Commit b43f8672 authored by Mikaël Salson's avatar Mikaël Salson

germlines: TRDD2*01 and TRDD3*01 are not retrieved from IMGT

For DD2/DD3 recombinations we need respectively upstream and downstream sequences of the two genes.
They are not included in IMGT, therefore we retrieve them from NCBI
parent 27cabf5a
......@@ -8,3 +8,6 @@ python buildBrowserGermline.py *.fa germlines.data ../browser/js/germline.js
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
......@@ -29,8 +29,6 @@ def verbose_open_w(name):
# Create isolated files for some sequences
SPECIAL_SEQUENCES = [
'TRDD2*01',
'TRDD3*01',
]
for l in sys.stdin:
......
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