Mercurial > repos > dfornika > screen_abricate_report
changeset 0:2ffd23634c1e draft
planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
| author | dfornika |
|---|---|
| date | Thu, 26 Sep 2019 19:37:27 -0400 |
| parents | |
| children | 40003338a8e8 |
| files | abricate_report_screening_files.loc.sample screen_abricate_report.py screen_abricate_report.xml test-data/abricate_report.tsv test-data/screen.tsv test-data/screen.yaml tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
| diffstat | 8 files changed, 175 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/abricate_report_screening_files.loc.sample Thu Sep 26 19:37:27 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 Thu Sep 26 19:37:27 2019 -0400 @@ -0,0 +1,46 @@ +#!/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_abricate_report_fieldnames(abricate_report): + with open(abricate_report) 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.screen) + abricate_report_fieldnames = get_abricate_report_fieldnames(args.abricate_report) + with open(args.abricate_report) as f: + reader = csv.DictReader(f, delimiter="\t", quotechar='"') + writer = csv.DictWriter(sys.stdout, delimiter="\t", quotechar='"', fieldnames=abricate_report_fieldnames) + writer.writeheader() + for row in reader: + for gene in screen: + if re.search(gene['regex'], row['GENE']): + writer.writerow(row) + + + +if __name__ == '__main__': + parser = argparse.ArgumentParser() + parser.add_argument("--screen", help="TSV file defining genes to screen for") + parser.add_argument("abricate_report", help="Abricate output") + args = parser.parse_args() + main(args)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/screen_abricate_report.xml Thu Sep 26 19:37:27 2019 -0400 @@ -0,0 +1,32 @@ +<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}' + --screen '${screening_file.fields.path}' + > '${output}' + ]]></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="output" type="data" format="tabular" label="Screened Abricate Report" /> + </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 Thu Sep 26 19:37:27 2019 -0400 @@ -0,0 +1,63 @@ +#FILE SEQUENCE START END GENE COVERAGE COVERAGE_MAP GAPS %COVERAGE %IDENTITY DATABASE ACCESSION PRODUCT +SRR9113479_assembly 1 188844 190331 tolC 1-1488/1488 =============== 0/0 100.00 99.73 card FJ768952:1-1489 card~~~tolC~~~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. +SRR9113479_assembly 1 212707 213528 bacA 1-822/822 =============== 0/0 100.00 98.66 card U00096.3:3203310-3204132 card~~~bacA~~~U00096.3:3203310-3204132 The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin. +SRR9113479_assembly 10 141472 142104 CRP 1-633/633 =============== 0/0 100.00 99.21 card AP009048.1:4153664-4154297 card~~~CRP~~~AP009048.1:4153664-4154297 CRP is a global regulator that represses MdtEF multidrug efflux pump expression. +SRR9113479_assembly 11 5292 8396 acrF 1-3105/3105 =============== 0/0 100.00 99.13 card U00096:3415033-3418138 card~~~acrF~~~U00096:3415033-3418138 AcrF is a inner membrane transporter similar to AcrB. +SRR9113479_assembly 11 8408 9565 acrE 1-1158/1158 =============== 0/0 100.00 98.96 card U00096:3413864-3415022 card~~~acrE~~~U00096:3413864-3415022 AcrE is a membrane fusion protein similar to AcrA. +SRR9113479_assembly 11 9964 10626 acrS 1-663/663 =============== 0/0 100.00 99.25 card U00096:3412803-3413466 card~~~acrS~~~U00096:3412803-3413466 AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux. +SRR9113479_assembly 12 1 422 evgS 1-422/3594 ==............. 