get-germline 712 Bytes
Newer Older
Mikaël Salson's avatar
Mikaël Salson committed
1 2 3
#!/bin/sh

cd $(dirname $0)
Mathieu Giraud's avatar
Mathieu Giraud committed
4
wget -O - http://www.imgt.org/download/GENE-DB/IMGTGENEDB-ReferenceSequences.fasta-nt-WithoutGaps-F+ORF+inframeP | python split-from-imgt.py 
Mikaël Salson's avatar
Mikaël Salson committed
5

6 7
wget -O - IMGT_RELEASE http://www.imgt.org/download/GENE-DB/RELEASE

8 9
wget -N http://rbx.vidjil.org/browser/germline/IGK-INTRON.fa
wget -N http://rbx.vidjil.org/browser/germline/IGK-KDE.fa
10 11 12

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