src/hg/makeDb/doc/calJac3.txt 1.6

Index: src/hg/makeDb/doc/calJac3.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/calJac3.txt,v
retrieving revision 1.5
retrieving revision 1.6
diff -b -B -U 4 -r1.5 -r1.6
--- src/hg/makeDb/doc/calJac3.txt	1 Apr 2010 17:28:00 -0000	1.5
+++ src/hg/makeDb/doc/calJac3.txt	1 Apr 2010 17:48:38 -0000	1.6
@@ -1298,4 +1298,49 @@
     #	in that pushQ entry walk through each entry and see if the
     #	sizes will set properly
 
 ############################################################################
+# ctgPos2 track - showing clone sequence locations on chromosomes
+#	(DONE - 2010-04-01 - Hiram)
+    mkdir /hive/data/genomes/calJac3/bed/ctgPos2
+    cd /hive/data/genomes/calJac3/bed/ctgPos2
+    cat << '_EOF_' > agpToCtgPos2.pl
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+my $argc = scalar(@ARGV);
+
+if ($argc != 1) {
+    printf STDERR "usage: zcat your.files.agp.gz | agpToCtgPos2.pl /dev/stdin > ctgPos2.tab\n";
+    exit 255;
+}
+
+my $agpFile = shift;
+
+open (FH, "<$agpFile") or die "can not read $agpFile";
+while (my $line = <FH>) {
+    next if ($line =~ m/^#/);
+    chomp $line;
+    my @a = split('\s+', $line);
+    next if ($a[4] =~ m/^N$/);
+    my $chrSize = $a[2]-$a[1]+1;
+    my $ctgSize = $a[7]-$a[6]+1;
+    die "sizes differ $chrSize != $ctgSize\n$line\n" if ($chrSize != $ctgSize);
+    printf "%s\t%d\t%s\t%d\t%d\t%s\n", $a[5], $chrSize, $a[0], $a[1]-1, $a[2], $a[4];
+}
+close (FH);
+'_EOF_'
+    # << happy emacs
+
+export S=../../genbank/Primary_Assembly/assembled_chromosomes/AGP
+cut -f2 ${S}/chr2acc | while read ACC
+do
+    C=`grep "${ACC}" ${S}/chr2acc | cut -f1`
+    zcat ${S}/AGP/chr${C}.agp.gz \
+        | sed -e "s/^${ACC}/chr${C}/"
+done | ./agpToCtgPos2.pl /dev/stdin > ctgPos2.tab
+
+    hgLoadSqlTab calJac3 ctgPos2 $HOME/kent/src/hg/lib/ctgPos2.sql ctgPos2.tab
+
+############################################################################