fxtools

A collection of fasta/fastq related tools that I've needed to write.

Installation

# from crates.io
cargo install fxtools

# from github
git clone https://github.com/noamteyssier/fxtools
cd fxtools
cargo install --path .

Commands

Unique

This is a command that will determine all unique sequences within a fastx file and split the records into either unique or duplicates. It will also count the number of unique/duplicate sequences/duplicate records and report those. By default all unique reads will be pushed to stdout unless piped to a file with the -o flag. Nulled reads will not be reported by default but can be written to a filepath with the -n flag.

fxtools unique \
  -i <input_fastx> \
  -o <optional_output_file_for_unique> \
  -n <optional_output_file_for_null>

sgRNA Table

This command will create a table mapping sgRNA names to their parent gene. This works by parsing the header of each record and currently it expects the header to be as follows:

# {gene}_{auxilliary sgrna description}

The command requires an input fasta/q file and will by default write a sgrna-to-gene table to stdout.

You can pipe the output table to a file with the -o flag.

You can also choose to include each records sequence with the -s flag.

You can also choose to reorder the columns to whatever format you'd like with the -r flag and provide a 3 character string (i.e. -r hsg or -r ghs) representing the [hH]eader, [sS]sequence, and [gG]ene.

By default the table's delimiter is tabs, but you can specify a separate delimiter with the -d flag.

fxtools sgrna-table \
  -i <input_fastx> \
  -o <s2g.txt> \
  -s \
  -r ghs \
  -d <character delim>