src/hg/utils/automation/makeGenomeDb.pl 1.21
1.21 2009/05/12 03:16:20 galt
maybe this is better ncbi url to fetch the chrM seq with
Index: src/hg/utils/automation/makeGenomeDb.pl
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/utils/automation/makeGenomeDb.pl,v
retrieving revision 1.20
retrieving revision 1.21
diff -b -B -U 4 -r1.20 -r1.21
--- src/hg/utils/automation/makeGenomeDb.pl 6 Mar 2009 23:33:26 -0000 1.20
+++ src/hg/utils/automation/makeGenomeDb.pl 12 May 2009 03:16:20 -0000 1.21
@@ -303,9 +303,11 @@
my $mitoFile = "$topDir/M/$mitoAcc.fa";
$bossScript->add(<<_EOF_
mkdir M
wget -O $mitoFile \\
- 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&rettype=fasta&id=$mitoAcc&retmode=text'
+ 'http://www.ncbi.nlm.nih.gov/sviewer/viewer.fcgi?db=nuccore&dopt=fasta&sendto=on&id=$mitoAcc'
+
+# old url 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&rettype=fasta&id=$mitoAcc&retmode=text'
# Make sure there's exactly one fasta record:
if (`grep '^>' $mitoFile | wc -l` != 1) then