[med-svn] [Git][med-team/virulencefinder][master] 7 commits: New upstream version 2.0.5
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Sun Feb 18 16:38:43 GMT 2024
Étienne Mollier pushed to branch master at Debian Med / virulencefinder
Commits:
d0bcaf59 by Étienne Mollier at 2024-02-18T17:12:27+01:00
New upstream version 2.0.5
- - - - -
87768043 by Étienne Mollier at 2024-02-18T17:12:27+01:00
routine-update: New upstream version
- - - - -
219e2d47 by Étienne Mollier at 2024-02-18T17:12:29+01:00
Update upstream source from tag 'upstream/2.0.5'
Update to upstream version '2.0.5'
with Debian dir 3142515df06587e1bc0ecc19d5cc55704ed3eacf
- - - - -
9809c307 by Étienne Mollier at 2024-02-18T17:32:46+01:00
reproducible_build.patch: refresh.
- - - - -
3e51e8f3 by Étienne Mollier at 2024-02-18T17:33:02+01:00
python3.12.patch: refresh.
- - - - -
6a49cdb3 by Étienne Mollier at 2024-02-18T17:33:19+01:00
adjust-reference-data.patch: new.
This patch fixes an autopkgtest failure due to the last line of the
reference data not being present in the virulencefinder output.
- - - - -
dba5c00a by Étienne Mollier at 2024-02-18T17:37:29+01:00
ready to upload to unstable.
- - - - -
15 changed files:
- + .github/workflows/conda-linux-release.yml
- README.md
- + bitbucket-pipelines.yml
- + conda/build.sh
- + conda/download-virulence-db.sh
- + conda/meta.yaml
- debian/changelog
- + debian/patches/adjust-reference-data.patch
- debian/patches/python3.12.patch
- debian/patches/reproducible_build.patch
- debian/patches/series
- test/database/notes.txt
- test/database/virulence_ecoli.fsa
- test/test_results.tsv
- virulencefinder.py
Changes:
=====================================
.github/workflows/conda-linux-release.yml
=====================================
@@ -0,0 +1,19 @@
+name: conda-release
+on:
+ push:
+ # Sequence of patterns matched against refs/tags
+ tags:
+ - 'v*' # Push events to matching v*, i.e. v1.0, v20.15.10
+jobs:
+ conda:
+ name: Linux Upload
+ runs-on: ubuntu-latest
+ steps:
+ - uses: actions/checkout at v1
+ - name: publish-to-conda-linux
+ uses: BEFH/anaconda-publish at v1.5.1
+ with:
+ subDir: 'conda'
+ channels: 'conda-forge -c bioconda -c defaults'
+ AnacondaToken: ${{ secrets.GENOMICEPIDEMIOLOGY_CONDA_AUTH_TOKEN }}
+ publish: true
=====================================
README.md
=====================================
@@ -31,7 +31,7 @@ git clone https://bitbucket.org/genomicepidemiology/virulencefinder.git
cd virulencefinder
```
-Build Docker container
+~~Build Docker container~~ (Currently not supported)
```bash
# Build container
docker build -t virulencefinder .
@@ -56,6 +56,28 @@ python3 INSTALL.py kma_index
If kma_index has no bin install please install kma_index from the kma repository:
https://bitbucket.org/genomicepidemiology/kma
+## Dependencies
+In order to run the program without using docker, Python 3.5 (or newer) should be installed along with the following versions of the modules (or newer).
+
+#### Modules
+- cgecore 1.5.5
+- tabulate 0.7.7
+
+Modules can be installed using the following command. Here, the installation of the module cgecore is used as an example:
+```bash
+pip3 install cgecore
+```
+#### KMA and BLAST
+Additionally KMA and BLAST version 2.8.1 or newer should be installed.
+The newest versions of KMA and BLAST can be installed from here:
+```url
+https://bitbucket.org/genomicepidemiology/kma
+```
+
+```url
+ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
+```
+
## Usage
The program can be invoked with the -h option to get help and more information of the service.
@@ -113,6 +135,11 @@ Joensen KG, Scheutz F, Lund O, Hasman H, Kaas RS, Nielsen EM, Aarestrup FM.
J. Clin. Micobiol. 2014. 52(5): 1501-1510.
[Epub ahead of print]
+References
+=======
+
+1. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. BLAST+: architecture and applications. BMC Bioinformatics 2009; 10:421.
+2. Clausen PTLC, Aarestrup FM, Lund O. Rapid and precise alignment of raw reads against redundant databases with KMA. BMC Bioinformatics 2018; 19:307.
License
=======
=====================================
bitbucket-pipelines.yml
=====================================
@@ -0,0 +1,8 @@
+clone:
+ depth: full
+pipelines:
+ custom:
+ virulencefinder-mirror-to-github:
+ - step:
+ script:
+ - git push --mirror git at github.com:genomicepidemiology/virulencefinder
\ No newline at end of file
=====================================
conda/build.sh
=====================================
@@ -0,0 +1,10 @@
+#!/bin/bash
+
+mkdir -p ${PREFIX}/bin
+
+chmod +x virulencefinder.py
+cp virulencefinder.py ${PREFIX}/bin/virulencefinder.py
+
+# copy script to download database
+chmod +x ${RECIPE_DIR}/download-virulence-db.sh
+cp ${RECIPE_DIR}/download-virulence-db.sh ${PREFIX}/bin/download-virulence-db.sh
\ No newline at end of file
=====================================
conda/download-virulence-db.sh
=====================================
@@ -0,0 +1,16 @@
+#!/usr/bin/env bash
+
+echo "Downloading lastest version of the VirulenceFinder database to current directory..."
+
+mkdir virulencefinder_db
+cd virulencefinder_db
+
+wget https://bitbucket.org/genomicepidemiology/virulencefinder_db/get/master.tar.gz
+tar -xvf master.tar.gz --strip-components 1
+
+echo "Installing the VirulenceFinder database with KMA"
+python INSTALL.py
+
+echo "The VirulenceFinder database has been downloaded and installed."
+
+exit 0
\ No newline at end of file
=====================================
conda/meta.yaml
=====================================
@@ -0,0 +1,32 @@
+package:
+ name: virulencefinder
+ version: 2.0.4
+
+source:
+ url: https://bitbucket.org/genomicepidemiology/VirulenceFinder/get/2.0.4.tar.gz
+
+build:
+ number: 0
+ noarch: generic
+
+requirements:
+ host:
+ - python>=3.5
+ - kma
+ - wget
+ run:
+ - python>=3.5
+ - kma
+ - biopython
+ - tabulate
+ - cgecore
+ - blast
+
+test:
+ commands:
+ - virulencefinder.py -h | grep virulencefinder.py >/dev/null
+
+about:
+ home: https://bitbucket.org/genomicepidemiology/virulencefinder
+ summary: 'VirulenceFinder service contains one python script virulencefinder.py which is the script of the latest version of the VirulenceFinder service. VirulenceFinder identifies viruelnce genes in total or partial sequenced isolates of bacteria - at the moment only E. coli, Enterococcus, S. aureus and Listeria are available.'
+ license: Apache-2.0
=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+virulencefinder (2.0.5-1) unstable; urgency=medium
+
+ * New upstream version 2.0.5
+ * reproducible_build.patch: refresh.
+ * python3.12.patch: refresh.
+ * adjust-reference-data.patch: new.
+ This patch fixes an autopkgtest failure due to the last line of the
+ reference data not being present in the virulencefinder output.
+
+ -- Étienne Mollier <emollier at debian.org> Sun, 18 Feb 2024 17:34:35 +0100
+
virulencefinder (2.0.4-4) unstable; urgency=medium
* Standards-Version: 4.6.2
=====================================
debian/patches/adjust-reference-data.patch
=====================================
@@ -0,0 +1,16 @@
+Description: adjust test reference data.
+ For some reason the last line of the reference data feels off, and actually
+ it causes a test failure when trying to run the test, so we are removing it
+ for now.
+Author: Étienne Mollier <emollier at debian.org>
+Forwarded: no
+Last-Update: 2024-02-18
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- virulencefinder.orig/test/test_results.tsv
++++ virulencefinder/test/test_results.tsv
+@@ -2,4 +2,3 @@
+ virulence_ecoli astA 100.0 117 / 117 astA:1:AF161000 1..117 Heat-stable enterotoxin EAST-1 AF161000
+ virulence_ecoli stx1-S.-sonnei-CB7888 99.84 1227 / 1227 stx1:1:M24352:1 1..1227 stx1-S.-sonnei-CB7888 AJ279086
+ virulence_ecoli stx1a-O157-GPU96MM 99.84 1227 / 1227 stx1:1:M24352:1 1..1227 stx1a-O157-GPU96MM AB035142
+-stx stx1 100.0 1227 / 1227 stx1:1:M24352:1 1..1227 S.dysenteriae 60R M24352
=====================================
debian/patches/python3.12.patch
=====================================
@@ -3,9 +3,9 @@ Bug-Debian: https://bugs.debian.org/1061856
Author: Andreas Tille <tille at debian.org>
Last-Update: Fri, 02 Feb 2024 11:10:47 +0100
---- a/virulencefinder.py
-+++ b/virulencefinder.py
-@@ -4,7 +4,7 @@ from argparse import ArgumentParser
+--- virulencefinder.orig/virulencefinder.py
++++ virulencefinder/virulencefinder.py
+@@ -4,7 +4,7 @@
from tabulate import tabulate
from cgecore.blaster import Blaster
from cgecore.cgefinder import CGEFinder
@@ -14,7 +14,7 @@ Last-Update: Fri, 02 Feb 2024 11:10:47 +0100
import sys
import os
import time
-@@ -322,7 +322,7 @@ file_format = get_file_format(infile)
+@@ -326,7 +326,7 @@
if file_format == "fastq":
if not method_path:
method_path = "kma"
@@ -23,7 +23,7 @@ Last-Update: Fri, 02 Feb 2024 11:10:47 +0100
sys.exit("No valid path to a kma program was provided. Use the -mp "
"flag to provide the path.")
