repseqio fromFasta

Creates boilerplate JSON library from existing fasta file.

Usage:

repseqio fromPaddedFasta [-f] \
    [--chains <chain>] \
    [--functionality-index <index>] \
    [--functionality-regexp <regexp>] \
    [--gene-feature <geneFeature>] \
    [--gene-type <gt>] \
    [--ignore-duplicates] \
    [--name-index <index>] \
    [--padding-character <char>] \
    [--species-name <species>] \
    [--taxon-id <id>] \
    [-Lkey=value]... \
    [-Pkey=value]... \
    input_padded.fasta \
    [output.fasta] \
    output.json[.gz]

Options:

-f, --force

Force overwrite of output file(s).

-c, --chain

Chain

-j, --functionality-index

Functionality mark index (0-based) in |-separated FASTA description line (e.g. 3 for IMGT files). If this option is omitted, all genes are considered functional.

--functionality-regexp

Functionality regexp, gene is considered functional if field defined by -j / --functionality-index parameter matches this expression. Default: [\(\[]?[Ff].?.

--gene-feature

Defines gene feature which sequences are contained in the file (e.g. VRegion, VGene, JRegion etc..).

-g, --gene-type

Gene type (V/D/J/C)

-i, --ignore-duplicates

Ignore duplicate genes. By default duplicate genes are not ignored.

-n, --name-index

Gene name index (0-based) in |-separated FASTA description line (e.g. 1 for IMGT files). Default: 0.

-s, --species-name

Species names (can be used multiple times). Default: [].

-t, --taxon-id

Taxon id

-L

Amino-acid pattern of anchor point. Has higher priority than -P for the same anchor point. The syntax is -Lkey=value.

-P

Positions of anchor points in padded / non-padded file. To define position relative to the end of sequence use negative values: -1 = sequence end, -2 = last but one letter. Example: -PFR1Begin=0 -PVEnd=-1, equivalent of --gene-feature VRegion.