PyamilySeq 0.3.0

PyamilySeq - A a tool to look for sequence-based gene families identified by clustering methods such as CD-HIT, DIAMOND, BLAST or MMseqs2.

PyamilySeq - !BETA!

PyamilySeq (Family Seek) is a Python tool for clustering gene sequences into families based on sequence similarity identified by tools such as CD-HIT, DIAMOND or MMseqs2. This work is an extension of the gene family / pangenome tool developed for the StORF-Reporter publication in NAR (https://doi.org/10.1093/nar/gkad814).

Features

• Clustering: Supports input from CD-HIT formatted files as well as TSV and CSV Edge List formats.
• Reclustering: Allows for the addition of new sequences post-initial clustering.
• Output: Generates a gene 'Roary' presence-absence CSV formatted file for downstream analysis.

Installation

PyamilySeq requires Python 3.6 or higher. Install dependencies using pip:

pip install PyamilySeq

Usage - Menu

usage: PyamilySeq_Species.py [-h] -c CLUSTERS -f {CD-HIT,CSV,TSV} [-w WRITE_FAMILIES] [-con CON_CORE] [-fasta FASTA] [-rc RECLUSTERED] [-st SEQUENCE_TAG]
                             [-groups CORE_GROUPS] [-gpa GENE_PRESENCE_ABSENCE_OUT] [-verbose {True,False}] [-v]

PyamilySeq v0.3.0: PyamilySeq Run Parameters.

Required Arguments:
  -c CLUSTERS           Clustering output file from CD-HIT, TSV or CSV Edge List
  -f {CD-HIT,CSV,TSV}   Which format to use (CD-HIT or Comma/Tab Separated Edge-List (such as MMseqs2 tsv output))

Output Parameters:
  -w WRITE_FAMILIES     Default - No output: Output sequences of identified families (provide levels at which to output "-w 99,95" - Must provide FASTA file
                        with -fasta
  -con CON_CORE         Default - No output: Output aligned and concatinated sequences of identified families - used for MSA (provide levels at which to
                        output "-w 99,95" - Must provide FASTA file with -fasta
  -fasta FASTA          FASTA file to use in conjunction with "-w" or "-con"

Optional Arguments:
  -rc RECLUSTERED       Clustering output file from secondary round of clustering
  -st SEQUENCE_TAG      Default - "StORF": Unique identifier to be used to distinguish the second of two rounds of clustered sequences
  -groups CORE_GROUPS   Default - ('99,95,15'): Gene family groups to use
  -gpa GENE_PRESENCE_ABSENCE_OUT
                        Default - False: If selected, a Roary formatted gene_presence_absence.csv will be created - Required for Coinfinder and other
                        downstream tools

Misc:
  -verbose {True,False}
                        Default - False: Print out runtime messages
  -v                    Default - False: Print out version number and exit

Clustering Analysis

To perform clustering analysis:

python pyamilyseq.py -c clusters_file -f format

Replace clusters_file with the path to your clustering output file and format with one of: CD-HIT, CSV, or TSV.

Reclustering

To add new sequences and recluster:

PyamilySeq -c clusters_file -f format --reclustered reclustered_file

Replace reclustered_file with the path to the file containing additional sequences.

Output

PyamilySeq generates various outputs, including:

• Gene Presence-Absence File: This CSV file details the presence and absence of genes across genomes.
• FASTA Files for Each Gene Family:

Gene Family Groups

After analysis, PyamilySeq categorizes gene families into several groups:

• First Core: Gene families present in all analysed genomes initially.
• Extended Core: Gene families extended with additional sequences.
• Combined Core: Gene families combined with both initial and additional sequences.
• Second Core: Gene families identified only in the additional sequences.
• Only Second Core: Gene families exclusively found in the additional sequences.