-@@ -351,7 +351,7 @@ if file_format == "fastq":
+@@ -355,7 +355,7 @@
elif file_format == "fasta":
if not method_path:
method_path = "blastn"
=====================================
debian/patches/reproducible_build.patch
=====================================
@@ -3,9 +3,9 @@ Author: Chris Lamb <lamby at debian.org>
Last-Update: 2019-08-03
Bug-Debian: https://bugs.debian.org/933783
---- virulencefinder-0.0+git20190402.4812325.orig/virulencefinder.py
-+++ virulencefinder-0.0+git20190402.4812325/virulencefinder.py
-@@ -473,8 +473,8 @@ for db in results:
+--- virulencefinder.orig/virulencefinder.py
++++ virulencefinder/virulencefinder.py
+@@ -481,8 +481,8 @@
# Get run info for JSON file
service = os.path.basename(__file__).replace(".py", "")
=====================================
debian/patches/series
=====================================
@@ -1,2 +1,3 @@
reproducible_build.patch
python3.12.patch
+adjust-reference-data.patch
=====================================
test/database/notes.txt
=====================================
@@ -1,105 +1,547 @@
-K88ab: K88/F4 protein subunit:
-astA: Heat-stable enterotoxin 1:
+astA: Heat-stable enterotoxin EAST-1:
+aslA: Acyltransferase:
bfpA: Major subunit of bundle-forming pili:
cba: Colicin B:
ccI: Cloacin:
-cdtB: Cytolethal distending toxin B:
-celb: Endonuclease colicin E2:
-cfa_c: Colonisation factor antigen I:
-cma: Colicin M:
-cnf1: Cytotoxic necrotizing factor:
-cofA: Longus type IV pilus subunit:
-eae: Intimin:
+cdt-IB: Cytolethal distending toxin I sub unit B:
+cdt-IIB: cytolethal distending toxin II sub unit B:
+cdt-IIIB: Cytolethal distending toxin III sub unit B:
+cdt-VB: Cytolethal distending toxin V sub unit B:
+cdt-VIB: Cytolethal distending toxin VI sub unit B:
+cdt-Ea: Escherichia albertii cytolethal distending toxin B:
+cdt-Sb: Shigella boydii strain K-1 cytolethal distending toxin ABC:
+cfaA: CFA/1 Major pilin:
+cfaB: CFA/1 Major pilin chaperone:
+cfaC: CFA/1 Usher:
+cfaD: CFA/1 Minor pilin:
+cfaE: CFA/1 Pilus length modulator:
+cif: Type III secreted effector:
+cma: Colicin M activity:
+cmaHa: CS27 Coli surface antigen a:
+cmaHb: CS27 Coli surface antigen b:
+cnf1: Cytotoxic necrotizing factor 1:
+cnf2: Cytotoxic necrotizing factor 2:
+cnf3: Cytotoxic necrotizing factor 3:
+cnmHa: CS28 Coli surface antigen a:
+cnmHb: CS28 Coli surface antigen b:
+cofR: CS8 Regulator:
+cofS: CS8 AraC-like protein:
+cofT: CS8 Unknown:
+cofA: CS8 Type IV pilin precursor; major pilin:
+cofB: CS8 Minor pilin:
+cofC: CS8 Unknown:
+cofD: CS8 Lipoprotein; secretin:
+cofE: CS8 Inner membrane accessory protein (IMAP):
+cofF: CS8 Inner membrane accessory protein (IMAP):
+cofG: CS8 Inner membrane accessory protein (IMAP):
+cofH: CS8 Nucleotide-binding protein; assembly ATPase:
+cofI: CS8 Integral membrane protein; inner membrane core protein (IMCP):
+cofJ: CS8 Secreted colonization factor:
+cofP: CS8 Prepilin peptidase:
+colE2: Colicin E2:
+colE2-like: Colicin lysis protein precursor E2-like:
+colE4: Colicin E4:
+colE5: Colicin E5 lysis protein Lys:
+colE6: Colicin E6:
+colE7: Colicin E7:
+colE8: Colicin E8:
+colE9: Colicin E9:
+cosA: PCFO71 Major fimbrial subunit:
+cosB: PCFO71 Periplasmic chaperone:
+cosC: PCFO71 Outer membrane usher:
+cosD: PCFO71 Minor fimbrial subunit:
+cooA: CS1 Major subunit:
+cooB: CS1 Chaperone:
+cooD: CS1 Chaperone:
+cooC: CS1 Usher:
+cotB: CS2 Major pilin chaperone:
+cotA: CS2 Major pilin chaperone:
+cotC: CS2 Usher:
+cotD: CS2 Chaperone:
+crsB: CS26 molecular chaperone:
+crsC: CS26 fimbria/pilus periplasmic chaperone:
+crsD: CS26 fimbrial biogenesis outer membrane usher protein:
+crsE: CS26 fimbria/pilus periplasmic chaperone:
+crsF: CS26 fimbrial protein:
+crsG: CS26 hypothetical protein:
+crsH: CS26 Coli surface antigen, type 1 fimbrial protein:
+crsS: CS26 Tyrosine-type DNA invertase:
+crsT: CS26 Tyrosine-type DNA invertase:
+csaA: CS4 Periplasmic chaperone-like protein:
+csaB: CS4: CS4 major fimbriae subunit:
+csaC: CS4 Usher protein:
+csaD: CS4 Deleted regulatory protein:
+csaE: CS4 Tip-associated protein:
+csbA: CS17 Fimbriae major subunit:
+csbB: CS17 Chaperone:
+csbC: CS17 Usher:
+csbD: CS17 Assembly protein/minor subunit:
+csdA: CS19 Major fimbrial subunit:
+csdB: CS19 Periplasmic chaperone:
+csdC: CS19 Outer membrane usher:
+csdD: CS19 Minor fimbrial subunit:
+cseA: CS22 Adhesin protein:
+csfA: CS5 major subunit:
+csfB: CS5 coli surface factor five B, Chaperone:
+csfC: CS5 Outer membrane usher protein:
+csfD: CS5 Minor fimbrial subunit:
+csfE: CS5 Pilus length modulator:
+csfF: CS5 Minor pilin chaperone:
+cshA: CS13 Minor pilin:
+cshB: CS13 Usher:
+cshC: CS13 Chaperone:
+cshD: CS13 Minor pilin:
+cshE: CS13 Pilin:
+cshF: CS13 Minor pilin:
+cshG: CS13 Minor pilin:
+csmA: CS30 Major subunit:
+csmB: CS30 Chaperone:
+csmC: CS30 Chaperone:
+csmD: CS30 Usher:
+csmE: CS30 Chaperone:
+csmF: CS30 Minor subunit:
+csmG: CS30 Fimbrial adhesin:
+csmS: CS30 Site specific recombinase:
+csmT: CS30 Site specific recombinase:
+csnA: CS20 Fimbria major subunit:
+csnB: CS20 Putative major subunit chaperone:
+csnC: CS20 Putative adhesin-specific chaperone:
+csnD: CS20 Putative outer membrane fimbrial usher:
+csnE: CS20 Putative chaperone-like:
+csnF: CS20 Putative minor subunit:
+csnG: CS20 Putative minor adhesive tip subunit:
+cssA: CS6 Structural subunit A:
+cssB: CS6 Structural subunit B:
+cssC: CS6 Periplasmic chaperone:
+cssD: CS6 Usher protein:
+cstA : CS3 Major pilin chaperone:
+cstBCDEF: CS3 Major pili usher:
+cstG: CS3 Major pilin:
+cstH: CS3 Major pilin reported but not found:
+csuA: CS14 Major fimbrial subunit:
+csuB: CS14 Periplasmic chaperone:
+csuC: CS14 Outer membrane usher:
+csuD: CS14 Minor fimbrial subunit:
+csvA: CS7 Major subunit:
+cswA: CS12 Major subunit:
+cswB: CS12 Chaperone:
+cswC: CS12 Chaperone:
+cswD: CS12 Outer membrane usher:
+cswE: CS12 Chaperone:
+cswF: CS12 Minor subunit:
+cswG: CS12 Putative adhesin:
+cswR: CS12 Transcriptional activator:
+dhaK: Dihydroxyacetone kinase (also designated ptnC):
+eae-a01-alpha 1 : Intimin-a01-alpha 1:
+eae-a02-alpha 2 : Intimin-a02-alpha 2:
+eae-a03-zeta : Intimin-a03-zeta:
+eae-a04-zeta : Intimin-a04-zeta:
+eae-a05a-nu : Intimin-a05a-nu:
+eae-a05b-nu : Intimin-a05b-nu:
+eae-a06-omicron : Intimin-a06-omicron:
+eae-a07-tau : Intimin-a07-tau:
+eae-a08-alpha 8 : Intimin-a08-alpha 8:
+eae-a09-alpha 9 : Intimin-a09-alpha 9:
+eae-a10-alpha 10 : Intimin-a10-alpha 10:
+eae-a11-alpha 11 : Intimin-a11-alpha 11:
+eae-a12-alpha 12 : Intimin-a12-alpha 12:
+eae-a13a-alpha 13 : Intimin-a13a-alpha 13:
+eae-a13b-alpha 13 : Intimin-a13b-alpha 13:
+eae-a14-alpha 14 : Intimin-a14-alpha 14:
+eae-a15-alpha 15 : Intimin-a15-alpha 15:
+eae-a16-alpha 16 : Intimin-a16-alpha 16:
