plaquette/pfasta repository overview

⁠corresponding github Repository: https://github.com/plaquette/pfasta_docker⁠

⁠pfasta Docker Container

This Docker container provides a set of tools for working with genetic sequences using the pfasta package (-> from: https://github.com/kloetzl/pfasta⁠ ). The tools offer various functionalities for fasta file manipulation and analysis.

⁠Examples

Running pfasta command to process a file:

docker run --rm -v /absolute/path/to/demo.fasta:/data/bad.fasta plaquette/pfasta:dev pfasta acgt /data/bad.fasta > /absolute/path/to/good.fasta

Replace /absolute/path/to/demo.fasta with the absolute path to your input demo.fasta file, and /absolute/path/to/good.fasta with the desired absolute path for the resulting good.fasta file.

This example demonstrates how to use the pfasta command to process a file (acgt subcommand is used in this case) and redirect the output to another file.

Starting an interactive session within the container:

docker run -it -v /absolute/path/to/demo.fasta:/data/demo.fasta plaquette/pfasta:dev /bin/bash

Replace /absolute/path/to/demo.fasta with the absolute path to your demo.fasta file.

This example showcases how to start an interactive session within the container and have the demo.fasta file mounted inside. It launches a bash shell (/bin/bash) for interactive usage within the container.

After starting the interactive session, you can navigate to the /data directory and access the demo.fasta file or execute other pfasta commands as needed.

⁠Available Tools (-> from: https://github.com/kloetzl/pfasta⁠ )

There is a wrapper program pfasta which bundles all of the tools at installation.

• acgt: Reduce residues to the four canonical bases.
• aln2dist: Convert an alignment to a distance matrix.
• aln2maf: Convert an alignment to MAF.
• cchar: Count the number of nucleotides.
• concat: Concatenate sequences.
• fancy_info: Print a fancy report.
• format: Format sequences.
• gc_content: Determine the GC content.
• n50: Compute the N50.
• revcomp: Compute the reverse complement.
• shuffle: Shuffle a set of sequences.
• sim: Simulate a set of genetic sequences.
• split: Split a FASTA file into multiple files on a sequence basis.
• validate: Check if a file conforms to the grammar given below.

Use the following command to format a file:

pfasta tool file.fasta

Replace file.fasta with the actual name of the file you want to format.