repseqio tsv

Export gene region coordinates to .tsv file. To output 1-based coordinates add -1 / --one-based option.

Usage:

repseqio tsv [-f] \
    [--chain <chain>] \
    [--gene-feature <geneFeature>] \
    [--name <regex>] \
    [--one-based] \
    [--species <species>] \
    [--taxon-id <id>] \
    input_library.json|default [output.txt]

Options:

-f, --force

Force overwrite of output file(s).

-c, --chain <chain>

Chain pattern, regexp string, all genes with matching chain record will be exported.

-g, --gene-feature <geneFeature>

Gene feature(s) to export (e.g. VRegion, JRegion, VTranscript, etc...). To specify several features use this option several times or separate multiple regions with commas.

-n, --name <regex>

Gene name pattern, regexp string, all genes with matching gene name will be exported.

-1, --one-based

Use one-based coordinates instead of zero-based and output inclusive end position. By default, zero-based coordinates are used.

-s, --species <species>

Species name, used in the same way as --taxon-id.

-t, --taxon-id <id>

Taxon id (filter multi-library file to leave single library for specified taxon id)