This script is intended to match potential antibiotic resistance found in WGS sample to the sequence in the WGS data and run a blast search to determine what species it may have come from. Returns a CSV file of the data. Designed for use at the Mills Lab @ UC Davis.
python resParse.py [HTM_FILE] [CONTIG_FILE] [SAMPLE_ID] [NUMBER_OF_MATCHES] [IDENTITY_THRESHOLD] [OUT_DIR]
python /home/sakre/projects/Res_BLAST/resParse.py test.htm final.contigs.fa DMDT001A 3 .9 /home/sakre/projects/Res_BLAST
Example bash file to run script titled 'resParse.sh'
Make sure to load biopython module, other dependencies are already loaded on the Farm Include full path to files needed Sample ID can be any string used to identify the input data Identity Threshold must be between 0 and 1
Currently runs on the NCBI database so I do not suggest running too many of these in parallel in order to not overload their servers
Sincerely,
Samir Akre
www.samirakre.com