+eae-a17-alpha 17 : Intimin-a17-alpha 17:
+eae-a18-alpha 18 : Intimin-a18-alpha 18:
+eae-b01a-beta 1a : Intimin-b01a-beta 1a:
+eae-b01b-beta 1b : Intimin-b01b-beta 1b:
+eae-b02a-beta 2a : Intimin-b02a-beta 2a:
+eae-b02b-beta 2b : Intimin-b02b-beta 2b:
+eae-b03-beta 3 : Intimin-b03-beta 3:
+eae-b04-delta : Intimin-b04-delta:
+eae-b05-Citrobacter : Intimin-b05-Citrobacter:
+eae-b06-beta 4 : Intimin-b06-beta 4:
+eae-b07-beta 7 : Intimin-b07-beta 7:
+eae-b08-kappa : Intimin-b08-kappa:
+eae-e01-epsilon 1 : Intimin-e01-epsilon 1:
+eae-e02-epsilon 2 : Intimin-e02-epsilon 2:
+eae-e03a-epsilon 3 : Intimin-e03a-epsilon 3:
+eae-e03b-epsilon 3 : Intimin-e03b-epsilon 3:
+eae-e04-epsilon 4 : Intimin-e04-epsilon 4:
+eae-e05-eta 1 : Intimin-e05-eta 1:
+eae-e06-eta 2 : Intimin-e06-eta 2:
+eae-e07-xi : Intimin-e07-xi:
+eae-e08-pi : Intimin-e08-pi:
+eae-e09-epsilon 9 : Intimin-e09-epsilon 9:
+eae-e10-epsilon 10 : Intimin-e10-epsilon 10:
+eae-e11-epsilon 11 : Intimin-e11-epsilon 11:
+eae-e12-eta 2 : Intimin-e12-eta 2:
+eae-g01-gamma 1 : Intimin-g01-gamma 1:
+eae-g02-theta : Intimin-g02-theta:
+eae-g03-mu : Intimin-g03-mu:
+eae-g04-sigma : Intimin-g04-sigma:
+eae-g05-gamma 5 : Intimin-g05-gamma 5:
+eae-g06-gamma 6 : Intimin-g06-gamma 6:
+eae-g07-gamma 7 : Intimin-g07-gamma 7:
+eae-g08-gamma 8 : Intimin-g08-gamma 8:
+eae-g09-gamma 9 : Intimin-g09-gamma 9:
+eae-i01-iota 1 : Intimin-i01-iota 1:
+eae-i02b-iota 2 : Intimin-i02b-iota 2:
+eae-i03-upsilon : Intimin-i03-upsilon:
+eae-l01-lambda 1 : Intimin-l01-lambda 1:
+eae-l02-lambda 2 : Intimin-l02-lambda 2:
+eae-l03-lambda 3 : Intimin-l03-lambda 3:
+eae-l04a-lambda 4 : Intimin-l04a-lambda 4:
+eae-l04b-lambda 4 : Intimin-l04b-lambda 4:
+eae-l05-lambda 5 : Intimin-l05-lambda 5:
+eae-r01-rho 1 : Intimin-r01-rho 1:
+eae-r02-rho 2 : Intimin-r02-rho 2:
+eae-r03-rho 3 : Intimin-r03-rho 3:
+eae-r04-rho 4 : Intimin-r04-rho 4:
+eatA: Mucin-degrading serine protease autotransporters of Enterobacteriaceae and ETEC (SPATE):
+efa1: EHEC factor for adherence; lymphostatin Efa1-LifA:
+ehxA: Enterohaemolysin:
+eltIAB-1: Heat-labile enterotoxin LTIh-1:
+eltIAB-2: Heat-labile enterotoxin LTIh-2:
+eltIAB-3: Heat-labile enterotoxin LTIh-3:
+eltIAB-4: Heat-labile enterotoxin LTIh-4:
+eltIAB-5: Heat-labile enterotoxin LTIh-5:
+eltIAB-6: Heat-labile enterotoxin LTIh-6:
+eltIAB-7: Heat-labile enterotoxin LTIh-7:
+eltIAB-8: Heat-labile enterotoxin LTIh-8:
+eltIAB-9: Heat-labile enterotoxin LTIh9:
+eltIAB-10: Heat-labile enterotoxin LTIh-10:
+eltIAB-11: Heat-labile enterotoxin LTIh-11:
+eltIAB-12: Heat-labile enterotoxin LTIh-12:
+eltIAB-13: Heat-labile enterotoxin LTIh-13:
+eltIAB-14: Heat-labile enterotoxin LTIh-14:
+eltIAB-15: Heat-labile enterotoxin LTIh-15:
+eltIAB-15b: Heat-labile enterotoxin LTIh-15b:
+eltIAB-16: Heat-labile enterotoxin LTIh-16:
+eltIAB-17: Heat-labile enterotoxin LTIh-17:
+eltIAB-18: Heat-labile enterotoxin LTIh-18:
+eltIAB-19: Heat-labile enterotoxin LTIh-19:
+eltIAB-20: Heat-labile enterotoxin LTIh-20:
+eltIAB-21: Heat-labile enterotoxin LTIh-21:
+eltIAB-22: Heat-labile enterotoxin LTIh-22:
+eltIAB-23: Heat-labile enterotoxin LTIh-23:
+eltIAB-24: Heat-labile enterotoxin LTIh-24:
+eltIAB-25: Heat-labile enterotoxin LTIh-25:
+eltIAB-26: Heat-labile enterotoxin LTIh-26:
+eltIAB-27: Heat-labile enterotoxin LTIh-27:
+eltIAB-28: Heat-labile enterotoxin LTIh-28:
+eltIAB-29: Heat-labile enterotoxin LTIh-29:
+eltIAB-30: Heat-labile enterotoxin LTIh-30:
+eltIAB-31: Heat-labile enterotoxin LTIh-31:
+eltIAB-33: Heat-labile enterotoxin LTIh-32:
+eltIAB-33: Heat-labile enterotoxin LTIh-33:
+eltIIAB-a: Heat-labile enterotoxin LTII-a:
+eltIIAB-b1: Heat-labile enterotoxin LTII-b1:
+eltIIAB-b2: Heat-labile enterotoxin LTII-b2:
+eltIIAB-c1: Heat-labile enterotoxin LTII-c1:
+eltIIAB-c2: Heat-labile enterotoxin LTII-c2:
+eltIIAB-c3: Heat-labile enterotoxin LTII-c3:
+eltIIAB-c4: Heat-labile enterotoxin LTII-c4:
+eltIIAB-c5: Heat-labile enterotoxin LTII-c5:
+eltIIAB-c6: Heat-labile enterotoxin LTII-c6:
+eltIIAB-c7: Heat-labile enterotoxin LTII-c7:
+eltIIAB-c8: Heat-labile enterotoxin LTII-c8:
+eltIIAB-c9: Heat-labile enterotoxin LTII-c9:
+eltIIAB-d1: Heat-labile enterotoxin LTII-d1:
+eltIIAB-d2: Heat-labile enterotoxin LTII-d2:
+eltIIAB-e: Heat-labile enterotoxin LTII-e:
+epeA: Serine protease autotransporters of Enterobacteriaceae (SPATE):
+espA: Type III secretions system:
+espA-Cr: Type III secretions system, C. rodentium:
espB: Secreted protein B:
-ehxA: Enterohaemolysin:
-f17-A: Subunit A of F17 fimbrial protein:
-f17-G: Adhesin subunit of F17 fimbriae:
-fanA: Involved in biogenesis of K99/F5 fimbriae:
-fasA: Fimbriae 987P/F6 subunit:
-fedA: Fimbrial protein F107 subunit A:
-fedF: Fimbrial adhesin AC precursor:
-fim41a: Mature Fim41a/F41 protein:
+espC: Escherichia coli enterotoxin EspC:
+espF: EPEC secreted protein F; Type III secretion system:
+espF-Cr: Citrobacter rodentium secreted protein F; Type III secretion system:
+espI: Serine protease autotransporters of Enterobacteriaceae (SPATE):
+espJ: Prophage-encoded type III secretion system effector:
+espP: Serine protease autotransporter EspP:
+estap-STa1: Heat-stable enterotoxin STa1 porcine variant:
+estah-STa2: Heat-stable enterotoxin STa2 human variant:
+estah-STa3: Heat-stable enterotoxin STa3 human variant:
+estap-STa4: Heat-stable enterotoxin STa4 porcine variant:
+estap-STa5: Heat-stable enterotoxin STa5 porcine variant:
+estap-STa6: Heat-stable enterotoxin STa6 porcine variant:
+estap-STa7: Heat-stable enterotoxin STa7 porcine variant:
+estap-STa8: Heat-stable enterotoxin STa8 porcine variant:
+estap-STa9: Heat-stable enterotoxin STa9 porcine variant:
+estb-STb1: Heat-stable enterotoxin STb1 porcine variant:
+estb-STb2: Heat-stable enterotoxin STb2 human variant:
+etpA: EtpA Invasin and adherence:
+etpB: EtpB Nonfimbrial adhesin/TPS transporter:
+etpC: EtpC Glycotransferase:
+etpD: Type II secretion protein EtpD:
+F17A: Major fimbrial subunit of F17:
+F17G: Minor adhesive subunit of F17 fimbriae:
+F17C: F17 Usher:
+F17D: F17 Chaperone:
+faeA: F4 (K88) Regulator:
+faeB: F4 (K88) Partial:
+faeC: F4 (K88) Minor fimbrial subunits:
+faeD: F4 (K88) Usher:
+faeE: F4 (K88) Chaperone:
+faeF: F4 (K88) Minor fimbrial subunit:
+faeGab: F4ab (K88) Major serotype specific fimbrial subunit:
+faeGab1: F4ab (K88) Major serotype specific fimbrial subunit, one of two copies in strain 2134E:
+faeGab2: F4ab (K88) Major serotype specific fimbrial subunit, second of two copies in strain 2134E:
+faeGac: F4ac (K88) Major serotype specific fimbrial subunit:
+faeGad: F4ad (K88) Major serotype specific fimbrial subunit:
+faeGW: F4W (K88) Major serotype specific fimbrial subunit:
