Version: 0.1.0
License: GPLv3
USAGE: python get_spa_type.py fasta_file.fa
Prints spa type to stdout - egenomics letter combination and then the ridom spa type.
If multiple pcr products are found will print spa types for each product.
Will download sparepeats.fasta and spatypes.txt from the ridom server to repository directory if files not provided or already in directory.
optional arguments:
-h, --help show this help message and exit
-r REPEAT_FILE, --repeat_file REPEAT_FILE
List of spa repeats
(http://spa.ridom.de/dynamic/sparepeats.fasta)
-o REPEAT_ORDER_FILE, --repeat_order_file REPEAT_ORDER_FILE
List spa types and order of repeats
(http://spaserver2.ridom.de/dynamic/spatypes.txt)
-f FASTA [FASTA ...], --fasta FASTA [FASTA ...]
List of one or more fasta files.
-g GLOB, --glob GLOB Uses unix style pathname expansion to run spa typing
on all files. If your shell autoexpands wildcards use
-f.
-s, --skip_enrich Skip enrichment (for already enriched (sanger) DNA).
-c, --clean_output Make output clean
--version show program's version number and exit
Just clone this repository or download the python script
Only requires python 2.7.x
If this script is unable to download files over HTTP you will need to provide the repeat sequence and order files from the ridom spa server.
The script searches for 50bp to 5000bp sequences produced by the following primer sets
TAAAGACGATCCTTCGGTGAG, CAGCAGTAGTGCCGTTTGCTT
AGACGATCCTTCGGTGAGC, GCTTTTGCAATGTCATTTACTG
ATAGCGTGATTTTGCGGTT, CTAAATATAAATAATGTTGTCACTTGGA
CAACGCAATGGTTTCATCCA, GCTTTTGCAATGTCATTTACTG
If an enriched sequence is found by a primer set, subsequent primer sets are not used.
The repeat sequences and repeat orders found on http://spaserver2.ridom.de/ are used to identify the spa type of each enriched sequence.
Ridom spa type and the egenomics repeat sequence are then reported back to the user.
written by mjsull.