0/0 11.74 98.58 card U00096:2484374-2487968 card~~~evgS~~~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. +SRR9113479_assembly 12 427 1041 evgA 1-615/615 =============== 0/0 100.00 99.02 card BA000007.3:3212026-3212641 card~~~evgA~~~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. +SRR9113479_assembly 12 1565 2620 emrK 1-1056/1056 =============== 0/0 100.00 99.72 card D78168:537-1593 card~~~emrK~~~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. +SRR9113479_assembly 12 2620 4158 emrY 1-1539/1539 =============== 0/0 100.00 99.67 card D78168:1592-3131 card~~~emrY~~~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. +SRR9113479_assembly 12 107325 108293 pmrF 1-969/969 =============== 0/0 100.00 99.28 card U00096:2367071-2368040 card~~~pmrF~~~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. +SRR9113479_assembly 14 22658 24124 mdtP 1-1467/1467 =============== 0/0 100.00 98.16 card AP009048.1:4303043-4304510 card~~~mdtP~~~AP009048.1:4303043-4304510 Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride +SRR9113479_assembly 14 24121 26172 mdtO 1-2052/2052 =============== 0/0 100.00 98.39 card AP009048.1:4304506-4306558 card~~~mdtO~~~AP009048.1:4304506-4306558 Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride +SRR9113479_assembly 14 26172 27203 mdtN 1-1032/1032 =============== 0/0 100.00 98.06 card AP009048.1:4306557-4307589 card~~~mdtN~~~AP009048.1:4306557-4307589 Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride. +SRR9113479_assembly 14 56559 58202 eptA 1-1644/1644 =============== 0/0 100.00 99.33 card AP009048:4338625-4340269 card~~~eptA~~~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. +SRR9113479_assembly 14 100409 101542 Escherichia_coli_ampC 1-1134/1134 =============== 0/0 100.00 97.35 card NC_000913.3:4377811-4378945 card~~~Escherichia_coli_ampC~~~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. +SRR9113479_assembly 16 18584 19810 mdtG 1-1227/1227 =============== 0/0 100.00 99.27 card CP000800.1:1191728-1192955 card~~~mdtG~~~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. +SRR9113479_assembly 16 28441 29649 mdtH 1-1209/1209 =============== 0/0 100.00 98.43 card U00096:1124118-1125327 card~~~mdtH~~~U00096:1124118-1125327 Multidrug resistance protein MdtH +SRR9113479_assembly 19 22628 24001 cpxA 1-1374/1374 =============== 0/0 100.00 98.62 card BA000007.3:4903689-4905063 card~~~cpxA~~~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. +SRR9113479_assembly 2 256854 258086 mdtM 1-1233/1233 =============== 0/0 100.00 96.27 card U00096.3:4567287-4568520 card~~~mdtM~~~U00096.3:4567287-4568520 Multidrug resistance protein MdtM +SRR9113479_assembly 24 23717 24075 Klebsiella_pneumoniae_KpnE 5-363/363 ========/====== 2/2 98.62 75.56 card AP006725.1:2483890-2484253 card~~~Klebsiella_pneumoniae_KpnE~~~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 +SRR9113479_assembly 24 24067 24391 Klebsiella_pneumoniae_KpnF 6-330/330 =============== 0/0 98.48 75.39 card AP006725.1:2484239-2484569 card~~~Klebsiella_pneumoniae_KpnF~~~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. +SRR9113479_assembly 25 12898 14144 tet(A) 1-1247/1275 =============== 0/0 97.80 100.00 card AF534183.1:2971-4246 card~~~tet(A)~~~AF534183.1:2971-4246 TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria. +SRR9113479_assembly 25 17540 18189 OXA-368 2072-2721/2721 ...........==== 0/0 23.89 99.08 card KT736121.1:1-2722 card~~~OXA-368~~~KT736121.1:1-2722 OXA-368 is a beta-lactamase found in Aeromonas sobria. From the Lahey list of OXA beta-lactamases. +SRR9113479_assembly 25 18254 19084 OXA-1 1-831/831 =============== 0/0 100.00 100.00 card JN420336.1:1400-2231 card~~~OXA-1~~~JN420336.1:1400-2231 OXA-1 is a beta-lactamase found in E. coli +SRR9113479_assembly 25 19222 19666 catB3 1-445/633 ===========.... 0/0 70.30 99.78 card JX101693.1:58201-58834 card~~~catB3~~~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 +SRR9113479_assembly 25 21029 21904 CTX-M-15 1-876/876 =============== 0/0 100.00 100.00 card AY044436:1436-2312 card~~~CTX-M-15~~~AY044436:1436-2312 CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family +SRR9113479_assembly 25 54292 54540 AAC(6')-Ib7 1-249/980 ====........... 