caspredict 0.3.1

Automatic detection and subtyping of CRISPR-Cas operons

CasPredict

Detect CRISPR-Cas genes and arrays, and predict the subtype based on both Cas genes and CRISPR repeat sequence.

Installation

Conda

It is advised to use miniconda or anaconda to install.

conda create -n caspredict -c conda-forge -c bioconda -c russel88 caspredict

pip

However, if you have the dependencies (Python >= 3.8, HMMER >= 3.2, Prodigal >= 2.6, grep, sed) in your PATH you can install with pip

python -m pip install caspredict

Download database

Conda

Coming soon...

pip

Coming soon...

How to run

Activate environment

conda activate caspredict

Run with a nucleotide fasta as input

caspredict genome.fa my_output

Use multiple threads

caspredict genome.fa my_output -t 20

Output

• CRISPR_Cas.tab: CRISPR_Cas loci
• cas_operons.tab: All certain Cas operons
• crisprs_all.tab: All CRISPR arrays
• crisprs_orphan.tab: Orphan CRISPRs (those not in CRISPR_Cas.tab)
• cas_operons_orphan.tab: Orphan Cas operons (those not in CRISPR_Cas.tab)
• cas_operons_putative.tab: Putative Cas operons, mostly false positives, but also some ambiguous and partial systems
• spacers.fa: Fasta file with all spacer sequences
• hmmer.tab: All HMM vs. ORF matches, raw unfiltered results
• arguments.tab: File with arguments given to CasPredict

Check the different options

caspredict -h

usage: caspredict [-h] [-t THREADS] [--prodigal {single,meta}] [--aa] [--skip_check] [--keep_tmp] [--log_lvl {DEBUG,INFO,WARNING,ERROR}] [--redo_typing] [--db DB] [--dist DIST]
                  [--overall_eval OVERALL_EVAL] [--overall_cov_seq OVERALL_COV_SEQ] [--overall_cov_hmm OVERALL_COV_HMM] [--two_gene_eval TWO_GENE_EVAL] [--two_gene_cov_seq TWO_GENE_COV_SEQ]
                  [--two_gene_cov_hmm TWO_GENE_COV_HMM] [--single_gene_eval SINGLE_GENE_EVAL] [--single_gene_cov_seq SINGLE_GENE_COV_SEQ] [--single_cov_hmm SINGLE_COV_HMM] [--vf_eval VF_EVAL]
                  [--vf_cov_hmm VF_COV_HMM] [--ccd CCD] [--kmer KMER]
                  input output

positional arguments:
  input                 Input fasta file
  output                Prefix for output directory

optional arguments:
  -h, --help            show this help message and exit
  -t THREADS, --threads THREADS
                        Number of parallel processes [4].
  --prodigal {single,meta}
                        Which mode to run prodigal in [single].
  --aa                  Input is a protein fasta. Has to be in prodigal format.
  --skip_check          Skip check of input.
  --keep_tmp            Keep temporary files (prodigal, hmmer, minced).
  --log_lvl {DEBUG,INFO,WARNING,ERROR}
                        Logging level [INFO].
  --redo_typing         Redo the typing. Skip prodigal and HMMER and load the hmmer.tab from the output dir.

data arguments:
  --db DB               Path to database.

cas threshold arguments:
  --dist DIST           Max allowed distance between genes in operon [3].
  --overall_eval OVERALL_EVAL
                        Overall E-value threshold [0.001].
  --overall_cov_seq OVERALL_COV_SEQ
                        Overall sequence coverage threshold [0.5].
  --overall_cov_hmm OVERALL_COV_HMM
                        Overall HMM coverage threshold [0.5].
  --two_gene_eval TWO_GENE_EVAL
                        Two-gene operon E-value threshold [1e-05].
  --two_gene_cov_seq TWO_GENE_COV_SEQ
                        Two-gene operon sequence coverage threshold [0.8].
  --two_gene_cov_hmm TWO_GENE_COV_HMM
                        Two-gene operon HMM coverage threshold [0.8].
  --single_gene_eval SINGLE_GENE_EVAL
                        Lonely gene E-value threshold [1e-10].
  --single_gene_cov_seq SINGLE_GENE_COV_SEQ
                        Lonely gene sequence coverage threshold [0.9].
  --single_cov_hmm SINGLE_COV_HMM
                        Lonely gene HMM coverage threshold [0.9].
  --vf_eval VF_EVAL     V-F Cas12 specific E-value threshold [1e-75].
  --vf_cov_hmm VF_COV_HMM
                        V-F Cas12 specific HMM coverage threshold [0.97].

crispr threshold arguments:
  --ccd CCD             Distance (bp) threshold to connect Cas operons and CRISPR arrays [10000.0].
  --kmer KMER           kmer size. Has to match training kmer size! [4].