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>

Upper

This command will convert your input fastx into an output fastx with all nucleotides converted to their uppercase. This will also validate to ensure there are no unexpected nucleotides found. Default will write to stdout, but you can provide an output file with the -o flag.

fxtools upper \
  -i <input_fastx> \
  -o <output_fastx>