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samplesheet-utils

Testing

samplesheet-utils (or samplesheetutils) is a collection of scripts and utilities for working with samplesheets and FASTA files at the command line. It is primarily designed for use within pipelines.

Installation

pip

pip3 install samplesheetutils

git

git clone https://github.com/Australian-Structural-Biology-Computing/create-samplesheet
cd create-samplesheet
pip3 install .

Commands

sample-name

This command is used to read the sample name(s) from a FASTA file. This is useful for dynamically creating directories based on the actual sample name.

sample-name [ARGS] [FASTA(s)]
  • -i --index: Index of the sample you wish to read the name from. This can be an integer, -1 for the last sample, or a range (1:5)
  • --sanitize --sanitise: Replaces any problematic characters in the sample name(s) with an underscore
  • -d --delim: Change the delimiter between each sample name. By default this is a new-line character

create-samplesheet

This command is used to create a samplesheet from different inputs, including string, and directories containing FASTA files

create-samplesheet [ARGS]
  • -a --aa-string: Input a single amino acid sequence
  • -d --directory: Input a directory containing FASTA files
  • -o --output-file: Samplesheet filename. Default is samplesheet.[ext] [ext] depends on mode
  • -j --json: Ouptut JSON formatted samplesheet
  • -y --yaml: Output YAML formatted samplesheet

TODO

  • Finish documentation