diff Y.sh @ 0:05c27700e5ca

initial commit

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Y.sh	Thu Sep 04 18:24:19 2014 -0400
@@ -0,0 +1,32 @@
+#!/bin/bash
+set -e;
+email_address_of_user=$1;
+echo "email: " $email_address_of_user;
+
+echo "Calculation of Y-linked genes started."
+./scripts/prepare_statistics.sh;
+echo "Statistics done";
+	
+#filter contigs, which are candidate Y genes - very divergent from their X counterparts
+perl scripts/filter_diverged_Y_contigs.pl scripts/statistics/stat_mother scripts/statistics/stat_father scripts/statistics/stat_daughter scripts/statistics/stat_son >Y_results.txt;
+perl scripts/get_sequences_based_on_ids.pl references/reference_male.fasta Y_list >Y_results_sequences.txt;
+
+if [[ -s Y_list ]] ; then
+	get_results_in_bam_file () 
+	{
+	  for ARG in "$@";
+	    do
+	    	./scripts/createBamFromResults.sh Y_list bam/aln_cleaned_sorted_deduplicated_${ARG}_male.bam bam/${ARG}_male.bam;
+	    	samtools index bam/${ARG}_male.bam;
+	    done;
+	}
+
+	get_results_in_bam_file mother father daughter son;
+	wait;
+	#send BAM files with corresponding contigs
+	mutt -s "LINKYX: Results of computation for Y-linked genes" $email_address_of_user -a bam/mother_male.bam -a bam/mother_male.bam.bai -a bam/father_male.bam -a bam/father_male.bam.bai -a bam/daughter_male.bam -a bam/daughter_male.bam.bai -a bam/son_male.bam -a bam/son_male.bam.bai < messages_to_user/message_results_sentBamY;
+else 
+		#we found NO genes
+		echo "No sequences found." >Y_results.txt;
+		echo "No sequences found." >Y_results_sequences.txt;
+fi
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