Package for checking for the presence/absence of markers against a set of samples
- Python >= 3.6
- Perl 5 (required for FASconCAT-G)
- ncbi-blast+ (makeblastdb and blastn must be in your $PATH)
- MUSCLE (muscle must be in your $PATH)
pip install seqPresenceAbsence
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: 0.2.0. 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.
This package includes a distribution of FASconCAT-G v1.04, developed by Patrick Kück.
- Kück P., Meusemann K. (2010): FASconCAT: Convenient handling of data matrices. Mol. Phylogen. Evol. 56:1115-1118
- Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput Nucleic Acids Res. 32(5):1792-1797
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