spatula mex2sptsv

Summary

TBA

Required options

TBA

Additional Options

TBA

Expected Output

TBA

Full Usage

The full usage of spatula mex2sptsv can be viewed with the --help option:

$ ./spatula mex2sptsv --help  
[./spatula mex2sptsv] -- Convert 10x Market Exchange (MEX) formatted DGE to Sparse TSV format in FICTURE2

 Copyright (c) 2022-2024 by Hyun Min Kang
 Licensed under the Apache License v2.0 http://www.apache.org/licenses/

Detailed instructions of parameters are available. Ones with "[]" are in effect:

Available Options:

== Key Input Options ==
   --in-dir                       [STR: ]             : Input directory containing the MEX files
   --bcd                          [STR: barcodes.tsv.gz] : Barcode file name
   --ftr                          [STR: features.tsv.gz] : Feature file name
   --mtx                          [STR: matrix.mtx.gz] : Matrix file name
   --icol-mtx                     [INT: 3]            : 1-based column index in the matrix file to use as the count

== Input Filtering Options ==
   --include-feature-list         [STR: ]             : A file containing a list of input genes to be included (feature name of IDs)
   --exclude-feature-list         [STR: ]             : A file containing a list of input genes to be excluded (feature name of IDs)
   --include-feature-regex        [STR: ]             : A regex pattern of feature/gene names to be included
   --exclude-feature-regex        [STR: ]             : A regex pattern of feature/gene names to be excluded
   --include-feature-substr       [STR: ]             : A substring of feature/gene names to be included
   --exclude-feature-substr       [STR: ]             : A substring of feature/gene names to be excluded
   --include-barcode-list         [STR: ]             : A file containing a list of input barcode IDs to be included (feature name of IDs)
   --exclude-barcode-list         [STR: ]             : A file containing a list of input barcode IDs to be excluded (feature name of IDs)
   --min-feature-count            [INT: 0]            : Minimum feature count to include in the output. Requires reading the input matrix twice

== Key Output Options ==
   --out                          [STR: ]             : Output prefix
   --out-suffix-meta              [STR: .json]        : Suffix for the metadata output file
   --out-suffix-tsv               [STR: .tsv]         : Suffix for the transcript output file
   --out-suffix-feature-counts    [STR: .feature.counts.tsv] : Suffix for the feature counts output file
   --colname-barcode-name         [STR: cell_id]      : Column name for barcode name
   --colname-random-key           [STR: random_key]   : Column name for random key
   --keyname-dictionary           [STR: dictionary]   : Key name for the dictionary in the metadata file
   --keyname-header-info          [STR: header_info]  : Key name for the header in the metadata file
   --keyname-n-features           [STR: n_features]   : Key name for the number of features in the metadata file
   --keyname-n-modalities         [STR: n_modalities] : Key name for the number of modalities in the metadata file
   --keyname-n-units              [STR: n_units]      : Key name for the number of units in the metadata file
   --keyname-offset-data          [STR: offset_data]  : Key name for the offset data in the metadata file

== Auxilary Output Options ==
   --seed                         [INT: 0]            : Random seed for the random key generation
   --use-gene-id                  [FLG: OFF]          : Use gene ID instead of gene name in the output
   --error-on-duplicate-gene-name [FLG: OFF]          : Report error on duplicate gene name in the feature file. If not set, the duplicate gene names will be renamed by combining with the gene IDs


NOTES:
When --help was included in the argument. The program prints the help message but do not actually run