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A package to detect IBS regions

Project description

IBSpy

Python package Maintainability

Python library to identify Identical By State regions

Installyng IBSpy

There easiest way to install IBSpy is to use pip3.

pip3 install IBSpy

If pip3 fails, you can clone the project and compiling it with:

pip3 install cython biopython pyfaidx
python3 setup.py develop

Then you should have the IBSpy command available.

Preparing the databases

IBSpy requires to have a kmer database from the sequencing files. Currently two formats are supported:

  1. Jellyfish: Follow the instructions in its website
  2. kmerGWAS: Has an adhoc file format that contains only the kmers in a binary representation, sorted. This option is faster than the jellyfish version, but creating the kmer table is less straight forward. The manual is here.

Running IBSPy

IBSpy has relatively few options, you can look at them with the ---help command.

IBSPy --help
usage: IBSPy [-h] [-w WINDOW_SIZE] [-k KMER_SIZE] [-d DATABASE] [-r REFERENCE]
             [-z] [-o OUTPUT] [-f {kmerGWAS,jellyfish}]

optional arguments:
  -h, --help            show this help message and exit
  -w WINDOW_SIZE, --window_size WINDOW_SIZE
                        window size to analyze
  -k KMER_SIZE, --kmer_size KMER_SIZE
                        Kmer size of the database
  -d DATABASE, --database DATABASE
                        Kmer database
  -r REFERENCE, --reference REFERENCE
                        The reference with the position of the kmers
  -z, --compress        When an ouput file is present, it is compressed as .gz
  -o OUTPUT, --output OUTPUT
                        Output file. If missing, the ouptut is sent to stdout
  -f {kmerGWAS,jellyfish}, --database_format {kmerGWAS,jellyfish}
                        Database format (kmerGWAS, jellyfish)

To generate the table with the number of observed kmers and variants run the following command, using the kmer database from kmerGWAS use the following command:

 IBSpy --output "kmer_windows_LineXXX.tsv.gz" -z --database kmers_with_strand  --reference arinaLrFor.fa --window_size 50000 --compress

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