stats_on_gff3
| Crates.io | stats_on_gff3 |
| lib.rs | stats_on_gff3 |
| version | 0.1.26 |
| source | src |
| created_at | 2023-04-26 14:54:10.130915 |
| updated_at | 2024-02-22 13:19:07.977065 |
| description | 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 |
| homepage | https://gitlab.in2p3.fr/penel/stats_on_gff3 |
| repository | https://gitlab.in2p3.fr/penel/stats_on_gff3 |
| max_upload_size | |
| id | 849448 |
| size | 120,307 |
Simon Penel (simonpenel)
documentation
README
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
Input data:
A Gff file and its associated fasta file from Ensembl. Fasta sequences should be in uppercase. (for NCBI data, see stats_on_gff3_ncbi https://crates.io/crates/stats_on_gff3_ncbi)