Jacques Dainat

Audio quality

5

Hi, I feel a huge difference in audio quality using this app according to what I can hear using the cast from the google chrome . Is there away to...

add BANpipe

GTF validation

1

Dear Jacques, Thank you very much for developing the tool AGAT. I am interested in validating the gtf prediction file generated from other tools like braker2 or maker. Is there...

Find a way to not count overlaping part when isoform present to the covering % of the genome

conda packaging

3

Hi, I'm thinking to make it available through conda. see here https://github.com/bioconda/bioconda-recipes/pull/29660 I would need to know if deps.sh statically compiles dependencies in. Could you let me know?

Update define-metadata.rst

1

update Skipping builds paragraph to clarify the use. I would like to improve the Skipping builds paragraph to give a better view of its use. I'm unsure about the list...

Each line of the file must be less than 65,536 characters

9

``` ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Each line of the file must be less than 65,536 characters. STACK: Error::throw STACK: Bio::Root::Root::throw /home/lgs6452/.conda/envs/exonerate_env/lib/site_perl/5.26.2/Bio/Root/Root.pm:447 STACK: Bio::DB::IndexedBase::_check_linelength /home/lgs6452/.conda/envs/exonerate_env/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm:757 STACK: Bio::DB::Fasta::_calculate_offsets /home/lgs6452/.conda/envs/exonerate_env/lib/site_perl/5.26.2/Bio/DB/Fasta.pm:227 STACK: Bio::DB::IndexedBase::_index_files...

Bio::Tools::GFF _gffX_string update

1

Hi, I would like to push some updates about the methods `_gff2_string` and `_gff25_string` to remove some inconsistency related to the format specifications ([Here](https://github.com/NBISweden/GAAS/blob/master/annotation/CheatSheet/gxf.md) a review of the specifications I...

Bio::DB issue on MAC using APFS (ssd hard drive).

18

Since I have updated my Mac to High Sierra, I cannot index properly the fasta files. There is problem with the IDs, when you print them you don't see any...

Update gaas_fasta_domain_extractor script to be more efficient.