Command line helper to manipulate RepSeq.IO formatted V/D/J/C reference data.
Install
brew install repseqio/all/repseqio
Upgrade
brew update
brew upgrade repseqio
Unpack zip file with latest release version to a folder and add it to your PATH variable or create symlink to repseqio script in /usr/local/bin, ~/bin or similar folder.
See this repository for actual references.
See this wiki page.
Here is the example pipeline starting from plain fasta files:
# Importing fasta file for each gene type
# (redundant meta information (species, chain, etc.) specified for each gene type is required because
# library produced on each step is self-contained and requires all meta fields to be defined)
repseqio fromFasta --taxon-id 9606 \
--species-name hs --species-name homsap \
--chain TRB --name-index 0 \
--gene-type V --gene-feature VRegion \
my_genes.v.fasta my_library.v.json
repseqio fromFasta --taxon-id 9606 \
--species-name hs --species-name homsap \
--chain TRB --name-index 0 \
--gene-type D --gene-feature DRegion \
my_genes.d.fasta my_library.d.json
repseqio fromFasta --taxon-id 9606 \
--species-name hs --species-name homsap \
--chain TRB --name-index 0 \
--gene-type J --gene-feature JRegion \
my_genes.j.fasta my_library.j.json
# Merging several libraries into single file
repseqio merge my_library.v.json my_library.d.json my_library.j.json my_library.json
# Inferring intermediate anchor points (like CDR3Begin) using automated homology-driven procedure;
# built-in repseqio library will be used as reference
repseqio inferPoints -g VRegion -g JRegion -f my_library.json my_library.jsonSee this wiki page.
Usage:
Usage: repseqio [options] [command] [command options]
Options:
-h, --help
Displays this help message.
--version
Output full version information.
-v
Output short version information.
Commands:
list Format JSON in library; sort libraries in multi-library files, sort genes inside libraries.
Usage: list [options] library.json[.gz]
Options:
-h, --help
Displays help for this command.
Default: false
filter Filter libraries and library records.
Usage: filter [options] input_library.json[.gz] output_library.json[.gz]
Options:
-c, --chain
Chain pattern, regexp string, all genes with matching chain record
will be collected.
-f, --force
Force overwrite of output file(s).
-h, --help
Displays help for this command.
Default: false
-s, --species
Species name, used in the same way as --taxon-id.
-t, --taxon-id
Taxon id (filter multi-library file to leave single library for
specified taxon id)
merge Merge several libraries into single library.
Usage: merge [options] [input1.json[.gz] [ input2.json[.gz] [...] ] ] output.json[.gz]
Options:
-f, --force
Force overwrite of output file(s).
-h, --help
Displays help for this command.
Default: false
compile Compile a library into self-contained compiled library file, by embedding sequence information into "sequenceFragments" section.
Usage: compile [options] input.json[.gz] output.json[.gz]
Options:
-f, --force
Force overwrite of output file(s).
-h, --help
Displays help for this command.
Default: false
-s, --surrounding
Length of surrounding sequences to include into library. Number of
upstream and downstream nucleotides around V/D/J/C segments to embed into
output library's "sequenceFragments" section. More nucleotides will be
included, more surrounding sequences will be possible to request using gene
features with offset (like JRegion(-12, +3)), at the same time size of
output file will be greater.
Default: 30
generateClones Generate synthetic clonotypes, and write in in jclns format.
Usage: generateClones [options] model_name|model_file_name [output.jclns]
Options:
-f, --force
Force overwrite of output file(s).
-h, --help
Displays help for this command.
Default: false
-a, --in-frame
In-frame clones only.
-b, --no-stops
Output clones without stop codons in CDR3 (valid only with -a /
--in-frame).
* -c, --number-of-clones
Number of clones to generate.
Default: 0
-s, --seed
Random generator seed (0 to use current time as random seed).
normalizeClones Normalize clone abundances in jclns file.
Usage: normalizeClones [options] [input.jclns [output.jclns]]
Options:
-f, --force
Force overwrite of output file(s).
-h, --help
Displays help for this command.
Default: false
exportCloneSequence Normalize clone abundances in jclns file.
Usage: exportCloneSequence [options] [input.jclns [output.jclns]]
Options:
-q, --abundance-factor
Repeat each clonal sequence round(f*clone.abundance) times, where
round means mathematical rounding of non-integer numbers.
-d, --add-description
Add description fields to fasta header (available values
NFeature[gene_feature], AAFeature[gene_feature] - for current
gene,NFeature[chain,gene_feature], AAFeature[chain,gene_feature] - for multi-gene clones, JSONClone,
JSONGene, JSONClone.field_name, JSONGene.field_name, Chain). Example:
NFeature[CDR3], AAFeature[FR3]
Default: []
-c, --chain
Which chains to export
Default: ALL
-f, --force
Force overwrite of output file(s).
