CampyCPS 1.0.2

Campylobacter CPS relevant gene analysis tool

CampyCPS

CampyCPS is a tool for Campylobacter CPS relevant genes identification.

usage: CampyCPS -i <genome assemble directory> -o <output_directory>

Author: Qingpo Cui(SZQ Lab, China Agricultural University)

optional arguments:
  -h, --help      show this help message and exit
  -i I            <input_path>: the PATH to the directory of assembled genome files. Could not use with -f
  -f F            <input_file>: the PATH of assembled genome file. Could not use with -i
  -o O            <output_directory>: output PATH
  -minid MINID    <minimum threshold of identity>, default=95
  -mincov MINCOV  <minimum threshold of coverage>, default=90
  -init      <initialize the reference database>
  -t T            <number of threads>: default=8
  -v, --version   Display version

Installation

Using pip

pip3 install CampyCPS

Using conda

comming soon...

Dependency

• BLAST+ >2.7.0

you should add BLAST in your PATH

Blast installation

Windows

Following this tutorial: Add blast into your windows PATH

Linux/Mac

The easyest way to install blast is:

conda install -c bioconda blast

Usage

The first time when running CampyCPS, you should use CampyCPS -init command to initialize your database.

The default database including the following genes.

CPS relevant genes

Loci	Gene/Aliases	Full name/product
CAMP1067	waaF	Heptosyltransferase II (K02843)
CAMP1326	cysC	Putative adenylylsulfate kinase (K00860)
CAMP1327	Cj1416c	Putative sugar nucleotidyltransferase
CAMP1328	Cj1417c	Putative amidotransferase (K07010)
CAMP1329	Cj1418c	Putative transferase
CAMP1330	Cj1419c	Putative methyltransferase
CAMP1331	Cj1420c	Putative methyltransferase
CAMP1332	Cj1421c	Putative sugar transferase
CAMP1333	Cj1422c	Putative sugar transferase
CAMP1334	hddC	Putative D-glycero-D-manno-heptose 1-phosphate guanosyltransferase (K15669)
CAMP1335	gmhA2	Phosphoheptose isomerase (K03271)
CAMP1336	hddA	Putative D-glycero-D-manno-heptose 7-phosphate kinase (K07031)
CAMP1337	Cj1426c	Putative methyltransferase family protein
CAMP1338	Cj1427c	Putative sugar-nucleotide epimerase/dehydratease
CAMP1339	fcl	GDP-L-fucose synthetase (K02377)
CAMP1340	Cj1429c	Hypothetical protein Cj1429c
CAMP1341	rfbC	Putative dTDP-4-dehydrorhamnose 3,5-epimerase (K01790)
CAMP1342	hddC	Capsular polysaccharide heptosyltransferase
CAMP1343	Cj1432c	Putative sugar transferase
CAMP1344	Cj1433c	Hypothetical protein Cj1433c
CAMP1345	Cj1434c	Putative sugar transferase
CAMP1346	Cj1435c	Putative phosphatase
CAMP1347	Cj1436c	Aminotransferase
CAMP1348	Cj1437c	Aminotransferase (K00817)
CAMP1349	Cj1438c	Putative sugar transferase
CAMP1350	glf	UDP-galactopyranose mutase (K01854)
CAMP1351	Cj1440c	Putative sugar transferase
CAMP1352	kfiD	UDP-glucose 6-dehydrogenase (K00012)
CAMP1353	Cj1442c	Putative sugar transferase
CAMP1354	kpsF	D-arabinose 5-phosphate isomerase (K06041)
CAMP1355	kpsD	Capsule polysaccharide export system periplasmic protein
CAMP1356	kpsE	Capsule polysaccharide export system inner membrane protein (K10107)
CAMP1357	kpsT	Capsule polysaccharide export ATP-binding protein (K09689)
CAMP1358	kpsM	Capsule polysaccharide export system inner membrane protein (K09688)

Example

# Single Genome Mode
CampyCPS -f /PATH_TO_ASSEBLED_GENOME/sample.fa -o PATH_TO_OUTPUT

# Batch Mode
CampyCPS -i /PATH_TO_ASSEBLED_GENOME_DIR -o PATH_TO_OUTPUT