0/0 25.41 99.60 card Y11946.1:1-981 card~~~AAC(6')-Ib7~~~Y11946.1:1-981 AAC(6')-Ib7 is a plasmid-encoded aminoglycoside acetyltransferase in E. cloacae and C. freundii +SRR9113479_assembly 25 54554 55027 dfrA17 1-474/474 =============== 0/0 100.00 100.00 card DQ838665:1-475 card~~~dfrA17~~~DQ838665:1-475 dfrA17 is an integron-encoded dihydrofolate reductase found in Escherichia coli +SRR9113479_assembly 25 55158 55946 aadA5 1-789/789 =============== 0/0 100.00 100.00 card AF137361:64-853 card~~~aadA5~~~AF137361:64-853 aadA5 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids transposons and integrons in E. coli K. pneumoniae Kluyvera georgiana P. aeruginosa and E. cloacae +SRR9113479_assembly 25 56493 57332 sul1 1-840/840 =============== 0/0 100.00 100.00 card JF969163:1054-1894 card~~~sul1~~~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. +SRR9113479_assembly 25 62643 63548 mphA 1-906/906 =============== 0/0 100.00 100.00 card D16251.1:1626-2532 card~~~mphA~~~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. +SRR9113479_assembly 29 29543 29926 marA 1-384/384 =============== 0/0 100.00 99.48 card AP009048.1:1621288-1621672 card~~~marA~~~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. +SRR9113479_assembly 3 120242 121990 msbA 1-1749/1749 =============== 0/0 100.00 99.37 card U00096.3:966621-968370 card~~~msbA~~~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. +SRR9113479_assembly 3 220771 222003 Escherichia_coli_mdfA 1-1233/1233 =============== 0/0 100.00 97.24 card JQ394987:1-1234 card~~~Escherichia_coli_mdfA~~~JQ394987:1-1234 Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter. +SRR9113479_assembly 31 2026 3669 yojI 1-1644/1644 =============== 0/0 100.00 98.11 card U00096.3:2306972-2308616 card~~~yojI~~~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. +SRR9113479_assembly 32 178 990 NDM-7 1-813/813 =============== 0/0 100.00 100.00 card JX262694:1-814 card~~~NDM-7~~~JX262694:1-814 NDM-7 is a beta-lactamase found in Escherichia coli +SRR9113479_assembly 32 994 1359 determinant_of_bleomycin_resistance 1-366/366 =============== 0/0 100.00 100.00 card KC503911.1:9884-10250 card~~~determinant_of_bleomycin_resistance~~~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. +SRR9113479_assembly 40 31611 34287 evgS 918-3594/3594 ...============ 0/0 74.49 99.48 card U00096:2484374-2487968 card~~~evgS~~~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. +SRR9113479_assembly 41 31495 31827 Escherichia_coli_emrE 1-333/333 =============== 0/0 100.00 91.89 card Z11877.1:486-819 card~~~Escherichia_coli_emrE~~~Z11877.1:486-819 Member of the small MDR (multidrug resistance) family of transporters; in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin; proton-dependent secondary transporter which exchanges protons for compound translocation +SRR9113479_assembly 43 24684 25214 emrR 1-531/531 =============== 0/0 100.00 100.00 card U00096.3:2810770-2811301 card~~~emrR~~~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. +SRR9113479_assembly 43 25341 26513 emrA 1-1173/1173 =============== 0/0 100.00 97.53 card AP009048:2810083-2811256 card~~~emrA~~~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. +SRR9113479_assembly 43 26530 28068 emrB 1-1539/1539 =============== 0/0 100.00 99.87 card U00096:2812616-2814155 card~~~emrB~~~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. +SRR9113479_assembly 44 22397 23069 kdpE 1-673/678 =============== 0/0 99.26 97.18 card U00096.3:721056-721734 card~~~kdpE~~~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. +SRR9113479_assembly 45 7769 8121 Nocardia_rifampin_resistant_beta-subunit_of_RNA_polymerase_(rpoB2) 2980-3332/3489 ......../...