Lib.rs

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#fasta #bioinformatics #gff3

app stats_on_gff3

Calculate statistics such as CDS GC3 ratio, intron GC ratio, flanking gene region GC ratio, first intron length, number of introns, CpG ratio, etc. Examples: stats_on_gff3 Homo_sapiens.GRCh38.109.chromosome.1.gff3 Homo_sapiens.GRCh38.dna.chromosome.1.fa zcat Ciona_savignyi.CSAV2.0.dna.toplevel.fa.gz | stats_on_gff3 Ciona_savignyi.CSAV2.0.109.gff3 stdin See https://gitlab.in2p3.fr/penel/stats_on_gff3

by Simon Penel

18 releases

0.1.18 Aug 1, 2023
0.1.17 Jul 28, 2023
0.1.13 Jun 19, 2023
0.1.4 Apr 28, 2023

#50 in Biology

Download history 107/week @ 2023-06-05 82/week @ 2023-06-12 57/week @ 2023-06-19 14/week @ 2023-06-26 39/week @ 2023-07-03 6/week @ 2023-07-10 13/week @ 2023-07-17 103/week @ 2023-07-24 38/week @ 2023-07-31 36/week @ 2023-08-07 18/week @ 2023-08-14 23/week @ 2023-08-21 9/week @ 2023-08-28 28/week @ 2023-09-04 11/week @ 2023-09-11 36/week @ 2023-09-18

106 downloads per month

CECILL-2.1

60KB
1K SLoC

Stats of gff3 files

Install :

cargo install stats_on_gff3

Crates: https://crates.io/crates/stats_on_gff3

Examples:

stats_on_gff3 --precision 1000 Homo_sapiens.GRCh38.109.chromosome.1.gff3 Homo_sapiens.GRCh38.dna.chromosome.1.fa 2>err

stats_on_gff3 --all Homo_sapiens.GRCh38.109.chromosome.1.gff3 Homo_sapiens.GRCh38.dna.chromosome.1.fa 2>err

zcat Ciona_savignyi.CSAV2.0.dna.toplevel.fa.gz | stats_on_gff3 --precision 100 Ciona_savignyi.CSAV2.0.109.gff3 stdin 2> err

Dependencies

~17MB
~306K SLoC