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
pip3 install CampyCPS
comming soon...
- BLAST+ >2.7.0
you should add BLAST in your PATH
Following this tutorial: Add blast into your windows PATH
The easyest way to install blast is:
conda install -c bioconda blast
The first time when running CampyCPS, you should use CampyCPS -init command to initialize your database.
The default database including the following 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) |
# 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