seqPresenceAbsence 0.2.2

Package for checking for the presence/absence of markers against a set of samples

seqPresenceAbsence

Requirements

• 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)

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: 0.2.0.

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.

Notes

This package includes a distribution of FASconCAT-G v1.04, developed by Patrick Kück.

References

• 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