#!/bin/sh

cd $(dirname $0)
wget -N https://www.imgt.org/download/GENE-DB/IMGTGENEDB-GeneList
wget -N https://www.imgt.org/download/GENE-DB/IMGTGENEDB-ReferenceSequences.fasta-nt-WithGaps-F+ORF+inframeP 
wget -N https://www.imgt.org/download/GENE-DB/IMGTGENEDB-ReferenceSequences.fasta-nt-WithoutGaps-F+ORF+allP


LOG=split-germlines.log
ERR=split-germlines.err
(python split-germlines.py IMGTGENEDB-ReferenceSequences.fasta-nt-WithGaps-F+ORF+inframeP IMGTGENEDB-ReferenceSequences.fasta-nt-WithoutGaps-F+ORF+allP IMGTGENEDB-GeneList | tee $LOG) 2> $ERR

wget -O IMGT_RELEASE https://www.imgt.org/download/GENE-DB/RELEASE

wget -N -P homo-sapiens https://www.vidjil.org/germline/IGK-INTRON.fa
wget -N -P homo-sapiens https://www.vidjil.org/germline/IGK-KDE.fa

cat $ERR