+faeH: F4 (K88) Fimbria minor subunit:
+faeH1: F4 (K88) Fimbria minor subunit, one of two copies in strain RHBSTW-00673:
+faeH2: F4 (K88) Fimbria minor subunit, second of two copies in strain RHBSTW-00673:
+faeI: F4 (K88) Fimbria minor subunit:
+faeI1: F4 (K88) Fimbria minor subunit, one of two copies in strain RHBSTW-00673:
+faeI2: F4 (K88) Fimbria minor subunit, second of two copies in strain RHBSTW-00673:
+faeJ: F4 (K88) Fimbria minor subunit:
+fanA: F5 (K99) Transcriptional regulator:
+fanB: F5 (K99) Regulator:
+fanC: F5 (K99) Major fimbrial subunit:
+fanD: F5 (K99) Usher:
+fanE: F5 (K99) Chaperone:
+fanF: F5 (K99) Minor fimbrial subunits:
+fanG: F5 (K99) Minor subunit:
+fanH: F5 (K99) Minor subunit:
+fasA: F6 (987P) Major subunit:
+fasB: F6 (987P) Major subunit chaperone:
+fasC: F6 (987P) Adhesin-specific chaperone:
+fasD: F6 (987P) Outer membrane usher:
+fasE: F6 (987P) Chaperone-like:
+fasF: F6 (987P) Minor subunit linker:
+fasG: F6 (987P) Minor adhesive subunit:
+fasH: F6 (987P) Positive regulator, previously fapR:
+fedAab: F18ab (F107) Major serotype specific fimbrial subunit A:
+fedAac: F18ac (F107) Major serotype specific fimbrial subunit A:
+fedAnt: F18 nontypeable (F107) Major serotype specific fimbrial subunit A:
+fedB: F18 (F107) Usher:
+fedC: F18 (F107) Chaperone:
+fedE: F18 (F107) Minor fimbrial subunits:
+fedF: F18 (F107) Minor adhesive subunit:
+fimF41: FimF41 Major fimbrial subunit:
+fimH: Type 1 fimbriae:
+fotA: CS18 Major subunit:
+fotB: CS18 Major chaperone:
+fotC: CS18 Minor chaperone:
+fotD: CS18 Usher:
+fotE: CS18 Minor chaperone:
+fotF: CS18 Minor subunit:
+fotG: CS18 Minor subunit-adhesin:
+fotS: CS18 Site-specific recombinase:
+fotT: CS18 Site-specific recombinase:
gad: Glutamate decarboxylase:
-hlyA: Haemolysin A:
-hlyE: Avian E.coli haemolysin:
+hlyA: Hemolysin A:
+hlyE: Avian E. coli haemolysin:
+hlyF: Hemolysin F:
+iha: Adherence protein:
ipaD: Invasion protein Shigella flexneri:
+ipaH: Invasion plasmid antigen: plasmid encoded:
+ipaH7.8: Invasion plasmid antigen: plasmid encoded:
ipaH9.8: Invasion plasmid antigen:
ireA: Siderophore receptor:
iroN: Enterobactin siderophore receptor protein:
iss: Increased serum survival:
-lngA: Longus type IV pilus:
-ltcA: Heat-labile enterotoxin A subunit:
+katP: Plasmid-encoded catalase peroxidase:
+lngX1: CS21:
+lngR: CS21 Putative papB-like regulator:
+lngS: CS21 Putative AraC-like regulator:
+lngT: CS21:
+lngX2: CS21:
+lngA: CS21 Major pilin:
+lngB: CS21:
+lngC: CS21:
+lngD: CS21 Putative outer membrane protein:
+lngE: CS21 Putative inner membrane protein:
+lngF: CS21 Putative inner membrane protein:
+lngG: CS21 Putative periplasmic protein:
+lngH: CS21 Putative nucleotide-binding protein:
+lngI: CS21 Putative inner membrane protein:
+lngJ: CS21 Putative ATPase-like:
+lngP: CS21 Putative prepilin peptidase:
+lpfA: Long polar fimbriae:
+lys: Colicin release protein:
mchB: Microcin H47 part of colicin H:
mchC: MchC protein:
mchF: ABC transporter protein MchF:
mcmA: Microcin M part of colicin H:
+nfaA: CS15 Nonfimbrial adhesin A:
nfaE: Diffuse adherence fibrillar adhesin gene:
-perA: EPEC adherence factor:
-pet: Autotransporter enterotoxin:
-senB: Plasmid-encoded enterotoxin:
-sfaS: S-fimbriae minor subunit:
-sta1: Heat-stabile enterotoxin ST-Ia:
-stb: Heat-stabile enterotoxin II:
-virF: VirF transcriptional activator:
-cif: Type III secreted effector:
-eatA: serine protease autotransporters of Enterobacteriaceae (SPATE):
-efa1: EHEC factor for adherence:
-epeA: serine protease autotransporters of Enterobacteriaceae (SPATE):
-espA: Type III secretions system:
-espC: serine protease autotransporters of Enterobacteriaceae (SPATE):
-espF: Type III secretion system:
-espI: serine protease autotransporters of Enterobacteriaceae (SPATE):
-espJ: Prophage-encoded type III secretion system effector:
-espP: Putative exoprotein precursor:
-etpD: Type II secretion protein:
-iha: Adherence protein:
-katP: Plasmid-encoded catalase peroxidase:
-lpfA: Long polar fimbriae:
nleA: Non-LEE encoded effector A:
nleB: Non-LEE encoded effector B:
nleC: Non-LEE encoded effector C:
+nlpI: lipoprotein NlpI precursor:
+perA: EPEC adherence factor:
+pet: Autotransporter enterotoxin:
pic: serine protease autotransporters of Enterobacteriaceae (SPATE):
+picU: Pic from uropathogenic E. coli (UPEC):
+pssA: Protease secreted by Shiga toxin-producing E. coli (STEC):
rpeA: serine protease autotransporters of Enterobacteriaceae (SPATE):
saa: Auto agglutinating adhesin:
sat: serine protease autotransporters of Enterobacteriaceae (SPATE):
-sepA: serine protease autotransporters of Enterobacteriaceae (SPATE):
-sigA: serine protease autotransporters of Enterobacteriaceae (SPATE):
+senB: Plasmid-encoded enterotoxin:
+sepA: serine protease autotransporters of Enterobacteriaceae (SPATE)-Shigella extracellular protein A:
+sfaS: S-fimbriae minor subunit:
+sigA: serine protease autotransporters of Enterobacteriaceae (SPATE),Shigella IgA-like protease homologue:
subA: Subtilase toxin subunit:
tccP: Tir-cytoskeleton coupling protein:
+tia: Tia Invasion determinant:
+tibA: TibA Adhesin/invasin (Glycoprotein):
+tibC: Glycosyltransferase:
tir: Translocated intimin receptor protein:
+tir-Cr: Translocated intimin receptor protein, C. rodentium:
+tleA: tsh-like ETEC autotransporter:
toxB: Toxin B:
-tsh: serine protease autotransporters of Enterobacteriaceae (SPATE):
+tsh: serine protease autotransporter of Enterobacteriaceae (SPATE)-Immunoglobulin A1 protease- Temperature-sensitive hemagglutinin:
+stx1a-O111-PH: stx1a-O111-PH:
+stx1a-O111-CB168: stx1a-O111-CB168:
+stx1a-O157-AI2001-52: stx1a-O157-AI2001-52:
+stx1a-O157-GPU96MM: stx1a-O157-GPU96MM:
+stx1a-O111-04-06263: stx1a-O111-04-06263:
+stx1a-O111-3385-00: stx1a-O111-3385-00:
+stx1-S.-sonnei-CB7888: stx1-S.-sonnei-CB7888:
+stx1a-O48-94C: stx1a-O48-94C:
+stx1a-O157-FLY16: stx1a-O157-FLY16:
+stx1a-O157-EDL933: stx1a-O157-EDL933:
+stx1a-O165-HI-2: stx1a-O165-HI-2:
+stx1a-ONT-HI-A: stx1a-ONT-HI-A:
+stx1c-Out-HI-N: stx1c-Out-HI-N:
+stx1c-ONT-HI-B: stx1c-ONT-HI-B:
+stx1c-ONT-HI-C: stx1c-ONT-HI-C:
+stx1c-ONT-BCN26: stx1c-ONT-BCN26:
+stx1c-O174-DG131-3: stx1c-O174-DG131-3:
+stx1d-ONT-92-1251: stx1d-ONT-92-1251:
+stx1d-ONT-92-1252: stx1d-ONT-92-1252:
+stx1d-ONT-AB8SF: stx1d-ONT-AB8SF:
+stx1d-ONT-MHI813: stx1d-ONT-MHI813:
+stx1e-E.-cloacae-M12X01451: stx1e-E.-cloacae-M12X01451:
+stx2a-A.-haemolyticus: stx2a-A.-haemolyticus:
+stx2a-E.-cloacae-95MV2: stx2a-E.-cloacae-95MV2:
+stx2a-O104-G5506: stx2a-O104-G5506:
+stx2a-O111-928-91: stx2a-O111-928-91:
+stx2a-O113-CL-3: stx2a-O113-CL-3:
+stx2a-O136-VTB60: stx2a-O136-VTB60:
+stx2a-O157-93-111: stx2a-O157-93-111:
+stx2a-O157-A397: stx2a-O157-A397:
