TranscriptToProtein.md

TranscriptToProtein tool help

TranscriptToProtein (2025_12-266-g396e1fe11)

Computes the protein sequence for each transcript name given.

Mandatory parameters:
  -out <file>       Output TSV file.

Optional parameters:
  -in <file>        Input file. If unset, reads from STDIN. Expects one transcript ID (ENSEMBLE or REFSEQ) per line.
                    Default value: ''
  -ref <file>       Reference genome FASTA file. If unset 'reference_genome' from the 'settings.ini' file is used.
                    Default value: ''
  -test             Uses the test database instead of on the production database.
                    Default value: 'false'
  -build <enum>     Genome build
                    Default value: 'hg38'
                    Valid: 'hg19,hg38'

Special parameters:
  --help            Shows this help and exits.
  --version         Prints version and exits.
  --changelog       Prints changeloge and exits.
  --tdx             Writes a Tool Definition Xml file. The file name is the application name with the suffix '.tdx'.
  --settings [file] Settings override file (no other settings files are used).

TranscriptToProtein changelog

TranscriptToProtein 2025_12-266-g396e1fe11

2026-05-04 Initial version

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