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Use same file selected in first bash process that has matching digits in it fot the second

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# 1  
Old 07-23-2016
Use same file selected in first bash process that has matching digits in it fot the second
In the below portion of a bash script the user selects a file from a directory.

Code:
select file in $(cd /home/cmccabe/Desktop/NGS/API/5-14-2016/bedtools;ls);do break;done

Code:
files in directory

123_base_counts.txt
456_base_counts.txt
789_base_counts.txt

second portion of bash currently (user manually selects the file)

Code:
select file in $(cd /home/cmccabe/Desktop/NGS/API/5-14-2016/annovar;ls);do break;done

What I am trying to do is if the user selects 123_base_counts.txt in the first select, then in the second select whatever the name of the file in the annovar directory, the one that starts with 123 is used. The files will always have a _ in them. However my attempt seems to have flaws in it that I am not sure how to fix. Thank you Smilie.

The directory in the second select has files names:

Code:
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
789_variant_strandbias_readcount.vcf.hg19_multianno_removed_final

Bash attempt
Code:
printf "please select a file to analyze with a panel \n"
select file in $(cd /home/cmccabe/Desktop/files;ls);do break;done # specify file
            echo $file
for file in /home/cmccabe/Desktop/files/$file; do
     bname=$(basename $file)
     pref=${bname%%.txt}
     done
printf "filtering vcf"
printf "\n\n"
nameNumeric=$(basename $file | awk -F'_' '{print $1}');
secondFile=$(ls /home/cmccabe/Desktop/files/${nameNumeric}*);
            echo $file
for file in /home/cmccabe/Desktop/annovar/$file; do
echo $file 
printf "will be filtered"
done

current output:
please select a file to analyze with a panel 
1) 123_base_counts.txt
2) 456_base_counts.txt
3) 789_base_counts.txt
#? 1
123_base_counts.txt
filtering vcf

/home/cmccabe/Desktop/files/123_base_counts.txt
/home/cmccabe/Desktop/annovar//home/cmccabe/Desktop/files/123_base_counts.txt

I can manually select each file but I am not sure how to automate the selection. Thank you Smilie.
Last edited by cmccabe; 07-23-2016 at 01:56 PM.. Reason: fixed format
# 2  
Old 07-23-2016
Hi - This is only rough but something like the below should work on your data:

Code:
#!/bin/bash
FILESDIR=/home/cmccabe/Desktop/files
ANNOVARDIR=/home/cmccabe/Desktop/annovar

PS3="please select a file to analyze with a panel: "
select file in ${FILESDIR}/*; do
        [[ -z ${file} ]] && printf "Pick a file" || break
done

filename=${file##*/}
file2=$(ls ${ANNOVARDIR}/${filename%%_*}*)
printf "File 1 is: ${file}\n"
printf "File 2 is: ${file2}\n"

This makes the assumption that:
  • There is only 1 file in the 'annovar' directory which has the same prefix (delimited by an underscore) as the associated file in the 'files' directory and it exists
  • This is not just applicable for '123_' but for all files
This User Gave Thanks to pilnet101 For This Post:
cmccabe
# 3  
Old 07-23-2016
That's a great start and close but I cannot seem to get the right syntax for basename .

Currently, the user gets:

Code:
1) /home/cmccabe/Desktop/files/123_base_counts.txt
2) /home/cmccabe/Desktop/files/456_base_counts.txt
3) /home/cmccabe/Desktop/files/789_base_counts.txt
please select a file to analyze with a panel:

If I didn't need the path before the filename where would basename be added?:

Code:
FILESDIR=/home/cmccabe/Desktop/files
ANNOVARDIR=/home/cmccabe/Desktop/annovar

PS3="please select a file to analyze with a panel: "
select file in ${FILESDIR}/*; do
bname=$(basename $file)
done

filename=${file##*/}
file2=$(ls ${ANNOVARDIR}/${filename%%_*}*)
printf "File 1 is: ${file}\n"
printf "File 2 is: ${file2}\n"

desired
Code:
1) 123_base_counts.txt
2) 456_base_counts.txt
3) 789_base_counts.txt
please select a file to analyze with a panel:

Thanks again Smilie
Last edited by jim mcnamara; 07-23-2016 at 10:24 PM.. Reason: added details code tag completion
# 4  
Old 07-23-2016
Sorry about that, I've amended the script slightly so it should work as expected now:

Code:
#!/bin/bash
FILESDIR=/home/cmccabe/Desktop/files
ANNOVARDIR=/home/cmccabe/Desktop/annovar

PS3="please select a file to analyze with a panel: "
select file in $(cd ${FILESDIR};ls *); do
        [[ -z ${file} ]] && printf "Pick a file" || break
done

file1=${FILESDIR}/${file}
file2=$(ls ${ANNOVARDIR}/${file%%_*}*)
printf "File 1 is: ${file1}\n"
printf "File 2 is: ${file2}\n"

It looks like basename isn't really required as you are dealing with the file names themselves straight from the select loop. Then when you create the file1 variable you append the directory in front of it.
This User Gave Thanks to pilnet101 For This Post:
cmccabe
# 5  
Old 07-23-2016
works perfect.... thank you for your help and explanations, I really appreciate them Smilie.
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