This software is used for identifying allele genes from polyploid genome.
Software:
Notice: these software should be added to the PATH Environment Variable or create an environment use conda with environment.yaml.
- Install latest release
# Download latest release
cd /path/to/install
wget https://github.com/sc-zhang/AlleleFinder/archive/refs/tags/V1.2.1.tar.gz
tar zxvf V1.2.1.tar.gz
chmod +x AlleleFinder-1.2.1/allelefinder.py- Install development version
# Clone development repository
cd /path/to/install
git clone https://github.com/sc-zhang/AlleleFinder.git
chmod +x AlleleFinder/allelefinder.py- Optional
# Optional, create environment with conda
conda env create -f environment.yaml
conda activate allelefinder_env
# Optional, add to PATH environment variable
echo 'export PATH=/path/to/install/AlleleFinder:$PATH' >> ~/.bash_profile
source ~/.bash_profileusage: allelefinder.py [-h] [-v] {construct,stat,cleanup,rescue,adjust} ...
options:
-h, --help show this help message and exit
-v, --version show program's version number and exit
Sub commands:
{construct,stat,cleanup,rescue,adjust}
construct Construct allele table
stat Statistic allele table
cleanup Remove duplicated sequences from cds, pep and gff3 files
rescue Rescue genes with duplicated sequences which be cleaned by "cleanup" method
adjust Adjust allele table with too many genes be marked as paralogusage: 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_ROUND] [--blast_threshold BLAST_THRESHOLD] [--reciprocal] [-e TE] [-j TE_OVERLAP] [--paralog_only] [-w WORKDIR]
[-t THREADS]
options:
-h, --help show this help message and exit
-r, --ref REF reference fasta
-d, --ref_cds REF_CDS
CDS fasta of ref
-f, --ref_gff3 REF_GFF3
GFF3 file of ref
-c, --cds CDS CDS fasta of polyploid
-g, --gff3 GFF3 GFF3 file of polyploid
-n, --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 coordinate overlap identified by GMAP, default: 0.8
-b, --blast_round BLAST_ROUND
blast round, default: 2
--blast_threshold BLAST_THRESHOLD
threshold of blast result which defined as matches*2/(query_length+reference_length), default: 0.5
--reciprocal add genes to allele table by blast with reciprocal, if set, blast_threshold would be ignored, default: False
-e, --TE TE TE gff3 for filtering, default: ""
-j, --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, default: wrkdir
-t, --threads THREADS
threads, default: 12Notice:
- 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.
- the gff3 files must contain "gene" records, or you can use "sed" command to change "mRNA" to "gene" for some downloaded gff3 files.
- there must no '-' in gene id.
-
Without TE filter
allele.adjusted.txt is the file contain all allele genes
allele.adjusted.*.stat are the statistics information of allele
-
With TE filter
allele.adjusted.nonTEs.txt is the file contain all allele genes
allele.adjusted.nonTEs.*.stat are the statistics information of allele
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- Cleanup sequence
If user want to remove the duplicate genes with same CDS/PEP 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 [--by_pep]
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
--by_pep filter by PEP sequencesNotice: CDS file and GFF3 file are required, PEP file is optional.
- Rescue genes which be cleaned up
If the cleanup method was applied, user may want to add genes which be cleanup onto allele table again, the rescue method would to do like this.
usage: allelefinder.py rescue [-h] -i INPUT --gff3 GFF3 --cds CDS [--pep PEP] -o OUTPUT
options:
-h, --help show this help message and exit
-i, --input INPUT Input allele table
--gff3 GFF3 Input GFF3 file before cleanup
--cds CDS Input CDS file before cleanup
--pep PEP Input PEP file before cleanup, required when cleanup was run with --by_pep
-o, --output OUTPUT Output rescued allele table- 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