Shell Programming and Scripting

123_base_counts.txt
456_base_counts.txt

123_variant_strandbias_readcount.vcf.hg19_multianno_removed_final (this one is automatically selected because it has the same starting digits as the original file)
456_variant_strandbias_readcount.vcf.hg19_multianno_removed_final

123_variant_strandbias_readcount.vcf.hg19_multianno_removed_final.txt
456_variant_strandbias_readcount.vcf.hg19_multianno_removed_final.txt

FILESDIR=/home/cmccabe/Desktop/NGS/API/5-14-2016/bedtools
ANNOVARDIR=/home/cmccabe/Desktop/NGS/API/5-14-2016/vcf/overall/annovar

PS3="please select a file1 to analyze with a panel: " # specify file
select file1 in $(cd ${FILESDIR};ls);do break;done
        file1=`basename ${FILESDIR}/${file1}`
        printf "FILE is: ${file1} and will be used to filter reads, identify target bases and genes less than 20 and 30 reads, create a low coverage bed for vizulization, calculate 20x and 30x coverage, and filter the vcf for the 98 gene epilepsy panel"
logfile=/home/cmccabe/Desktop/NGS/API/5-14-2016/process.log
for file1 in /home/cmccabe/Desktop/NGS/API/5-14-2016/bedtools/$file1; do
     bname=$(basename $file1)
     pref=${bname%%.txt}
     grep -wFf /home/cmccabe/Desktop/NGS/panels/EPILEPSY_unix_trim.bed $file1 > /home/cmccabe/Desktop/NGS/API/5-14-2016/panel/reads/${pref}_EPILEPSY.txt
     done >> "$logfile"
# filter vcf
printf "\n\n"
printf "These are all vcf files in the directory:  \n"
ls ${ANNOVARDIR}
file1=`basename ${FILESSDIR}/${file1}`  # file matched
file2=`basename ${ANNOVARDIR}/${file1%%_*}`
path=${ANNOVARDIR}/${file1%%_*}
     printf "The matching identifier for file2 is: ${file2} and will be used filtered using the epilepsy genes\n"
     echo "The full filename is $path"

1) 123_base_counts.txt
2) 456_base_counts.txt 
please select a file1 to analyze with a panel: 1
FILE is: 123_base_counts.txt and will be used to filter reads, identify target bases and genes less than 20 and 30 reads, create a low coverage bed for vizulization, calculate 20x and 30x coverage, and filter the vcf for the 98 gene epilepsy panel

These are all vcf files in the directory:  
123_variant_strandbias_readcount.vcf.hg19_multianno_removed_final.txt
456_variant_strandbias_readcount.vcf.hg19_multianno_removed_final.txt

The matching identifier for file2 is: 123 and will be used filtered using the epilepsy genes
The full file name is /home/cmccabe/Desktop/NGS/API/5-14-2016/vcf/overall/annovar/123

123_base_counts.txt
456_base_counts.txt

123_variant_strandbias_readcount.vcf.hg19_multianno_removed_final.txt
456_variant_strandbias_readcount.vcf.hg19_multianno_removed_final.txt

# manual selection of file
FILESDIR=/home/cmccabe/Desktop/NGS/API/5-14-2016/bedtools
ANNOVARDIR=/home/user

PS3="please select a file to analyze with a panel: " # specify file1
select file1 in $(cd ${FILESDIR};ls);do break;done
          file1=`basename ${FILESDIR}/${file1}`
          printf "FILE is: ${file1} and will be used

# automatic file based on match
FILESDIR=/home/cmccabe/Desktop/NGS/API/5-14-2016/bedtools # match directory
ANNOVARDIR=/home/cmccabe/Desktop/NGS/API/5-14-2016/vcf/overall/annovar # search directory
printf "\n\n"
printf "These are all vcf files in the directory: \n"
ls ${ANNOVARDIR}
file1=`basename ${FILESSDIR}/${file1}`  # file matched
file2=(${ANNOVARDIR}/${file1%%_*}*)
     printf "file2 is: ${file2} and will be used

1) 123_base_counts.txt 
2) 456_base_counts.txt 

please select a file to analyze with a panel: 1
FILE is: 123_base_counts.txt and will be used to filter reads, identify target bases and genes less than 20 and 30 reads, create a low coverage bed for visualization, calculate 20x and 30x coverage, and filter the vcf for the 98 gene epilepsy panel

These are all files in the new directory: 
123_variant_strandbias_readcount.vcf.hg19_multianno_removed_final.txt
456_variant_strandbias_readcount.vcf.hg19_multianno_removed_final.txt
file2 is: /home/cmccabe/Desktop/NGS/API/5-14-2016/vcf/overall/annovar/123_variant_strandbias_readcount.vcf.hg19_multianno_removed_final.txt and will be used 

second time results
1) 123_base_counts.txt  
2) 456_base_counts.txt


please select a file to analyze with a panel: 2
FILE is: 456_base_counts.txt and will be used

These are all files in the new directory: 
123_variant_strandbias_readcount.vcf.hg19_multianno_removed_final.txt
456_variant_strandbias_readcount.vcf.hg19_multianno_removed_final.txt
file2 is: /home/user/123_variant_strandbias_readcount.vcf.hg19_multianno_removed_final.txt and will be used

bash -xv your_script_name

#!/bin/ksh
# manual selection of file
ANNOVARDIR=/home/cmccabe/Desktop/NGS/API/5-14-2016/vcf/overall/annovar
FILESDIR=/home/cmccabe/Desktop/NGS/API/5-14-2016/bedtools
PS3="please select a file to analyze with a panel: "

cd "$FILESDIR"
select file1 in $(ls)
do	[ "$file1" != "" ] && break
done
printf "FILE is: ${file1} and will be used\n\n"

# automatic file based on match
cd "$ANNOVARDIR"
printf "These are all vcf files in the directory:\n"
ls
file2=("${file1%%_*}"*)
file2=$PWD/$file2
printf "file2 is: $file2 and will be used\n"