* -g, --gene-feature
Gene feature to export (e.g. CDR3, VDJRegion, VDJTranscript,
VDJTranscript+CExon1 etc...)
-h, --help
Displays help for this command.
Default: false
fasta Export sequences of genes to fasta file.
Usage: fasta [options] input_library.json|default [output.fasta]
Options:
-c, --chain
Chain pattern, regexp string, all genes with matching chain record
will be exported.
-f, --force
Force overwrite of output file(s).
* -g, --gene-feature
Gene feature to export (e.g. VRegion, JRegion, VTranscript, etc...)
-h, --help
Displays help for this command.
Default: false
-n, --name
Gene name pattern, regexp string, all genes with matching gene name
will be exported.
-s, --species
Species name, used in the same way as --taxon-id.
-t, --taxon-id
Taxon id (filter multi-library file to leave single library for
specified taxon id)
tsv Export genes region coordinates to TSV file. To output 1-based coordinates add `-1` / `--one-based` option.
Usage: tsv [options] input_library.json|default [output.txt]
Options:
-c, --chain
Chain pattern, regexp string, all genes with matching chain record
will be exported.
-f, --force
Force overwrite of output file(s).
* -g, --gene-feature
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.
-h, --help
Displays help for this command.
Default: false
-n, --name
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.
Default: false
-s, --species
Species name, used in the same way as --taxon-id.
-t, --taxon-id
Taxon id (filter multi-library file to leave single library for
specified taxon id)
inferPoints Try to infer anchor point positions from gene sequences of other libraries. If no reference libraries are specified, built-in library will be used.
Usage: inferPoints [options] input_library.json [reference_library1.json [reference_library2.json [....]]] output.json
Options:
-f, --force
Force overwrite of output file(s).
* -g, --gene-feature
Reference gene feature to use (e.g. VRegion, JRegion, VTranscript,
etc...). This feature will be used to align target genes with reference
genes. Target genes must have this gene feature. This option can be used
several times, to specify several target gene features. Inference will be
performed in order options are specified.
-h, --help
Displays help for this command.
Default: false
-m, --min-score
Absolute minimal score. Alignment is performed using amino acid
sequences (target is queried using all three reading frames) using BLOSUM62
matrix. (default 200 for V gene, 50 for J gene)
-n, --name
Gene name pattern, regexp string, all genes with matching gene name
will be exported.
-o, --only-modified
Output only modified records.
debug Outputs extensive information on genes in the library.
Usage: debug [options] input_library.json[.gz]
Options:
-a, --all
Check all genes, used with -p option.
-h, --help
Displays help for this command.
Default: false
-n, --name
Gene name pattern, regexp string, all genes with matching gene name
will be exported.
-p, --problems
Print only genes with problems, checks only functional genes by
default (see -a option).
format Format JSON in library; sort libraries in multi-library files, sort genes inside libraries.
Usage: format [options] library.json[.gz]
Options:
-c, --compact
Compact.
-h, --help
Displays help for this command.
Default: false
stat Print library statistics.
Usage: stat [options] input_library.json
Options:
-h, --help
Displays help for this command.
Default: false
fromFasta Creates boilerplate JSON library from existing fasta file.
Usage: fromFasta [options] input.fasta output.json
Options:
* -c, --chain
Chain.
-f, --force
Force overwrite of output file(s).
-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 sequecnes are contained in the file
(e.g. VRegion, VGene, JRegion etc..).
* -g, --gene-type
Gene type (V/D/J/C)
-h, --help
Displays help for this command.
Default: false
-i, --ignore-duplicates
Ignore duplicate genes
* -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. Have higher priority than -P
for the same anchor point.
Syntax: -Lkey=value
Default: {}
-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
Syntax: -Pkey=value
Default: {}
fromPaddedFasta Converts library from padded fasta file (IMGT-like) to json library. This command can operate in two modes
(1) if 3 file-parameters are specified, it will create separate non-padded fasta and put links inside newly created library pointing to it,
(2) if 2 file-parameters are specified, 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: fromPaddedFasta [options] input_padded.fasta [output.fasta] output.json[.gz]
Options:
* -c, --chain
Chain.
-f, --force
Force overwrite of output file(s).
-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 sequecnes are contained in the file
(e.g. VRegion, VGene, JRegion etc..).
* -g, --gene-type
Gene type (V/D/J/C)
-h, --help
Displays help for this command.
Default: false
-i, --ignore-duplicates
Ignore duplicate genes
* -n, --name-index
Gene name index (0-based) in `|`-separated FASTA description line
(e.g. 1 for IMGT files).
Default: 0
-p, --padding-character
Padding character
Default: .
-s, --species-name
Species names (can be used multiple times)
Default: []
* -t, --taxon-id
Taxon id
-L
Amino-acid pattern of anchor point. Have higher priority than -P
for the same anchor point.
Syntax: -Lkey=value
Default: {}
-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
Syntax: -Pkey=value
Default: {}