1 unstable release
0.1.0 | Aug 2, 2023 |
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#42 in #dna
14KB
240 lines
rust-gc-count
cargo build --release
target/release/gccount --input in.fa --output out.wig
Description
A tool for generating wiggle files of GC from DNA written in Rust.
Help
Calculate GC and write into a wiggle file
Usage: gccount [OPTIONS] --input <INPUT> --output <OUTPUT>
Options:
--input <INPUT> FASTA formatted file (can be gziped) to calculate GC from
--output <OUTPUT> Output wiggle file. One file will be produced
--window <WINDOW> Window size to calculate GC over [default: 5]
--omit-tail Remove any trailing sequence and do not calcualte GC. Default behaviour is to retain the leftover sequence. GC is calculated over the remaining sequence length
--write-chrom-sizes Write a chrom.sizes file into the current directory. Use --chrom-sizes-path to configure location
--chrom-sizes-path <CHROM.SIZES> Path of the chrom.sizes file. Defaults to chrom.sizes [default: chrom.sizes]
--verbose Be verbose
-h, --help Print help
-V, --version Print version
Checksum calculator
target/release/checksumseq --input in.fa --output chrom.file
Another binary for calculating sequence lengths and checksums from a file. The resulting file is formted as tab separated with the following columns:
- Sequence ID as it appears in the FASTA file
- Sequence length
- Refget ga4gh identifier (SQ.sha512t24u)
- MD5 checksum hex encoded
The resulting file can be used as a chrom.sizes
file too.
Command line
Iterates through a FASTA file calclating checksums and sequence length
Usage: checksumseq [OPTIONS]
Options:
--input <INPUT> FASTA formatted file to calculate checksums from (- mean STDIN). Reads gzipped FASTA if the filename ends with .gz (including bgzip files) [default: -]
--output <OUTPUT> Output file (- means STDOUT). Each line is tab separated reporting "ID Length sha512t24u md5" [default: -]
--verbose Be verbose
-h, --help Print help
-V, --version Print version
Level of code quality
The code developed here has not been extensively tested but has been verified as producing correct and expected output.
Dependencies
~2.7–3.5MB
~70K SLoC