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Mask Dna

Summary

Mask an input fasta file for sequences that could be RNA viral (or mistaken for such).

Description

Mask an input fasta file for sequences that could be RNA viral (or mistaken for such).

Usage

rolypoly mask-dna [OPTIONS]

Options

  • -o, --output: Output file name (type: TEXT; required; default: Sentinel.UNSET)
  • -f, --flatten: Attempt to kcompress.sh the masked file (type: BOOLEAN; default: False)
  • -i, --input: Input fasta file (type: TEXT; required; default: Sentinel.UNSET)
  • -a, --aligner: Which tool to use for identifying shared sequence (minimap2, mmseqs2, diamond, bbmap) (type: TEXT; default: mmseqs2)
  • -mlc, --mask-low-complexity: Whether to mask low complexity regions using bbduks entropy masking (type: BOOLEAN; default: False)
  • -r, --reference: Provide an input fasta file to be used for masking, instead of the pre-generated collection of RNA viral sequences (type: TEXT; default: /home/neri/Documents/Github/rolypoly/src/rolypoly/data/contam/masking/combined_entropy_masked.fasta.gz)
  • -drvh, --dont-remove-viral-headers: Whether to remove entried from the fasta input with 'virus' sounding headers (sequence names/ids in the fasta input). (type: BOOLEAN; default: False)
  • -dcs, --dont-clean-spaces-from-input: removed everything after the first space in the fasta header (sequence name/id). USEFUL AS mmseqs sam output doesn't seem to retain that, and then bbnmask won't find the seqid without the space... (type: BOOLEAN; default: False)
  • --tmpdir: Temporary directory to use (default: output file's parent/tmp - if you have enough RAM, you can set this to /dev/shm/ or /tmp/ for faster I/O) (type: TEXT)
  • -t, --threads: Number of worker threads. (type: INTEGER RANGE; default: 1)
  • -M, --memory: Memory limit, for example 8g. (type: MEMORY; default: 8g)