fxtools
A collection of fasta/fastq related tools that I've needed to write.
Installation
# from crates.io
# from github
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.
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.