+stx2a-O157-EDL933: stx2a-O157-EDL933:
+stx2a-O157-I6581: stx2a-O157-I6581:
+stx2a-O157-SF-258-98: stx2a-O157-SF-258-98:
+stx2a-O178-TS22-08: stx2a-O178-TS22-08:
+stx2a-O22-EBC217: stx2a-O22-EBC217:
+stx2a-O26-126814: stx2a-O26-126814:
+stx2a-O26-FD930: stx2a-O26-FD930:
+stx2a-O48-94C: stx2a-O48-94C:
+stx2a-O8-BMH-17-0027: stx2a-O8-BMH-17-0027:
+stx2a-O8-VTB178: stx2a-O8-VTB178:
+stx2a-O83-N1135: stx2a-O83-N1135:
+stx2a-O88-N2688: stx2a-O88-N2688:
+stx2a-ONT-23765: stx2a-ONT-23765:
+stx2a-ONT-EBC210: stx2a-ONT-EBC210:
+stx2a-ONT-EK9900: stx2a-ONT-EK9900:
+stx2b-O111-PH: stx2b-O111-PH:
+stx2b-O111-S-1: stx2b-O111-S-1:
+stx2b-O111-S-3: stx2b-O111-S-3:
+stx2b-O118-EH250: stx2b-O118-EH250:
+stx2b-O128-24196-97: stx2b-O128-24196-97:
+stx2b-O146-BMH-17-0036: stx2b-O146-BMH-17-0036:
+stx2b-O174-031: stx2b-O174-031:
+stx2b-O22-3143-97: stx2b-O22-3143-97:
+stx2b-O40-5293-98: stx2b-O40-5293-98:
+stx2b-O8-S-9: stx2b-O8-S-9:
+stx2b-O93-S-5: stx2b-O93-S-5:
+stx2b-O96-S-10: stx2b-O96-S-10:
+stx2b-O96-S-6: stx2b-O96-S-6:
+stx2b-O96-S-7: stx2b-O96-S-7:
+stx2b-ONT-I7606: stx2b-ONT-I7606:
+stx2b-Out-HI-N: stx2b-Out-HI-N:
+stx2b-Out-S-4: stx2b-Out-S-4:
+stx2c-O157-020324: stx2c-O157-020324:
+stx2c-O157-310: stx2c-O157-310:
+stx2c-O157-469: stx2c-O157-469:
+stx2c-O157-A75: stx2c-O157-A75:
+stx2c-O157-C394-03: stx2c-O157-C394-03:
+stx2c-O157-E32511: stx2c-O157-E32511:
+stx2c-O157-FLY16: stx2c-O157-FLY16:
+stx2c-O157-G5101: stx2c-O157-G5101:
+stx2c-O157-V20: stx2c-O157-V20:
+stx2c-O157-Y350-: stx2c-O157-Y350-:
+stx2c-O171-EBC287: stx2c-O171-EBC287:
+stx2c-O171-VTB46: stx2c-O171-VTB46:
+stx2c-O174-031: stx2c-O174-031:
+stx2c-O177-06-5121: stx2c-O177-06-5121:
+stx2c-O177-CB7126: stx2c-O177-CB7126:
+stx2c-ONT-EBC219: stx2c-ONT-EBC219:
+stx2c-ONT-EBC289: stx2c-ONT-EBC289:
+stx2c-OR-TS27-08: stx2c-OR-TS27-08:
+stx2d-C.-freundii-LM76: stx2d-C.-freundii-LM76:
+stx2d-O103-CVM9322: stx2d-O103-CVM9322:
+stx2d-O113-TS03-07: stx2d-O113-TS03-07:
+stx2d-O113-TS21-08: stx2d-O113-TS21-08:
+stx2d-O157-7279: stx2d-O157-7279:
+stx2d-O174-EC1720a: stx2d-O174-EC1720a:
+stx2d-O174-EC173b: stx2d-O174-EC173b:
+stx2d-O2-EC604a: stx2d-O2-EC604a:
+stx2d-O22-KY-O19: stx2d-O22-KY-O19:
+stx2d-O28-MT71: stx2d-O28-MT71:
+stx2d-O55-5905: stx2d-O55-5905:
+stx2d-O6-NV206: stx2d-O6-NV206:
+stx2d-O73-C165-02: stx2d-O73-C165-02:
+stx2d-O8-C466-01B: stx2d-O8-C466-01B:
+stx2d-ONT-EBC275: stx2d-ONT-EBC275:
+stx2d-ONT-EC1871a: stx2d-ONT-EC1871a:
+stx2d-OR-TS06-08: stx2d-OR-TS06-08:
+stx2d1-O91-B2F1: stx2d1-O91-B2F1:
+stx2d2-O91-B2F1: stx2d2-O91-B2F1:
+stx2e-O100-TS01-07: stx2e-O100-TS01-07:
+stx2e-O101-CB10394: stx2e-O101-CB10394:
+stx2e-O101-E-D42: stx2e-O101-E-D42:
+stx2e-O101-E-D43: stx2e-O101-E-D43:
+stx2e-O101-E-D53: stx2e-O101-E-D53:
+stx2e-O101-E-D68: stx2e-O101-E-D68:
+stx2e-O121-NP9621: stx2e-O121-NP9621:
+stx2e-O138-NN: stx2e-O138-NN:
+stx2e-O139-S1191: stx2e-O139-S1191:
+stx2e-O22-3615-99: stx2e-O22-3615-99:
+stx2e-O26-R107: stx2e-O26-R107:
+stx2e-O8-1509W52833: stx2e-O8-1509W52833:
+stx2e-O89-1810F65304: stx2e-O89-1810F65304:
+stx2e-O9-1706T56070: stx2e-O9-1706T56070:
+stx2e-ONT-26725-97: stx2e-ONT-26725-97:
+stx2e-ONT-2771: stx2e-ONT-2771:
+stx2e-ONT-TS03-08: stx2e-ONT-TS03-08:
+stx2e-ONT-TS29-08: stx2e-ONT-TS29-08:
+stx2e-OR-TS09-07: stx2e-OR-TS09-07:
+stx2f-O115-F08-101-31: stx2f-O115-F08-101-31:
+stx2f-O128-T4-97: stx2f-O128-T4-97:
+stx2f-O128-HI8: stx2f-O128-HI8:
+stx2g-O2-7v: stx2g-O2-7v:
+stx2g-O2-HI-11: stx2g-O2-HI-11:
+stx2g-O2-S86: stx2g-O2-S86:
+stx2g-Out-S-8: stx2g-Out-S-8:
+stx2h-O102-STEC299: stx2h-O102-STEC299:
+stx2i-O9-CB10366: stx2i-O9-CB10366:
+stx2j-O101-O101-2012C-4221: stx2j-O101-O101-2012C-4221:
+stx2j-O33-PNUSAE005447: stx2j-O33-PNUSAE005447:
+stx2k-O159-12GZSW01: stx2k-O159-12GZSW01:
+stx2k-O48-STEC309: stx2k-O48-STEC309:
+stx2l-O65-1610T27873: stx2l-O65-1610T27873:
+stx2l-O8-FHI-1106-1092: stx2l-O8-FHI-1106-1092:
+stx2m-O96-2001F31428: stx2m-O96-2001F31428:
+stx2n-O23-2017C-4317: stx2n-O23-2017C-4317:
+stx2o-O85-03-3638: stx2o-O85-03-3638:
+vat-EXPEC: Vacuolating autotransporter toxin from extra-intestinal pathogenic E. coli(EXPEC):
vat: serine protease autotransporters of Enterobacteriaceae (SPATE):
-stx1Aa: Shiga toxin 1, subunit A, variant a:
-stx1Ab: Shiga toxin 1, subunit A, variant b:
-stx1Ac: Shiga toxin 1, subunit A, variant c:
-stx1Ad: Shiga toxin 1, subunit A, variant d:
-stx1Ae: Shiga toxin 1, subunit A, variant e:
-stx1Af: Shiga toxin 1, subunit A, variant f:
-stx1Ba: Shiga toxin 1, subunit B, variant a:
-stx1Bb: Shiga toxin 1, subunit B, variant b:
-stx1Bc: Shiga toxin 1, subunit B, variant c:
-stx1Bd: Shiga toxin 1, subunit B, variant d:
-stx1Be: Shiga toxin 1, subunit B, variant e:
-stx1Bf: Shiga toxin 1, subunit B, variant f:
-stx2Aa: Shiga toxin 2, subunit A, variant a:
-stx2Ab: Shiga toxin 2, subunit A, variant b:
-stx2Ac: Shiga toxin 2, subunit A, variant c:
-stx2Ad: Shiga toxin 2, subunit A, variant d:
-stx2Ae: Shiga toxin 2, subunit A, variant e:
-stx2Af: Shiga toxin 2, subunit A, variant f:
-stx2Ag: Shiga toxin 2, subunit A, variant g:
-stx2Ba: Shiga toxin 2, subunit B, variant a:
-stx2Bb: Shiga toxin 2, subunit B, variant b:
-stx2Bc: Shiga toxin 2, subunit B, variant c:
-stx2Bd: Shiga toxin 2, subunit B, variant d:
-stx2Be: Shiga toxin 2, subunit B, variant e:
-stx2Bf: Shiga toxin 2, subunit B, variant f:
-stx2Bg: Shiga toxin 2, subunit B, variant g:
-stx1A: Shiga toxin 1, subunit A:
-stx1B: Shiga toxin 1, subunit B:
-stx2A: Shiga toxin 2, subunit A:
-stx2B: Shiga toxin 2, subunit B:
+virF: VirF transcriptional activator:
+aalR: CS23 Putative transcriptional regulator:
+aalA: CS23 Minor structural subunit:
+aalB: CS23 Usher:
+aalC: CS23 Chaperone:
+aalD: CS23 Minor structural subunit:
+aalE: CS23 Major structural subunit:
+aalF: CS23 Minor structural subunit:
+aalG: CS23 Minor structural subunit:
+aalH: CS23 Minor structural subunit:
ElrA::
SrtA::
ace:collagen adhesin precursor:
@@ -286,197 +728,195 @@ essC:type VII secretion protein EssC:
esaC:EsaC protein within ESAT-6 gene cluster:
esxB:virulence factor EsxB family protein:
vwb:von Willebrand factor-binding protein:
-stx11:S.dysenteriae 60R
-stx12:ONTNA, variant a
-stx13:S.dysenteriae 3818T
-stx14:O111 PH, variant a
-stx15:O111 CB168, variant a
-stx16:O157 AI2001 52, variant a
-stx17:O157 GPU96MM, variant a
-stx18:O111 04-06263, variant a
-stx19:O111 3385-00, variant a
-stx110:S.sonnei CB7888
-stx111:O48 94C, variant a
-stx112:O157 FLY16, variant a
-stx113:O157 EDL933, variant a
-stx114:O165 HI-2, variant a
-stx115:ONT HI-A, variant a
-stx116:Out HI-N, variant c
-stx117:ONT HI-B, variant c
-stx118:ONT HI-C, variant c
-stx119:ONT BCN26, variant c
-stx120:O174 DG131-3, variant c
