AlleleFinder: a tool for identifying allele genes from polyploid genome.

Introduction

This software is used for identifying allele genes from polyploid genome.

Overview

Dependencies

Software:

• MCScanX
• GMAP
• NCBI BLAST+

Notice: these software should be added to the PATH Environment Variable.

Installation

cd /path/to/install
git clone https://github.com/sc-zhang/AlleleFinder.git
chmod +x AlleleFinder/allelefinder.py
# Optional
echo 'export PATH=/path/to/install/AlleleFinder:$PATH' >> ~/.bash_profile
source ~/.bash_profile

Usage

1. main program

usage: allelefinder.py [-h] {construct,cleanup,stat,adjust} ...

options:
  -h, --help            show this help message and exit

Sub commands:
  {construct,cleanup,stat,adjust}
    construct           Construct allele table
    cleanup             Remove same CDS from cds, pep and gff3 files
    stat                Statistic allele table
    adjust              Adjust allele table with too many genes be marked as paralog

2. construct allele table

Usage

usage: allelefinder.py construct [-h] -r REF -d REF_CDS -f REF_GFF3 -c CDS -g GFF3 -n NUM_ALLELE [-m] [--ovlp_ratio OVLP_RATIO] [-b BLAST_COUNT] [--blast_identity BLAST_IDENTITY] [-e TE] [-j TE_OVERLAP] [--paralog_only] [-w WORKDIR] [-t THREADS]

options:
  -h, --help            show this help message and exit
  -r REF, --ref REF     reference fasta
  -d REF_CDS, --ref_cds REF_CDS
                        CDS fasta of ref
  -f REF_GFF3, --ref_gff3 REF_GFF3
                        GFF3 file of ref
  -c CDS, --cds CDS     CDS fasta of polyploid
  -g GFF3, --gff3 GFF3  GFF3 file of polyploid
  -n NUM_ALLELE, --num_allele NUM_ALLELE
                        number of allele
  -m, --is_mono         if your reference fasta is mono assembly of polyploid, add this argument
  --ovlp_ratio OVLP_RATIO
                        threshold of gene pair overlap regions identified by GMAP, default: 0.8
  -b BLAST_COUNT, --blast_count BLAST_COUNT
                        blast count, default: 2
  --blast_identity BLAST_IDENTITY
                        threshold of blast identity, default: 80
  -e TE, --TE TE        TE gff3 for filtering, default: ""
  -j TE_OVERLAP, --TE_overlap TE_OVERLAP
                        threshold of TE overlap, default: 0.3, only effect when TE is not NULL
  --paralog_only        do TE filter only on paralog genes
  -w WORKDIR, --workdir WORKDIR
                        workdir, default: wrkdir
  -t THREADS, --threads THREADS
                        threads, default: 12

Notice:

1. the name of Chromosomes should be like: Chr01X, "X" means consecutive uppercase letters from A to Z, indicates different alleles, for example, if there are 4 alleles, the names should be: Chr01A,Chr01B,Chr01C,Chr01D.
2. the gff3 files must contain "gene" records, or you can use "sed" command to change "mRNA" to "gene" for some downloaded gff3 files.
3. there must no '-' in gene id.

Results

1. Without TE filter

   allele.adjusted.txt is the file contain all allele genes

   allele.adjusted.*.stat are the statistics information of allele

2. With TE filter

   allele.adjusted.nonTEs.txt is the file contain all allele genes

   allele.adjusted.nonTEs.*.stat are the statistics information of allele

3. Statistic

usage: allelefinder.py stat [-h] -i INPUT -g GFF3 -o OUTPUT

options:
  -h, --help            show this help message and exit
  -i INPUT, --input INPUT
                        Input allele table
  -g GFF3, --gff3 GFF3  GFF3 file of polyploid
  -o OUTPUT, --output OUTPUT
                        Prefix of output file

4. Additional

• Cleanup sequence

If user want to remove the duplicate genes with same CDS sequence, the "cleanup" would deal with them and only one gene would be kept randomly.

usage: allelefinder.py cleanup [-h] --in_cds IN_CDS [--in_pep IN_PEP] --in_gff3 IN_GFF3 --out_cds OUT_CDS [--out_pep OUT_PEP] --out_gff3 OUT_GFF3

options:
  -h, --help           show this help message and exit
  --in_cds IN_CDS      Input CDS file
  --in_pep IN_PEP      Input PEP file
  --in_gff3 IN_GFF3    Input GFF3 file
  --out_cds OUT_CDS    Output CDS file
  --out_pep OUT_PEP    Output PEP file
  --out_gff3 OUT_GFF3  Output GFF3 file

Notice: CDS file and GFF3 file are required, PEP file is optional.

• Adjust paralog genes

If there are too many genes be marked with paralog, you can use command below to pull them down as new alleles

usage: allelefinder.py adjust [-h] -i INPUT -m MIN_NUM -o OUTPUT

options:
  -h, --help            show this help message and exit
  -i INPUT, --input INPUT
                        Input allele table
  -m MIN_NUM, --min_num MIN_NUM
                        Minium number of genes, which means the number of genes marked as paralog that distribute in different allele should be pulled down as new allele genes
  -o OUTPUT, --output OUTPUT
                        Output allele table