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repseqio fromPaddedFasta

Converts library from padded fasta file (IMGT-like) to json library. This command can operate in two modes:

  1. if three input files are specified, it will create separate non-padded fasta and put links inside newly created library pointing to it.

  2. if 2 input files are specified, it will create only library file, and embed sequences directly into it.

To use library generated using mode (1) one need both output files, (see also repseqio compile). If library is intended for further editing and/or submission to version control system option (1) is recommended.

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>
Chain.
-j, --functionality-index <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 <regexp>
Functionality regexp, gene is considered functional if field defined by -j / --functionality-index parameter matches this expression. Default: [\(\[]?[Ff].?.
--gene-feature <geneFeature>
Defines gene feature which sequences are contained in the file(e.g. VRegion, VGene, JRegion etc..).
-g, --gene-type <gt>
Gene type (V/D/J/C)
-i, --ignore-duplicates
Ignore duplicate genes. Default behavior: duplicates are not ignored.
-n, --name-index <index>
Gene name index (0-based) in |-separated FASTA description line(e.g. 1 for IMGT files). Default is 0.
-p, --padding-character <char>
Padding character. Default: ..
-s, --species-name <species>
Species names (can be used multiple times)
-t, --taxon-id <id>
Taxon id
-L
Amino-acid pattern of anchor point. Has higher priority than -P for the same anchor point. 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.