT(3'')-IIa is a aminoglycoside nucleotidyltransferase identified in Acinetobacter spp. via horizontal gene transfer mechanisms. aminoglycoside +SAMN13042171.fasta contig00035 10991 11741 - AAC(6')-Ib7 234-980/980 ...=====/====== 2/4 76.22 96.67 card Y11946.1:1-981 AAC(6')-Ib7 is a plasmid-encoded aminoglycoside acetyltransferase in E. cloacae and C. freundii aminoglycoside +SAMN13042171.fasta contig00035 14582 15457 + 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 +SAMN13042171.fasta contig00035 20098 20754 + QnrS1 1-657/657 =============== 0/0 100.00 100.00 card DQ485529.1:1-658 QnrS1 is a plasmid-mediated quinolone resistance protein found in Shigella flexneri fluoroquinolone +SAMN13042171.fasta contig00063 2129 2494 - 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 +SAMN13042171.fasta contig00063 2498 3310 - NDM-1 1-813/813 =============== 0/0 100.00 100.00 card FN396876:2407-3220 NDM-1 is a metallo-beta-lactamase isolated from Klebsiella pneumoniae with nearly complete resistance to all beta-lactam antibiotics. cephalosporin/penam/carbapenem/cephamycin diff -r 000000000000 -r b2d56a44a872 test-data/SAMN13042171_abricate_report_screened.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SAMN13042171_abricate_report_screened.tsv Thu Oct 31 15:43:15 2019 -0400 @@ -0,0 +1,2 @@ +#FILE SEQUENCE START END STRAND GENE COVERAGE COVERAGE_MAP GAPS %COVERAGE %IDENTITY DATABASE ACCESSION PRODUCT RESISTANCE +SAMN13042171.fasta contig00063 2498 3310 - NDM-1 1-813/813 =============== 0/0 100.00 100.00 card FN396876:2407-3220 NDM-1 is a metallo-beta-lactamase isolated from Klebsiella pneumoniae with nearly complete resistance to all beta-lactam antibiotics. cephalosporin/penam/carbapenem/cephamycin diff -r 000000000000 -r b2d56a44a872 test-data/SAMN13042171_gene_detection_status.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SAMN13042171_gene_detection_status.tsv Thu Oct 31 15:43:15 2019 -0400 @@ -0,0 +1,4 @@ +gene_name detected +KPC False +NDM True +OXA-48 False diff -r 000000000000 -r b2d56a44a872 test-data/abricate_report_screening_files.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abricate_report_screening_files.loc Thu Oct 31 15:43:15 2019 -0400 @@ -0,0 +1,6 @@ +# Tab separated with three columns: +# - value (Galaxy records this in the Galaxy DB) +# - name (Galaxy shows this in the UI) +# - path (folder name containing the Kraken DB) +# +test_entry "Test Screening File" ${__HERE__}/screening_file.tsv \ No newline at end of file diff -r 000000000000 -r b2d56a44a872 test-data/screening_file.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/screening_file.tsv Thu Oct 31 15:43:15 2019 -0400 @@ -0,0 +1,4 @@ +gene_name regex +KPC KPC +NDM NDM +OXA-48 OXA\-48 diff -r 000000000000 -r b2d56a44a872 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Thu Oct 31 15:43:15 2019 -0400 @@ -0,0 +1,8 @@ + + + + + value, name, path + +
+ diff -r 000000000000 -r b2d56a44a872 tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Thu Oct 31 15:43:15 2019 -0400 @@ -0,0 +1,8 @@ + + + + + value, name, path + +
+