=== 4/6 10.03 75.56 card AP006618.1:4835200-4838689 card~~~Nocardia_rifampin_resistant_beta-subunit_of_RNA_polymerase_(rpoB2)~~~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. +SRR9113479_assembly 47 23039 24196 mdtE 1-1158/1158 =============== 0/0 100.00 99.74 card AP009048.1:3980026-3981184 card~~~mdtE~~~AP009048.1:3980026-3981184 MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA. +SRR9113479_assembly 47 24221 27334 mdtF 1-3114/3114 =============== 0/0 100.00 98.49 card U00096:3660414-3663528 card~~~mdtF~~~U00096:3660414-3663528 MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex. +SRR9113479_assembly 47 27697 28425 gadW 1-729/729 =============== 0/0 100.00 94.38 card CP015085.1:2551712-2552441 card~~~gadW~~~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. +SRR9113479_assembly 47 28793 29617 gadX 1-825/825 =============== 0/0 100.00 97.94 card AP009048.1:3974605-3975430 card~~~gadX~~~AP009048.1:3974605-3975430 GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. +SRR9113479_assembly 5 4886 5299 H-NS 1-414/414 =============== 0/0 100.00 99.52 card BA000007.3:1737691-1738105 card~~~H-NS~~~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. +SRR9113479_assembly 50 24357 25523 ugd 1-1167/1167 ========/====== 6/12 99.49 84.57 card U00096:2098447-2099614 card~~~ugd~~~U00096:2098447-2099614 PmrE 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 +SRR9113479_assembly 6 113576 114050 mphB 3-477/477 =============== 0/0 99.58 97.47 card AE005174.2:3397371-3397848 card~~~mphB~~~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. +SRR9113479_assembly 6 135287 138400 acrD 1-3114/3114 =============== 0/0 100.00 99.07 card AP009048.1:2586251-2589365 card~~~acrD~~~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. +SRR9113479_assembly 6 169518 170822 Escherichia_coli_ampC1_beta-lactamase 1-1305/1305 =============== 0/0 100.00 98.62 card FN649414.1:2765051-2766356 card~~~Escherichia_coli_ampC1_beta-lactamase~~~FN649414.1:2765051-2766356 An ampC-like beta-lactamase identified from Escherichia coli. +SRR9113479_assembly 7 42780 44027 mdtA 1-1248/1248 =============== 0/0 100.00 98.16 card U00096:2154016-2155264 card~~~mdtA~~~U00096:2154016-2155264 MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC. +SRR9113479_assembly 7 44027 47149 mdtB 1-3123/3123 =============== 0/0 100.00 99.78 card U00096:2155263-2158386 card~~~mdtB~~~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. +SRR9113479_assembly 7 47150 50227 mdtC 1-3078/3078 =============== 0/0 100.00 98.57 card U00096:2158386-2161464 card~~~mdtC~~~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. +SRR9113479_assembly 7 51640 53043 baeS 1-1404/1404 =============== 0/0 100.00 98.08 card AP009048:2165013-2166417 card~~~baeS~~~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. +SRR9113479_assembly 7 53040 53762 baeR 1-723/723 =============== 0/0 100.00 99.45 card AP009048.1:2166413-2167136 card~~~baeR~~~AP009048.1:2166413-2167136 BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes. +SRR9113479_assembly 8 79721 80914 Escherichia_coli_acrA 1-1194/1194 =============== 0/0 100.00 99.75 card U00096.3:484426-485620 card~~~Escherichia_coli_acrA~~~U00096.3:484426-485620 AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli. +SRR9113479_assembly 8 80937 84086 acrB 1-3150/3150 =============== 0/0 100.00 99.08 card U00096.3:481254-484404 card~~~acrB~~~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. +SRR9113479_assembly 8 168988 170145 Escherichia_coli_ampH 1-1158/1158 =============== 0/0 100.00 99.40 card AP012030.1:395554-396712 card~~~Escherichia_coli_ampH~~~AP012030.1:395554-396712 AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/screen.tsv Thu Sep 26 19:37:27 2019 -0400 @@ -0,0 +1,4 @@ +gene regex +KPC KPC +NDM NDM +OXA OXA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/screen.yaml Thu Sep 26 19:37:27 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/tool_data_table_conf.xml.sample Thu Sep 26 19:37:27 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 Thu Sep 26 19:37:27 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>