extract blasttest method

bash/bioinfo_utils.sh

@@ -120,3 +120,4 @@ createCuffDbTrickyDisk(getwd(), gtfFile, genomeBuild)
 ' | R -q --no-save --no-restore  --args $1 $2
 }
 export -f MakeCuffDB
+

bash/lsf_bioinfo_utils.sh

@@ -44,3 +44,34 @@ mmCountFastGzReads(){
 export -f mmCountFastGzReads
 
 
+
+
+##http://www.biostars.org/p/16471/
+## estimate blast progress for fasta-query files. Result files are assumed to have the fasta id in column 1
+BlastProgress(){
+    if [ $# -eq 0 ]; then echo "Usage: BlastProgress <blast_query_fasta>+"; return; fi
+
+
+   for query in $* ; do
+#        query=$1
+        blast=$query.blast.out
+    #    echo "the blast out is: "$blast
+        #echo "the fasta query is: "$query
+
+        #curquery=$(tail -1 $blast | cut -f 1)
+        # http://tldp.org/LDP/abs/html/fto.html
+        if [ -s $blast ]; then
+    #        echo "file exists and has non-zero size"
+            curquery=$(tail -1 $blast | cut -f 1)
+            curline=$(grep -n $curquery"$" $query |  cut -f 1 -d ':')
+        else
+    #        echo "file does not yet exist or is empty"
+            curline=0
+        fi
+
+        nblines=$(wc -l $query | cut -f 1 -d " ")
+        percent=$(echo "($curline/$nblines) *100" | bc -l | cut -c 1-4)
+        echo "Approximately $percent % of $query were processed."
+    done
+}
+export -f BlastProgress