PR changed for annotate_bed.sh

README.md

@@ -1,6 +1,6 @@
 # eggd_coverage_report
 
-This is a tool to generate coverage statistics for NGS data, and combine these into an  interactive HTML report. This gives both summary level and in depth information as to the coverage of the data, including various tables and plots to visualise the data. Examples of the output statistics files and report may be found in `data/example`.<br>
+This is a tool to generate coverage statistics for NGS data, and combine these into an interactive HTML report. This gives both summary level and in depth information as to the coverage of the data, including various tables and plots to visualise the data. Examples of the output statistics files and report may be found in `data/example`.<br>
 
 It is written to take in per base coverage data (as output from tools such as mosdepth and samtools mpileup) as input to calculate coverage for target regions defined in a bed file. <br></br>
 

bin/annotate_bed.sh

@@ -8,15 +8,15 @@ Help()
 {
    # Display Help
     echo "
-    This script may be used to perform bedtools intersect commands to generate the required tsv file
+    This script may be used to perform bedtools intersect commands to generate the required annotated bed file
     for generating single sample coverage statistics."
     echo ""
     echo "Usage:"
     echo ""
     echo "-i    Input bed file; must have columns chromosome, start position, end position, transcript."
     echo "-g    Exons nirvana file, contains required gene and exon information."
     echo "-b    Per base coverage file (output from mosdepth or similar)."
-    echo "-o    Output file name prefix, will have the .tsv suffix."
+    echo "-o    Output file name prefix, will have the .bed suffix."
     echo "-h    Print this Help."
     echo ""
 
@@ -43,26 +43,25 @@ while getopts ":i:g:b:o:h" option; do
             exit
         ;;
         \*) # incorrect option
-
         ;;
    esac
 done
 
-# check for no and incorrect args given
-if  [ -z $input_bed ] || 
-    [ -z $gene_file  ] || 
-    [ -z $bp_coverage ] || 
+# check for no and incorrect args given a
+if  [ -z $input_bed ] ||
+    [ -z $gene_file  ] ||
+    [ -z $bp_coverage ] ||
     [ -z $outfile ]; then
-    
+
     echo "Error: Missing arguments, please see usage below."
         Help
         exit 0
 fi
 
 # add gene and exon annotation to bed file from exons nirvana tsv
-bedtools intersect -a $input_bed -b $gene_file -wa -wb | awk 'OFS="\t" {if ($4 == $9) print}' | cut -f 1,2,3,8,9,10 > $(tmp).txt
+bedtools intersect -a $input_bed -b $gene_file -wa -wb | awk 'OFS="\t" {if ($4 == $9) print}' | cut -f 1,2,3,8,9,10 > ${tmp}.txt
 
 # add coverage annotation from per base coverage bed file
-bedtools intersect -wa -wb -a $tmp.txt -b $bp_coverage | cut -f 1,2,3,4,5,6,8,9,10 > $outfile.tsv
+bedtools intersect -wa -wb -a $tmp.txt -b $bp_coverage | cut -f 1,2,3,4,5,6,8,9,10 > $outfile.bed
 
-echo "Done. Output file: " $outfile.tsv
+echo "Done. Output file: " $outfile.bed