src/hg/makeDb/doc/felCatV17e.txt 1.7

Index: src/hg/makeDb/doc/felCatV17e.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/felCatV17e.txt,v
retrieving revision 1.6
retrieving revision 1.7
diff -b -B -U 4 -r1.6 -r1.7
--- src/hg/makeDb/doc/felCatV17e.txt	31 Mar 2010 21:32:36 -0000	1.6
+++ src/hg/makeDb/doc/felCatV17e.txt	1 Apr 2010 16:37:14 -0000	1.7
@@ -72,19 +72,19 @@
    # For unplaced scalfolds, named them as chrUn_xxxxxxxx
    #   where xxxxxx is the original access id as: chrUn_ACBE01000381.1 
    # and put it into chrUn.* files 
    # copy all the comment lines (start with #)
+S=Primary_Assembly/unplaced_scaffolds
 zcat ${S}/AGP/unplaced.scaf.agp.gz | grep "^#" > ucscChr/chrUn.agp
    # append the gap records
 zcat ${S}/AGP/unplaced.scaf.agp.gz | grep -v "^#" \
         | sed -e "s/^/chrUn_/" >> ucscChr/chrUn.agp
 gzip ucscChr/chrUn.agp &
 
-S=Primary_Assembly/unplaced_scaffolds
 zcat ${S}/FASTA/unplaced.scaf.fa.gz \
         | sed -e "s#^>.*|gb|#>chrUn_#; s#|.*##" | gzip > ucscChr/chrUn.fa.gz
    # about 104034 sequences in the unplaced
-zcat chrUn.fa.gz | grep "^>" | wc
+zcat ucscChr/chrUn.fa.gz | grep "^>" | wc
    #  104034  104034 2275648
 
    # Check them with faSize 
    faSize Primary_Assembly/unplaced_scaffolds/FASTA/unplaced.scaf.fa.gz 
@@ -96,8 +96,21 @@
 
 
 ##########################################################################
 # Initial genome build (Done - 2010-03-03 -Chin)
+
+# decide the right order by
+ hgsql -e "select orderKey,name from dbDb order by orderKey;" \
+ hgcentraltest | less
+    # 168     cavPor3
+    # 169     cavPor2
+    # 189     oryCun2
+    # 190     oryCun1
+    # 191     ochPri2
+    # 200     eriEur1
+    # 217     felCat3
+ 
+
     cd /hive/data/genomes/felCatV17e
 
     cat << '_EOF_' > felCatV17e.config.ra
 # Config parameters for makeGenomeDb.pl: