Package for checking for the presence/absence of markers against a set of samples
Project description
seqPresenceAbsence
Requirements
- Python 3.6
- ncbi-blast+ (makeblastdb and blastn must be in your $PATH)
Installation
pip install seqPresenceAbsence
Usage
Usage: seqPresenceAbsence [OPTIONS]
seqPresenceAbsence is a simple script for querying an input nucleotide
FASTA file against a database of sequences. Will return an .xlsx and .csv
report of presence/absence of the sequences. Version: 0.1.3.
Options:
-i, --indir PATH Path to directory containing FASTA files you want
to query [required]
-t, --targets PATH Path to multi-FASTA containing targets of
interest [required]
-o, --outdir PATH Root directory to store all output files
[required]
-p, --perc_identity FLOAT Equivalent to the -perc_identity argument in
blastn. Defaults to 95.00.
-k, --keep_db_seqs Set this flag to keep the target sequence in
addition to the query sequence from BLAST.
-v, --verbose Set this flag to enable more verbose logging.
--version Specify this flag to print the version and exit.
--help Show this message and exit.
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