-stx121:ONT 92-1251, variant d
-stx122:ONT 92-1252, variant d
-stx123:ONT AB8SF, variant d
-stx124:ONT MHI813, variant d
-stx21:O113 TS17-08, variant a
-stx22:O22 EBC217, variant a
-stx23:ONT 23765, variant a
-stx24:O113 TS18-08, variant a
-stx25:O88 N2688, variant a
-stx26:ONT N5578, variant a
-stx27:O153 TS20-08, variant a
-stx28:O130 TS07-07, variant a
-stx29: 178 TS02-07, variant a
-stx210:O48 94C, variant a
-stx211:OR TS05-07, variant a
-stx212:E.cloacae 95MV2, variant a
-stx213:O101 EBC201, variant a
-stx214:O26 126814, variant a
-stx215:O157 SF-258-98, variant a
-stx216:O178 TS22-08, variant a
-stx217:O178 TS24-08, variant a
-stx218:O104 G5506, variant a
-stx219:O8 VTB178, variant a
-stx220:O83 N1135, variant a
-stx221:ONT EK9900, variant a
-stx222:ONT EBC210, variant a
-stx223:O26 FD930, variant a
-stx224:O157 SF-3573-98, variant a
-stx225:O157 A397, variant a
-stx226:O157 I6581, variant a
-stx227:O136 VTB60, variant a
-stx228:A.haemolyticus, variant a
-stx229:O111 928-91, variant a
-stx230:O157 93-111, variant a
-stx231:O157 EDL933, variant a
-stx232:O113 CL-3, variant a
-stx233:O157 G5101, variant c
-stx234:ONT pVTEC9, variant c
-stx235:O174 031, variant c
-stx236:O157 E32511, variant c
-stx237:O177 CB7126, variant c
-stx238:O174 EC1720a, variant d
-stx239:ONT EBC219, variant c
-stx240:O177 06-5121, variant c
-stx241:O157 CB8028, variant c
-stx242:O157 A580, variant c
-stx243:O157 469, variant c
-stx244:O157 A75, variant c
-stx245:O157 310, variant c
-stx246:O177 VTB323, variant c
-stx247:O157 020324, variant c
-stx248:O157 C394-03, variant c
-stx249:O157 V20, variant c
-stx250:O157 CS1718, variant c
-stx251:O157 Y350 , variant c
-stx252:O157 FLY16, variant c
-stx253:O171 EBC287, variant c
-stx254:O171 VTB46, variant c
-stx255:ONT EBC289, variant c
-stx256:OR TS27-08, variant c
-stx257:ONT EBC275, variant d
-stx258:O91 B2F1, variant d1
-stx259:O83 N15432, variant d
-stx260:O113 VTB75, variant d
-stx261:O77 VTB91, variant d
-stx262:O103 pVTEC7, variant d
-stx263:OR TS06-08, variant d
-stx264:ONT EC1871a, variant d
-stx265:O15 88 1509, variant d
-stx266:O113 TS03-07, variant d
-stx267:O174 EC173b, variant d
-stx268:O8 C466-01B, variant d
-stx269:O91 B2F1, variant d2
-stx270:C.freundii LM76, variant d
-stx271:O103 CVM9322, variant d
-stx272:O157 7279, variant d
-stx273:O55 5905, variant d
-stx274:O55 06-5231, variant d
-stx275:O6 NV206, variant d
-stx276:O2 EC604a, variant d
-stx277:O28 MT71, variant d
-stx278:O73 C165-02, variant d
-stx279:O22 KY-O19, variant d
-stx280:O113 TS28-08, variant d
-stx281:O113 TS21-08, variant d
-stx282:Out S-4, variant b
-stx283:O8 S-9, variant b
-stx284:Out HI-N, variant b
-stx285:O93 S-5, variant b
-stx286:O111 S-3, variant b
-stx287:O96 S-10, variant b
-stx288:O111 S-1, variant b
-stx289:O96 S-7, variant b
-stx290:O96 S-6, variant b
-stx291:O22 3143-97, variant b
-stx292:O118 EH250, variant b
-stx293:O40 5293-98, variant b
-stx294:ONT I7606, variant b
-stx295:O128 24196-97, variant b
-stx296:O111 PH, variant b
-stx297:O174 031, variant b
-stx298:O8 FHI-1106-1092, variant e
-stx299:Out S-8, variant g
-stx2100:O2 7v, variant g
-stx2101:O2 HI-11, variant g
-stx2102:O2 S86, variant g
-stx2103:O115 F08-101-31, variant f
-stx2104:O128 T4-97, variant f
-stx2105:O89 HI8, variant f
-stx2106:O101 E-D42, variant e
-stx2107:O22 3615-99, variant e
-stx2108:OR TS09-07, variant e
-stx2109:O26 R107, variant e
-stx2110:O139 S1191, variant e
-stx2111:O101 E-D43, variant e
-stx2112:O101 E-D68, variant e
-stx2113:O101 E-D53, variant e
-stx2114:ONT TS29-08, variant e
-stx2115:ONT TS03-08, variant e
-stx2116:O138 NN, variant e
-stx2117:O101 CB10394, variant e
-stx2118:O100 TS01-07, variant e
-stx2119:O121 NP9621, variant e
-stx2120:ONT 26725-97, variant e
-stx2121:ONT 2771, variant e
-astA: EAST-1 heat-stable toxin
-pet: Plasmid-encoded toxin
-sigA: Shigella IgA-like protease homologue
-Pic: Protease involved in intestinal colonization
-sepA: Shigella extracellular protein A
-tsh: Temperature-sensitive hemagglutinin
-sat: Secreted autotransporter toxin
-espC: EPEC secreted protein C
-espP: Extracellular serine protease plasmid-encoded
-pssA: Protease secreted by Shiga toxin-producing E. coli (STEC)
-picU: Pic from uropathogenic E. coli (UPEC)
-vat: Vacuolating autotransporter toxin
-vat-EXPEC: Vacuolating autotransporter toxin from extra-intestinal pathogenic E. coli(EXPEC)
-eatA: enterotoxigenic E. coli (ETEC) autotransporter A
-epeA: enterohemorrhagic E. coli EHEC plasmid-encoded autotransporter
-boa: Protease from Salmonella bongori
-ORF3: Isoprenoid Biosynthesis
-ORF4: Putative isopentenyl-diphosphate delta-isomerase
-aap: Dispersin, antiaggregation protein
-aaiC: Type VI secretion protein
-aggR: AraC transcriptional activator
-aatA: Dispersin transporter protein
-agg4A: AAF/IV major fimbrial subunit
-aggA: AAF/I major fimbrial subunit
-aafA: AAF/II major fimbrial subunit
-agg3A: AAF/III major fimbrial subunit
-agg3C: Usher, AAF/III assembly unit
-agg3D: Chaperone, AAF/III assembly unit
-agg3B: AAF/III minor adhesin. Enterobacteria AfaD invasin protein
-aafC: Usher, AAF/II assembly unit
-aafD: Chaperone, AAF/II assembly unit
-aafB: AAF/II minor adhesin. Enterobacteria AfaD invasin protein
-agg4C: Usher, AAF/IV assembly unit
-agg4D: Chaperone, AAF/IV assembly unit
-agg4B: AAF/IV minor adhesin. Enterobacteria AfaD invasin protein
-aggC: Usher, AAF/I assembly unit
-aggD: Chaperone, AAF/I assembly unit
-aggB: AAF/I minor adhesin. Enterobacteria AfaD invasin protein
-aar: AggR-activated regulator
-anr: AraC negative regulator
-eilA: Salmonella HilA homolog
-capU: Hexosyltransferase homolog
-air: Enteroaggregative immunoglobulin repeat protein
-clpK:
-mrk:
-ClpK:
+stx11:S.dysenteriae 60R:
+stx12:ONTNA, variant a:
+stx13:S.dysenteriae 3818T:
+stx14:O111 PH, variant a:
+stx15:O111 CB168, variant a:
+stx16:O157 AI2001 52, variant a:
+stx17:O157 GPU96MM, variant a:
+stx18:O111 04-06263, variant a:
+stx19:O111 3385-00, variant a:
+stx110:S.sonnei CB7888:
+stx111:O48 94C, variant a:
+stx112:O157 FLY16, variant a:
+stx113:O157 EDL933, variant a:
+stx114:O165 HI-2, variant a:
+stx115:ONT HI-A, variant a:
+stx116:Out HI-N, variant c:
+stx117:ONT HI-B, variant c:
+stx118:ONT HI-C, variant c:
+stx119:ONT BCN26, variant c:
+stx120:O174 DG131-3, variant c:
+stx121:ONT 92-1251, variant d:
+stx122:ONT 92-1252, variant d:
+stx123:ONT AB8SF, variant d:
+stx124:ONT MHI813, variant d:
+stx125:E. cloacae M12X01451, variant e:
+stx21:O113 TS17-08, variant a:
+stx22:O22 EBC217, variant a:
+stx23:ONT 23765, variant a:
+stx24:O113 TS18-08, variant a:
+stx25:O88 N2688, variant a:
+stx26:ONT N5578, variant a:
+stx27:O153 TS20-08, variant a:
+stx28:O130 TS07-07, variant a:
