Metadata-Version: 2.1
Name: seqPresenceAbsence
Version: 0.2.2
Summary: Package for checking for the presence/absence of markers against a set of samples
Home-page: https://github.com/bfssi-forest-dussault/SeqPresenceAbsence
Author: Forest Dussault
Author-email: forest.dussault@canada.ca
License: UNKNOWN
Description: # seqPresenceAbsence
        
        ### Requirements
        - Python >= 3.6
        - Perl 5 (required for FASconCAT-G)
        - [ncbi-blast+](https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download) (makeblastdb and blastn must be in your $PATH)
        - [MUSCLE](https://www.drive5.com/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
Platform: UNKNOWN
Requires-Python: ~=3.6
Description-Content-Type: text/markdown
