Commit 60418f92 authored by Mikaël Salson's avatar Mikaël Salson

germline: TRDD2/TRDD3 upstream and downstream sequences are now retrieved by split_from_imgt.py

parent 300394b0
......@@ -200,10 +200,10 @@ void MultiGermline::build_incomplete_set(string path, int max_indexing)
add_germline(new Germline("VdJa", 'a', path + "/TRDV.fa", path + "/TRDD.fa", path + "/TRAJ.fa", -10, 80, max_indexing), SEED_S13);
add_germline(new Germline("VdJa", 'a', path + "/TRDD_upstream.fa", "", path + "/TRAJ.fa", -10, 80, max_indexing), SEED_S13);
// DD2-DD3
add_germline(new Germline("TRD+", 'd', path + "/TRDD2-01.fa", "", path + "/TRDJ.fa", -10, 60, max_indexing), SEED_9);
add_germline(new Germline("TRD+", 'd', path + "/TRDV.fa", "", path + "/TRDD3-01.fa", -10, 50, max_indexing), SEED_9);
add_germline(new Germline("TRD+", 'd', path + "/TRDD2-01.fa", "", path + "/TRDD3-01.fa", -10, 50, max_indexing), SEED_9);
// DD-JD + DD2-DD3
add_germline(new Germline("TRD+", 'd', path + "/TRDD_upstream.fa", "", path + "/TRDJ.fa", -10, 60, max_indexing), SEED_9);
add_germline(new Germline("TRD+", 'd', path + "/TRDV.fa", "", path + "/TRDD3_downstream.fa", -10, 50, max_indexing), SEED_9);
add_germline(new Germline("TRD+", 'd', path + "/TRDD2_upstream.fa", "", path + "/TRDD3_downstream.fa", -10, 50, max_indexing), SEED_9);
// DH-JH
add_germline(new Germline("IGH+", 'h', path + "/IGHD_upstream.fa", "", path + "/IGHJ.fa", -10, 20, max_indexing), SEED_S12);
......
......@@ -7,6 +7,3 @@ wget -O IMGT_RELEASE http://www.imgt.org/download/GENE-DB/RELEASE
wget -N http://rbx.vidjil.org/browser/germline/IGK-INTRON.fa
wget -N http://rbx.vidjil.org/browser/germline/IGK-KDE.fa
wget -q -O - 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=M22153&rettype=fasta&retmode=text&to=42' | sed '1s/>gb\|/>gb|TRDD2*01/' > TRDD2-01.fa
wget -q -O - 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=M22152&rettype=fasta&retmode=text&from=214&to=258' | sed '1s/>gb\|/>gb|TRDD3*01/' > TRDD3-01.fa
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