GitLab

backed out changes to deal with component seq_regions mapping to more than one assembly coord_system

Check if a particular key/value pair exists before trying to store it; warn and don't store if it's already there.

    1) For some species, the SPTREMBL file was pulled in with the
       source_id of Swiss-Prot.

    2) The RefSeq DNA and peptide sources for microbat were confused
       (the peptide files had the source_id of RefSeq_dna).

    3) Same problem, but inversed, for yeast.

    4) RefSeq files for microbat were fetched from the wrong
       FTP directory at NCBI (vertibrate_other rather than
       vertibrate_mammalian).

make it so in the generation of 'xref.txt' as well (was empty string).
Thanks to sd3 for spotting this.

Readability formatting of related code.

- determine deleted genes/transcripts by comparing old and new db, rather than reading from file lists\n- this also fixes a potential issue when deleting both whole genes and individual transcripts\n- increment gene version where individual transcripts were deleted

find the release info.  Fixed.

http://www.ebi.ac.uk/GOA/uniprot_release.html

used together with pipline code ( prevent that dbcon to pipeline db will be cleared as well)

new routines for getting the sql querys and their times. Note you need to uncomment the relevant sections to use this. By default this is all commented out as intended fro debuging and profiling