GitLab

Integration of select query (from sp-mapping-dump.sh) in gene-description.pl.
Next step, integrate sp-description.pl in gene-description.pl, so gene description can be manage through one command :)

Then identified bug in Accession Number parsing, when in more than one line for an entry, script was getting the first
AC of the last parsed line. But we want the first AC of the first parsed line. Fixed now. Added possibility of parsing

This  script is now deprecated. It has been integrated in gene-descriptions.pl

Now does two different mapping, one for the prediction and one for the known genes... it will allow us to be more free to tickle the parameters

added peptide ---> contig coordinate mapping on Transcript. Not tested. Mainly to make sure I shift the code off my laptop

same fixes as in branch-4: get_Genes_by_Type treats nicely the supp_evidence and invert() preserves the db object in contig

Not much gain to see so far, all alignments look ungapped.
Probably still buggy.

not ready yet.

Adaptor to store in db and retrieve.

Added a specific option in the mapping_conf file for NCBI prediction. Flaged the different entries retrieved in get_Xmapping.pl; KNOWN for SPTR and curated Refseq, XREF for all of the entries retrieved from the KNOWN matches and then PRED for all of the sequences predicted by other teams (in that case NCBI for human but can be anything).

Feature are not storable.