+stx29: 178 TS02-07, variant a:
+stx210:O48 94C, variant a:
+stx211:OR TS05-07, variant a:
+stx212:E.cloacae 95MV2, variant a:
+stx213:O101 EBC201, variant a:
+stx214:O26 126814, variant a:
+stx215:O157 SF-258-98, variant a:
+stx216:O178 TS22-08, variant a:
+stx217:O178 TS24-08, variant a:
+stx218:O104 G5506, variant a:
+stx219:O8 VTB178, variant a:
+stx220:O83 N1135, variant a:
+stx221:ONT EK9900, variant a:
+stx222:ONT EBC210, variant a:
+stx223:O26 FD930, variant a:
+stx224:O157 SF-3573-98, variant a:
+stx225:O157 A397, variant a:
+stx226:O157 I6581, variant a:
+stx227:O136 VTB60, variant a:
+stx228:A.haemolyticus, variant a:
+stx229:O111 928-91, variant a:
+stx230:O157 93-111, variant a:
+stx231:O157 EDL933, variant a:
+stx232:O113 CL-3, variant a:
+stx233:O157 G5101, variant c:
+stx234:ONT pVTEC9, variant c:
+stx235:O174 031, variant c:
+stx236:O157 E32511, variant c:
+stx237:O177 CB7126, variant c:
+stx238:O174 EC1720a, variant d:
+stx239:ONT EBC219, variant c:
+stx240:O177 06-5121, variant c:
+stx241:O157 CB8028, variant c:
+stx242:O157 A580, variant c:
+stx243:O157 469, variant c:
+stx244:O157 A75, variant c:
+stx245:O157 310, variant c:
+stx246:O177 VTB323, variant c:
+stx247:O157 020324, variant c:
+stx248:O157 C394-03, variant c:
+stx249:O157 V20, variant c:
+stx250:O157 CS1718, variant c:
+stx251:O157 Y350 , variant c:
+stx252:O157 FLY16, variant c:
+stx253:O171 EBC287, variant c:
+stx254:O171 VTB46, variant c:
+stx255:ONT EBC289, variant c:
+stx256:OR TS27-08, variant c:
+stx257:ONT EBC275, variant d:
+stx258:O91 B2F1, variant d1:
+stx259:O83 N15432, variant d:
+stx260:O113 VTB75, variant d:
+stx261:O77 VTB91, variant d:
+stx262:O103 pVTEC7, variant d:
+stx263:OR TS06-08, variant d:
+stx264:ONT EC1871a, variant d:
+stx265:O15 88 1509, variant d:
+stx266:O113 TS03-07, variant d:
+stx267:O174 EC173b, variant d:
+stx268:O8 C466-01B, variant d:
+stx269:O91 B2F1, variant d2:
+stx270:C.freundii LM76, variant d:
+stx271:O103 CVM9322, variant d:
+stx272:O157 7279, variant d:
+stx273:O55 5905, variant d:
+stx274:O55 06-5231, variant d:
+stx275:O6 NV206, variant d:
+stx276:O2 EC604a, variant d:
+stx277:O28 MT71, variant d:
+stx278:O73 C165-02, variant d:
+stx279:O22 KY-O19, variant d:
+stx280:O113 TS28-08, variant d:
+stx281:O113 TS21-08, variant d:
+stx282:Out S-4, variant b:
+stx283:O8 S-9, variant b:
+stx284:Out HI-N, variant b:
+stx285:O93 S-5, variant b:
+stx286:O111 S-3, variant b:
+stx287:O96 S-10, variant b:
+stx288:O111 S-1, variant b:
+stx289:O96 S-7, variant b:
+stx290:O96 S-6, variant b:
+stx291:O22 3143-97, variant b:
+stx292:O118 EH250, variant b:
+stx293:O40 5293-98, variant b:
+stx294:ONT I7606, variant b:
+stx295:O128 24196-97, variant b:
+stx296:O111 PH, variant b:
+stx297:O174 031, variant b:
+stx298:O8 FHI-1106-1092, variant e:
+stx299:Out S-8, variant g:
+stx2100:O2 7v, variant g:
+stx2101:O2 HI-11, variant g:
+stx2102:O2 S86, variant g:
+stx2103:O115 F08-101-31, variant f:
+stx2104:O128 T4-97, variant f:
+stx2105:O89 HI8, variant f:
+stx2106:O101 E-D42, variant e:
+stx2107:O22 3615-99, variant e:
+stx2108:OR TS09-07, variant e:
+stx2109:O26 R107, variant e:
+stx2110:O139 S1191, variant e:
+stx2111:O101 E-D43, variant e:
+stx2112:O101 E-D68, variant e:
+stx2113:O101 E-D53, variant e:
+stx2114:ONT TS29-08, variant e:
+stx2115:ONT TS03-08, variant e:
+stx2116:O138 NN, variant e:
+stx2117:O101 CB10394, variant e:
+stx2118:O100 TS01-07, variant e:
+stx2119:O121 NP9621, variant e:
+stx2120:ONT 26725-97, variant e:
+stx2121:ONT 2771, variant e:
+stx2122:O102 STEC299, variant h:
+stx2123:O9 CB10366, variant i:
+stx2124:O33 PNUSAE005447, variant j:
+stx2125:O101 2012C-4221, variant j:
+stx2126:O159 12GZSW01, variant k:
+stx2127:O65 1610T27873, variant l:
+stx2128:O96 2001F31428, variant m:
+stx2130:O8 BMH-17-0027, variant a:
+stx2131:O146 BMH-17-0036, variant b:
+stx2132:O23 2017C-4317, variant n:
+stx2133:O85 03-3638, variant o:
+stx2135:O48STEC309, variant k:
+stx2136:O8 1509W52833, variant e:
+stx2137:O89 1810F65304, variant e:
+stx2138:O9 1706T56070, variant e:
+boa: Protease from Salmonella bongori:
+ORF3: Isoprenoid Biosynthesis:
+ORF4: Putative isopentenyl-diphosphate delta-isomerase:
+aap: Dispersin, antiaggregation protein:
+aaiC: Type VI secretion protein:
+aggR: AraC transcriptional activator:
+aatA: Dispersin transporter protein:
+agg4A: AAF/IV major fimbrial subunit:
+aggA: AAF/I major fimbrial subunit:
+aafA: AAF/II major fimbrial subunit:
+agg3A: AAF/III major fimbrial subunit:
+agg3C: Usher, AAF/III assembly unit:
+agg3D: Chaperone, AAF/III assembly unit:
+agg3B: AAF/III minor adhesin. Enterobacteria AfaD invasin protein:
+aafC: Usher, AAF/II assembly unit:
+aafD: Chaperone, AAF/II assembly unit:
+aafB: AAF/II minor adhesin. Enterobacteria AfaD invasin protein:
+agg4C: Usher, AAF/IV assembly unit:
+agg4D: Chaperone, AAF/IV assembly unit:
+agg4B: AAF/IV minor adhesin. Enterobacteria AfaD invasin protein:
+aggC: Usher, AAF/I assembly unit:
+aggD: Chaperone, AAF/I assembly unit:
+aggB: AAF/I minor adhesin. Enterobacteria AfaD invasin protein:
+aar: AggR-activated regulator:
+anr: AraC negative regulator:
+eilA: Salmonella HilA homolog:
+capU: Hexosyltransferase homolog:
+air: Enteroaggregative immunoglobulin repeat protein:
tst: toxic shock syndrome toxin-1:
ACME:arginine catabolic mobile element:
aur:aureolysin:
@@ -485,7 +925,6 @@ edinB:epidermal cell differentiation inhibitor B:
edinC:epidermal cell differentiation inhibitor C:
seb:enterotoxin B:
sea:enterotoxin A:
-sep:enterotoxin P:
sec:enterotoxin C:
sed:enterotoxin D:
see:enterotoxin E:
@@ -501,4 +940,110 @@ seo:enterotoxin O:
sep:enterotoxin P:
seq:enterotoxin Q:
ser:enterotoxin R:
-seu:enterotoxin U:
\ No newline at end of file
+seu:enterotoxin U:
+afaA: Transcriptional regulator:
+afaB: Periplasmic chaperone:
+afaC: Outer membrane usher protein:
+afaD: Afimbrial adhesion:
+afaE: Adhesin protein:
+cea: Colicin E1:
+chuA: Outer membrane hemin receptor:
+cia: Colicin ia:
+cib: Colicin ib:
+clbB: Hybrid non-ribosomal peptide / polyketide megasynthase:
+cvaC: Microcin C:
+etsC: Putative type I secretion outer membrane protein:
+focC: S fimbrial/F1C minor subunit:
+focCsfaE: S fimbrial/F1C minor subunit:
+focG: F1C adhesion:
+focI: S fimbrial/F1C minor subunit:
+fyuA: Siderophore receptor:
+hra: Heat-resistant agglutinin:
+ibeA: Invasin of brain endothelial cells:
+irp2: High molecular weight protein 2 non-ribosomal peptide synthetase:
+iucC: Aerobactin synthetase:
+iutA: Ferric aerobactin receptor:
+kpsE: Capsule polysaccharide export inner-membrane protein:
+kpsM: Polysialic acid transport protein:
+mcbA: Bacteriocin microcin B17:
