# 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](http://82.157.185.121:22300/shares/BevQrP0j8EXn76p7CwfheA)
### 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
```
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"description": "# CampyCPS\n\n\nCampyCPS is a tool for Campylobacter CPS relevant genes identification.\n\n```\nusage: CampyCPS -i <genome assemble directory> -o <output_directory>\n\nAuthor: Qingpo Cui(SZQ Lab, China Agricultural University)\n\noptional arguments:\n -h, --help show this help message and exit\n -i I <input_path>: the PATH to the directory of assembled genome files. Could not use with -f\n -f F <input_file>: the PATH of assembled genome file. Could not use with -i\n -o O <output_directory>: output PATH\n -minid MINID <minimum threshold of identity>, default=95\n -mincov MINCOV <minimum threshold of coverage>, default=90\n -init <initialize the reference database>\n -t T <number of threads>: default=8\n -v, --version Display version\n```\n\n\n## Installation\n### Using pip\npip3 install CampyCPS\n\n### Using conda\ncomming soon...\n\n## Dependency\n- BLAST+ >2.7.0\n\n**you should add BLAST in your PATH**\n\n\n## Blast installation\n### Windows\n\n\nFollowing this tutorial:\n[Add blast into your windows PATH](http://82.157.185.121:22300/shares/BevQrP0j8EXn76p7CwfheA)\n\n### Linux/Mac\nThe easyest way to install blast is:\n\n```\nconda install -c bioconda blast\n```\n\n## Usage\n\nThe first time when running CampyCPS, you should use **CampyCPS -init** command to initialize your database.\n\n**The default database including the following genes.**\n\n### CPS relevant genes\n| Loci | Gene/Aliases | Full name/product |\n|----------|----------------|-----------------------------------------------------------------------------|\n| CAMP1067 | waaF | Heptosyltransferase II (K02843) |\n| CAMP1326 | cysC | Putative adenylylsulfate kinase (K00860) |\n| CAMP1327 | Cj1416c | Putative sugar nucleotidyltransferase |\n| CAMP1328 | Cj1417c | Putative amidotransferase (K07010) |\n| CAMP1329 | Cj1418c | Putative transferase |\n| CAMP1330 | Cj1419c | Putative methyltransferase |\n| CAMP1331 | Cj1420c | Putative methyltransferase |\n| CAMP1332 | Cj1421c | Putative sugar transferase |\n| CAMP1333 | Cj1422c | Putative sugar transferase |\n| CAMP1334 | hddC | Putative D-glycero-D-manno-heptose 1-phosphate guanosyltransferase (K15669) |\n| CAMP1335 | gmhA2 | Phosphoheptose isomerase (K03271) |\n| CAMP1336 | hddA | Putative D-glycero-D-manno-heptose 7-phosphate kinase (K07031) |\n| CAMP1337 | Cj1426c | Putative methyltransferase family protein |\n| CAMP1338 | Cj1427c | Putative sugar-nucleotide epimerase/dehydratease |\n| CAMP1339 | fcl | GDP-L-fucose synthetase (K02377) |\n| CAMP1340 | Cj1429c | Hypothetical protein Cj1429c |\n| CAMP1341 | rfbC | Putative dTDP-4-dehydrorhamnose 3,5-epimerase (K01790) |\n| CAMP1342 | hddC | Capsular polysaccharide heptosyltransferase |\n| CAMP1343 | Cj1432c | Putative sugar transferase |\n| CAMP1344 | Cj1433c | Hypothetical protein Cj1433c |\n| CAMP1345 | Cj1434c | Putative sugar transferase |\n| CAMP1346 | Cj1435c | Putative phosphatase |\n| CAMP1347 | Cj1436c | Aminotransferase |\n| CAMP1348 | Cj1437c | Aminotransferase (K00817) |\n| CAMP1349 | Cj1438c | Putative sugar transferase |\n| CAMP1350 | glf | UDP-galactopyranose mutase (K01854) |\n| CAMP1351 | Cj1440c | Putative sugar transferase |\n| CAMP1352 | kfiD | UDP-glucose 6-dehydrogenase (K00012) |\n| CAMP1353 | Cj1442c | Putative sugar transferase |\n| CAMP1354 | kpsF | D-arabinose 5-phosphate isomerase (K06041) |\n| CAMP1355 | kpsD | Capsule polysaccharide export system periplasmic protein |\n| CAMP1356 | kpsE | Capsule polysaccharide export system inner membrane protein (K10107) |\n| CAMP1357 | kpsT | Capsule polysaccharide export ATP-binding protein (K09689) |\n| CAMP1358 | kpsM | Capsule polysaccharide export system inner membrane protein (K09688) |\n\n### Example\n```\n# Single Genome Mode\nCampyCPS -f /PATH_TO_ASSEBLED_GENOME/sample.fa -o PATH_TO_OUTPUT\n\n# Batch Mode\nCampyCPS -i /PATH_TO_ASSEBLED_GENOME_DIR -o PATH_TO_OUTPUT\n```\n\n\n",
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