diff estimate_unique_counts.sh @ 2:14d6929f8aa1 draft default tip

Tool tests or/and test-data are missing.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/estimate_unique_counts.sh	Thu Sep 11 08:30:05 2014 -0400
@@ -0,0 +1,86 @@
+#!/bin/bash
+
+############################################################
+#Create table of fragments containing coordinates[RNA molecule, start,end], number of mapped reads, number of unique barcodes and 3'most nucleotide of cDNA (on that was ligated to)
+############################################################
+#Remove untemplated nucleotides and create positions_temp file 
+
+#defaults
+output_dir="output_dir"
+priming_pos=-1
+
+#parse input
+while getopts hf:b:p:o: myarg
+do	case "$myarg" in
+	h)	echo "Usage: estimate_unique_counts.sh -f <bam_file> -b <barcodes_file> -o <output_dir>"
+		exit ;;
+	f)	bamfile="$OPTARG" ;; #required
+	b)	barcodes="$OPTARG" ;; #required
+	p)	priming_pos="$OPTARG" ;; #optional
+	o)	output_dir="$OPTARG" ;;	#optional
+	[?])	echo "Usage: estimate_unique_counts.sh -f <myfile.bam> -b <barcodes.txt>"
+		exit 1 ;;
+	esac
+done
+
+mkdir $output_dir
+
+samtools view $bamfile |  awk 'BEGIN{OFS="\t"}{if(substr($0,1,1)!="@"){print}}' - | awk -v out="${output_dir}/trimming_stats.txt" 'BEGIN{OFS="\t";counter[0]=0;counter[1]=0;counter[2]=0;counter[3]=0}
+function abs(value){return(value<0?-value:value)}
+($2==99 && /[\s\t]MD:Z:/ && !/MD:Z:([012][ACGT])/)  {print($1, $3, $4+0, $4+abs($9)-1);counter[0]++;next};
+($2==99 && /[\s\t]MD:Z:0[ACGT]/ && !/MD:Z:0[ACGT][01][ACGT]/) {print($1, $3, $4+1, $4+abs($9)-1);counter[1]++;next};
+($2==99 && (/[\s\t]MD:Z:1[ACGT]/ && !/MD:Z:1[ACGT]0[ACGT]/ || (/MD:Z:0[ACGT]0[ACGT]/ && !/MD:Z:0[ACGT]0[ACGT]0[ACGT]/))) {print($1, $3, $4+2, $4+abs($9)-1);counter[2]++;next};
+($2==99 && ((/[\s\t]MD:Z:1[ACGT]0[ACGT]/)||(/MD:Z:0[ACGT]1[ACGT]/)||(/MD:Z:0[ACGT]0[ACGT]0[ACGT]/)||(/MD:Z:2[ACGT]/))) {print($1, $3, $4+3, $4+abs($9)-1);counter[3]++;next}
+END{print("No trimming:",counter[0],"1 nt trimmed:", counter[1],"2 nt trimmed:", counter[2],"3 nt trimmed:",counter[3]) > out}' | sort -k1,1 | gzip > positions_temp_sorted.gz &
+
+# Computing barcode length (Use the first line and compute the string length of the second column
+
+TMP=`head -1 $barcodes | awk '{print $2}'`
+BAR_LEN=`echo ${#TMP}`
+
+# Remove "@" from barcodes and sort them
+sed 's/^.//' $barcodes | sort -k1,1 | gzip > barcodes_temp_sorted.gz &
+
+wait 
+
+# Merge poistions and barcodes
+join -1 1 <(zcat positions_temp_sorted.gz) <(zcat barcodes_temp_sorted.gz) | cut -f 2,3,4,5 -d " " | awk '{if($4 !~ /N/){print}}' | awk -v bar_len="${BAR_LEN}" '{if(length($4)==bar_len){print}}' | gzip > merged_temp.gz
+
+#### If priming flag is set....
+if [ $priming_pos != -1 ]; then
+    zcat merged_temp.gz | awk -v pos="${priming_pos}" '{print $1, $2, pos, $4}' - > merged_temp2
+    cat merged_temp2 | gzip > merged_temp.gz
+    rm merged_temp2
+fi
+
+#File summary.gz columns: RNA_ID, Start, End, barcode sequence, sequenced_count[=number of sequenced fragments fulfilling previous requiremnts]
+
+zcat merged_temp.gz | awk '{barcode[$1][$2][$3][$4]++}END{
+for(RNA in barcode){
+for(start_position in barcode[RNA]){
+for(end_position in barcode[RNA][start_position]){
+for(barseq in barcode[RNA][start_position][end_position]){print RNA,start_position,end_position,barseq,barcode[RNA][start_position][end_position][barseq]}}}}}' > $output_dir/summary.txt
+
+#File unique_barcodes columns: RNA_ID, Start, End, number of unique barcodes observed for this fragment [PROBLEM: How to treat the different 3cdns for the same fragment? if the template was homogenous then it should be always the same]
+
+awk '{barcode[$1][$2][$3]++}END{
+for(RNA in barcode){
+for(start_position in barcode[RNA]){
+for(end_position in barcode[RNA][start_position]){print RNA,start_position,end_position,barcode[RNA][start_position][end_position]}}}}' $output_dir/summary.txt > $output_dir/unique_barcodes.txt &
+
+#read_counts.gz colums: RNA_ID, Start, End, sequenced_count
+
+zcat merged_temp.gz | awk '{barcode[$1][$2][$3]++}END{
+for(RNA in barcode){
+for(start_position in barcode[RNA]){
+for(end_position in barcode[RNA][start_position]){print RNA,start_position,end_position,barcode[RNA][start_position][end_position]}}}}' > $output_dir/read_counts.txt &
+
+wait
+
+##Remove temporary files - didn't do it, in case debugging needed.
+
+rm positions_temp_sorted.gz
+rm barcodes_temp_sorted.gz
+#rm merged_temp.gz
+
+##End of remove temp files