+neuC: Polysialic acid capsule biosynthesis protein:
+ompT: Outer membrane protease (protein protease 7):
+papC: Outer membrane usher P fimbriae:
+sfaD: S fimbrial/F1C minor subunit:
+sfaE: S fimbrial/F1C minor subunit:
+sitA: Iron transport protein:
+tcpC: Tir domain-containing protein:
+terC: Tellurium ion resistance protein:
+traJ: Protein TraJ (Positive regulator of conjugal transfer operon):
+traT: Outer membrane protein complement resistance:
+usp: Uropathogenic specific protein:
+yfcV: Fimbrial protein:
+kpsMII: Polysialic acid transport protein; Group 2 capsule:
+kpsMIII: ABC-type polysaccharide/polyol phosphate export systems permease; Group 3 capsule:
+kpsM_K19K23: ABC-type polysaccharide/polyol phosphate export systems permease; Group 3 capsule:
+kpsM_K19: ABC-type polysaccharide/polyol phosphate export systems permease; Group 3 capsule:
+kpsM_K11: ABC-type polysaccharide/polyol phosphate export systems permease; Group 3 capsule:
+kpsMII_K94: Polysialic acid transport protein; Group 2 capsule:
+kpsMII_K52: Polysialic acid transport protein; Group 2 capsule:
+kpsMII_K23: Polysialic acid transport protein; Group 2 capsule:
+kpsMII_K5: Polysialic acid transport protein; Group 2 capsule:
+kpsMII_K4: Polysialic acid transport protein; Group 2 capsule:
+kpsMIII_K98: ABC-type polysaccharide/polyol phosphate export systems permease; Group 3 capsule:
+kpsMIII_K96: ABC-type polysaccharide/polyol phosphate export systems permease; Group 3 capsule:
+kpsMIII_K10: ABC-type polysaccharide/polyol phosphate export systems permease; Group 3 capsule:
+kpsM_K15: Polysialic acid transport protein; Group 3 capsule:
+kpsMII_K1: Polysialic acid transport protein; Group 2 capsule:
+kpsMII_K24: Polysialic acid transport protein; Group 2 capsule:
+papA_feiA_F8: Major pilin subunit F8:
+papA_ffiA_F15: Major pilin subunit F15:
+papA_ffoA_F14: Major pilin subunit F14:
+papA_fsiA_F16: Major pilin subunit F16:
+papA_fteA_F10: Major pilin subunit F10:
+papA_F12: Major pilin subunit F12:
+papA_F48: Major pilin subunit F48:
+papA_F40: Major pilin subunit F40:
+papA_F536: Major pilin subunit F536:
+papA_F7-1: Major pilin subunit F7-1:
+papA_F11: Major pilin subunit F11:
+papA_F1651A: Major pilin subunit F1651A:
+papA_F9: Major pilin subunit F9:
+papA_F43: Major pilin subunit F43:
+papA_F14: Major pilin subunit F14:
+papA_F13: Major pilin subunit F13:
+papA_F7-2: Major pilin subunit F7-2:
+papA_prsA_F12: Major pilin subunit F12:
+papA_F19: Major pilin subunit F19:
+papA_F20: Major pilin subunit F20:
+yehA: Outer membrane lipoprotein, YHD fimbriael cluster:
+yehB: Usher, YHD fimbriael cluster:
+yehC: Chaperone, YHD fimbriael cluster:
+yehD: Major pilin subunit, YHD fimbriael cluster:
+csgA: curlin major subunit CsgA:
+clpK1: heat shock survival AAA family ATPase ClpK. thermal stress survival:
+clpK2: heat shock survival AAA family ATPase ClpK. thermal stress survival:
+espy3: Non-LEE-encoded type III secreted effector:
+espy2: Non-LEE-encoded type III secreted effector:
+mrkA: type 3 fimbrial major subunit:
+aamR: AggR activated metabolic regulator:
+fdeC: intimin-like adhesin FdeC:
+shiA: homologs of the Shigella flexneri SHI-2 pathogenicity island gene shiA:
+shiB: homologs of the Shigella flexneri SHI-2 pathogenicity island gene shiA:
+C719-09_SefB: Chaperone:
+C719-09_sefC: Usher:
+C719-09_CS22: Colonization factor (CF), CS22:
+hha: hemolysin expression modulator Hha (previous rmoA):
+afpA: Major structural subunit of bundle-forming pilus, AFP fimbrial cluster:
+afpG: hypothetical protein, AFP fimbrial cluster:
+afpB: membrane protein, AFP fimbrial cluster:
+afpC: hypothetical protein, AFP fimbrial cluster:
+afpU: hypothetical protein, AFP fimbrial cluster:
+afpD: DNA binding protein type II/IV SS family protein, AFP fimbrial cluster:
+afpE: type II SS protein, AFP fimbrial cluster:
+afpF: type II/IV SS family protein, AFP fimbrial cluster:
+afpP: prepilin peptidase, AFP fimbrial cluster:
+afpH: lytic transglycosylase, AFP fimbrial cluster:
+afpI: hypothetical protein, AFP fimbrial cluster:
+afpJ: hypothetical protein, AFP fimbrial cluster:
+afpK: hypothetical protein, AFP fimbrial cluster:
+afpL: hypothetical protein, AFP fimbrial cluster:
+afpA2: major structural subunit of bundle-forming pilus, AFP fimbrial cluster:
\ No newline at end of file
=====================================
test/database/virulence_ecoli.fsa
=====================================
The diff for this file was not included because it is too large.
=====================================
test/test_results.tsv
=====================================
@@ -1,4 +1,5 @@
Database Virulence factor Identity Query / Template length Contig Position in contig Protein function Accession number
-virulence_ecoli astA 100.0 117 / 117 astA:1:AF161000 1..117 EAST-1 heat-stable toxin AF161000
-virulence_ecoli stx1A 99.79 948 / 948 stx1:1:M24352:1 1..948 Shiga toxin 1, subunit A, variant a EF079675
-virulence_ecoli stx1B 100.0 270 / 270 stx1:1:M24352:1 958..1227 Shiga toxin 1, subunit B, variant a AM230663
+virulence_ecoli astA 100.0 117 / 117 astA:1:AF161000 1..117 Heat-stable enterotoxin EAST-1 AF161000
+virulence_ecoli stx1-S.-sonnei-CB7888 99.84 1227 / 1227 stx1:1:M24352:1 1..1227 stx1-S.-sonnei-CB7888 AJ279086
+virulence_ecoli stx1a-O157-GPU96MM 99.84 1227 / 1227 stx1:1:M24352:1 1..1227 stx1a-O157-GPU96MM AB035142
+stx stx1 100.0 1227 / 1227 stx1:1:M24352:1 1..1227 S.dysenteriae 60R M24352
=====================================
virulencefinder.py
=====================================
@@ -180,6 +180,10 @@ parser.add_argument("-x", "--extented_output",
"template and query hits in fasta and a tab "
"seperated file with gene profile results"),
action="store_true")
+parser.add_argument("--overlap",
+ help=("Genes are allowed to overlap this number of"
+ "nucleotides."),
+ default=30)
parser.add_argument("--speciesinfo_json",
help=("Argument used by the cge pipeline. It takes a list"
" in json format consisting of taxonomy, from "
@@ -362,7 +366,8 @@ elif file_format == "fasta":
# Call BLASTn
method_obj = Blaster(infile, databases, db_path, tmp_dir,
- min_cov, threshold, method_path, cut_off=False)
+ min_cov, threshold, method_path, cut_off=False,
+ allowed_overlap=args.overlap)
else:
sys.exit("Input file must be fastq or fasta format, not " + file_format)
View it on GitLab: https://salsa.debian.org/med-team/virulencefinder/-/compare/13e201e80cd2cd995d0bef811ebcffe96d036da6...dba5c00acbdeec8328def9e4fb8684d808eb3405
--
View it on GitLab: https://salsa.debian.org/med-team/virulencefinder/-/compare/13e201e80cd2cd995d0bef811ebcffe96d036da6...dba5c00acbdeec8328def9e4fb8684d808eb3405
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