Bash script to compute the splicing events on a core database and to write

the results in the same core database. Use LSF to run the jobs on a farm.

misc-scripts/alternative_splicing/as_event_computations.sh

+#!/bin/bash
+
+#################################################
+#                                               #
+# Sanger Ensembl specific script to compute and #
+# store Alternative splicing events in a core   #
+# database.                                     #
+# Author: Gautier Koscielny                     #
+# e-mail: ensembl-dev mailing list              #
+#                                               #
+#################################################
+ 
+port=3306
+host=""
+password=""
+user=""
+species=""
+db=""
+core=""
+output_dir="/tmp"
+
+print_help () { 
+    echo "Usage:";
+    echo "    as_event_computations.sh -h <dbhost> [-P <dbport>] -u <dbuser> [-p <dbpass>] -s <species> [-d <dbname>] [-o <output_dir>]";
+    echo "";
+    echo "If the species name is passed, the script will find the corresponding core database on <dbhost>.";
+    echo "If the database name <dbname> is passed, the script will use this database as the core database.";
+    echo "By default, all intermediate results will be written in the /tmp directory.";
+    echo "Please use the -o parameter to pass a different existing writable directory.";
+}
+
+echo "Parsing parameters..."
+
+while getopts ":h:u:p:P:s:d:o:" optname
+  do
+    #echo $optname
+    case "$optname" in
+      "h")
+        echo "Hostname=$OPTARG";
+				host=$OPTARG;
+				echo $host
+        ;;
+      "o")
+        echo "Output directory=$OPTARG";
+				output_dir=$OPTARG;
+        ;;
+      "P")
+        echo "Port=$OPTARG";
+				port=$OPTARG;
+        ;;
+      "p")
+        echo "Password=$OPTARG";
+				password=$OPTARG;
+        ;;
+      "u")
+        echo "User=$OPTARG";
+				user=$OPTARG
+        ;;
+      "d")
+        echo "Database=$OPTARG";
+				db=$OPTARG
+        ;;
+      "s")
+        echo "Species=$OPTARG";
+				species=$OPTARG
+        ;;
+      "?")
+        echo "Unknown option $OPTARG";
+				print_help;
+        ;;
+      ":")
+        echo "No argument value for option $OPTARG"
+				print_help;
+        ;;
+      *)
+      # Should not occur
+        echo "Unknown error while processing options"
+        ;;
+    esac
+    #echo "OPTIND is now $OPTIND"
+  done
+
+if [[ -n "$host" && -n "$user" ]]
+then
+  if [ -z "$db" ]
+  then 
+    if  [ -n "$species" ]
+    then
+      ## Find a core database for this species on the specified server.
+	  if [[ -n "$password" && $password != "" ]]
+	  then
+				core=`mysql -h ${host} -P ${port} -u ${user} -p ${password} -s --skip-column-names -e "show databases like '${species}_core_%'"`
+	  else
+				core=`mysql -h${host} -P${port} -u${user} -s --skip-column-names -e "show databases like '${species}_core_%'"`
+	  fi
+    else
+				echo "Species or/and database name are required." ;
+				print_help;
+				exit 1;
+    fi
+  else
+			core=${db};
+  fi
+else
+		echo "Hostname and username are required."
+		print_help;
+		exit 1;
+fi
+
+# count how many databases match this name
+
+y=0;
+
+for X in ${core}
+do
+		y=$[$y+1];
+done
+
+if [[ ${y} -eq 0 ]]
+then
+		echo "Check your parameters, there is no database matching species '${species}'";
+		exit 1;
+fi
+
+
+if [[ ${y} -gt 1 ]]
+then
+		echo "Check your parameters, there are ${y} databases matching species '${species}':";
+		echo "$core";
+		exit 1;
+fi
+
+
+# Otherwise, start the pipeline
+
+NOW=$(date +"%Y-%m-%d-%H-%M-%S")
+
+echo "Starting pipeline with timestamp '${NOW}'";
+if [ -n "$password" ]
+then
+		bsub -q normal -o ${output_dir}/as_gff_${species}_${NOW}.out -e ${output_dir}/as_gff_${species}_${NOW}.err -J as_gff_${species}_${NOW} "perl Fetch_gff.pl -dbname ${db} -dbhost ${host} -dbport ${port} -dbuser ${user} -dbpass ${password} -o ${output_dir}/${species}_${NOW}_variants.gff"
+else
+		bsub -q normal -o ${output_dir}/as_gff_${species}_${NOW}.out -e ${output_dir}/as_gff_${species}_${NOW}.err -J as_gff_${species}_${NOW} "perl Fetch_gff.pl -dbname ${db} -dbhost ${host} -dbport ${port} -dbuser ${user} -o ${output_dir}/${species}_${NOW}_variants.gff"
+fi
+
+bsub -q small -o ${output_dir}/as_compute_${species}_${NOW}.out -e ${output_dir}/as_compute_${species}_${NOW}.err -w "done(\"as_gff_${species}_${NOW}\")" -J as_compute_${species}_${NOW} "altSpliceFinder -i ${output_dir}/${species}_${NOW}_variants.gff -o ${output_dir}/${species}_${NOW}_events.gff --relax --statistics"
+
+if [ -n "$password" ]
+then
+bsub -q normal -o ${output_dir}/as_populate_${species}_${NOW}.out -e ${output_dir}/as_populate_${species}_${NOW}.err -w "done(\"as_compute_${species}_${NOW}\")" -J as_populate_${species}_${NOW} "perl load_alt_splice_gff.pl -file ${output_dir}/${species}_${NOW}_events.gff -host ${host} -user ${user} -pass ${password} -dbname ${core}"
+else 
+		echo "Sorry, you did not provide any password. The script can't populate the database with the Alternative splicing information.";
+		echo "However, the results are available in ${output_dir}/${species}_${NOW}_events.gff";
+fi
+
+