kmerator2 0.4.1b0

Find specific gene or transcript kmers. And more.

Kmerator2

Prototype for decomposition of transcript or gene sequences and extraction of their specific k-mers

Kmerator is a prototype tool designed for the prediction of specific k-mers (also called tags) from input sequences, considering a reference genome and an ENSEMBL-like transcriptome. From these specific k-mers, it also outputs their corresponding specific contigs which are sequences of consecutive k-mers (overlapping length between k-mers must be k-1, otherwise, it's a new contig). Kmerator first uses Jellyfish [1] to create 2 requestable indexes from the reference genome and transcriptome, and second, decomposes your input transcript or gene sequences to count the occurences of each k-mer in the genome and transcriptome. Number of occurrences are then interpreted, in different manners, to select specific k-mer from your input.

Kmerator strictly depends on a reference genome (fasta or jellyfish index format) and on an Ensembl fasta format transcriptome, you can find it there: https://www.ensembl.org/info/data/ftp/index.html. For a more complete k-mer filtering, we advice to merge the coding (cDNA) and non-coding (ncRNA) as one unique reference transcript.

Kmerator2 is new version of kmerator, written in python3 (julia with first version), several options have changed. It is compatible with last versions of Ensembl transcriptome (version 103 max for kmerator). The output is improved and a file report is produced.

Dependencies

• Python >= v3.6
• Jellyfish >= 2.0

Installation

Solution 1 (preferred)

Install with pip

pip3 install kmerator2

If installed as user, ensure the directory $HOME/.local/bin is in your $PATH.

Solution 2

Installation from github

git clone https://github.com/Transipedia/kmerator2.git
cp kmerator2/kmerator/kmerator.py /usr/local/bin/kmerator2  # or somewhere in your $PATH
cp kmerator2/kmerator/ktools.py /usr/local/bin/ktools       # or somewhere in your $PATH

Usage

kmerator2 [-h] (-s SELECTION [SELECTION ...] | -f FASTA_FILE) -g GENOME -t TRANSCRIPTOME   
			-l {gene,transcript,chimera} [-a APPRIS] [-u] [-k KMER_LENGTH] [--stringent]  
			[--threshold THRESHOLD] [-o OUTPUT] [-c CORES] [--verbose] [-v]

How use kmerator2

There are two main cases:

• you find for specific k-mers for annotated genes or transcripts : use the --selection option, followed by:
  • the list of gene and/or transcripts
  • or a file with the list of genes/transcripts
• you find for specific k-mers of unannotated sequences : use the --fasta-file option, followed by a fasta file containing yours requests. In case of you focuses on chimeras, add the --chimera option

Differences between genes and transcripts

• When you find for a gene (symbol or Ensembl name), kmerator fetch sequence of its canonical transcript, extracts kmers and keep those that found only in the gene.
• When you find for a transcript, kmerator only keeps the kmer found in the transcript, and only in that transcript. If isoforms completely cover the transcript, no kmer will be kept.

arguments

optional arguments:
  -h, --help            show this help message and exit
  -s SELECTION [SELECTION ...], --selection SELECTION [SELECTION ...]
                        list of gene IDs or transcript IDs (ENST, ENS or gene Symbol) to select
                        inside your fasta transcriptome file and that you want to
                        extract specific kmers from. For genes, kmerator search specific kmers
                        along the gene. For transcripts, it search specific kmers to
                        the transcript. You can also give a file with yours genes/transcripts
                        separated by space, tab or newline. If you want to use your
                        own unannotated sequences, you must give your fasta file with 
                        --fasta_file option.
  -f FASTA_FILE, --fasta-file FASTA_FILE
                        Use this option when yours sequences are unannonated or provided by a
                        annotation file external from Ensembl. Otherwise, use 
                        --selection option.
  -g GENOME, --genome GENOME
                        genome fasta file or jellyfish index (.jf) to use for k-mers requests.
  -t TRANSCRIPTOME, --transcriptome TRANSCRIPTOME
                        transcriptome fasta file (ENSEMBL fasta format ONLY) to use for k-mers
                        request and transcriptional variants informations.
  -j JELLYFISH_TRANSCRIPTOME, --jellyfish-transcriptome JELLYFISH_TRANSCRIPTOME
                        if your transcriptome (-t option) has already been converted by
                        jellyfish as a jf file, this avoids redoing the operation (be
                        careful,it must be the same transcriptome!). if not set, kmerator find
                        for a jellyfish index with the same name (extension .fa -> .jl), and if
                        not it creates a index in the output directory (-o).
  -c SPECIE, --specie SPECIE
                        indicate a specie referenced in Ensembl, to help, follow the link
                        https://rest.ensembl.org/documentation/info/species. You can use
                        the 'name', the 'display_name' or any 'aliases'. For example human,
                        homo_sapiens or homsap are valid.
  -k KMER_LENGTH, --kmer-length KMER_LENGTH
                        k-mer length that you want to use (default 31).
  --chimera             Only if with --fasta-file option.
  --stringent           FOR ANNOTATED GENE ONLY: use this option if you want to select 
  						 gene-specific k-mers present in ALL known transcripts for your gene.
                        If false, a k-mer is considered as gene-specific if present in at least
                        one isoform of your gene of interest.
  --threshold THRESHOLD
                        FOR ANNOTATED GENE ONLY: minimum fraction of annotated transcripts, for
                        a given gene, containing this kmer to keep it (default: 0)
  -o OUTPUT, --output OUTPUT
                        output directory (default: 'output')
  -p PROCS, --procs PROCS
                        run n processes simultaneously (default: 1)
  -d, --debug           if you want some details while Kmerator is running.
  --keep                keep intermediate files (sequences, indexes, separate tags and contigs 
                        files).
  -v, --version         show program's version number and exit

Nota: kmerator2 has lost the --level option specifying the level (gene, transcript or chimera). It's now semi-automatic: if you give a gene symbol or a ENSGxxx the level is gene, if you give a ENSTxxx the level is transcript. You can mix gene symbols, ENSGxxxx and ENSTxxx. You need to use the --fasta-file in association with --chimera to operate at chimera level.

ktools, a companion tool for kmerator

ktools can help you with some kmerator related tasks. For example, build the transcriptome could be tricky and repetitive (updated quaterly).

usage: ktools [-h] [-v] {mk-transcripts} ...

positional arguments:
  {mk-transcripts}
    mk-transcripts  make transcriptome

optional arguments:
  -h, --help        show this help message and exit
  -v, --version     show program's version number and exit

build transcriptome

ktools get cDNA and ncRNA Ensembl transcriptome fasta files (last release by default), it concatene this files and remove alternative chromosomes.

References

[1] Guillaume Marçais, Carl Kingsford, A fast, lock-free approach for efficient parallel counting of occurrences of k-mers, Bioinformatics, Volume 27, Issue 6, 15 March 2011, Pages 764–770, https://doi.org/10.1093/bioinformatics/btr011 [2] Rodriguez JM, et al. Nucleic Acids Res. Database issue; 2017 Oct 23