/home/cmccabe/f1/file is the path to file (which has all the necessary information for the move, (folder name, ids).
The for loop on RDIR was for trimming the R_2019 in file to match the folder name in /home/cmccabe/f2 but is undefined and maybe should be /home/cmccabe/f1/file. The FILE2=$(awk '{print $2}' $f') was then intended to read each id from file1 in FILE2. The code executes but nothing is moved and set -x shows the variables not being populated correctly as you already knew .I indented the code above but add comments to help me learn and help me in my logic. Thank you for your help.
I rewrote the script (well a portion) and most of the variables seem good: $STRING is the same as FILE2, I just changed the name to hopefully be more clear as I am looking for a string. However, the loop is not working so only the first id is retained in $STRING. I think I am on the right track but is there a better way? Thank you .
Code:
set -x
DIR=/home/cmccabe/f1
DEST=/home/cmccabe/f2
for file in "$DIR"/variants/*.vcf ; do
bname=$(basename $file) # strip of path
VCF="$(echo $bname|cut -d. -f1)" # remove .vcf extension
for f in "$DIR"/file; do STRING=( $(awk '{for(i=2; i<=NF; i++) print $i}' "$DIR"/file) ); echo "This is the string" "$STRING"; done
done
set -x
Code:
cmccabe@Satellite-M645:~$ set -x
cmccabe@Satellite-M645:~$ DIR=/home/cmccabe/f1
+ DIR=/home/cmccabe/f1
cmccabe@Satellite-M645:~$ DEST=/home/cmccabe/f2
+ DEST=/home/cmccabe/f2
cmccabe@Satellite-M645:~$ for file in "$DIR"/variants/*.vcf ; do
> bname=$(basename $file) # strip of path
> VCF="$(echo $bname|cut -d. -f1)" # remove .vcf extension
> for f in "$DIR"/file; do STRING=( $(awk '{for(i=2; i<=NF; i++) print $i}' "$DIR"/file) ); echo "This is the string" "$STRING"; done
> done
+ for file in '"$DIR"/variants/*.vcf'
++ basename /home/cmccabe/f1/variants/19-0000-LastName-FirstName.vcf
+ bname=19-0000-LastName-FirstName.vcf
++ echo 19-0000-LastName-FirstName.vcf
++ cut -d. -f1
+ VCF=19-0000-LastName-FirstName
+ for f in '"$DIR"/file'
+ STRING=($(awk '{for(i=2; i<=NF; i++) print $i}' "$DIR"/file))
++ awk '{for(i=2; i<=NF; i++) print $i}' /home/cmccabe/f1/file
+ echo 'This is the string' 19-0000-LastName-FirstName
This is the string 19-0000-LastName-FirstName
+ for file in '"$DIR"/variants/*.vcf'
++ basename /home/cmccabe/f1/variants/19-0002-L-F.vcf
+ bname=19-0002-L-F.vcf
++ echo 19-0002-L-F.vcf
++ cut -d. -f1
+ VCF=19-0002-L-F
+ for f in '"$DIR"/file'
+ STRING=($(awk '{for(i=2; i<=NF; i++) print $i}' "$DIR"/file))
++ awk '{for(i=2; i<=NF; i++) print $i}' /home/cmccabe/f1/file
+ echo 'This is the string' 19-0000-LastName-FirstName
This is the string 19-0000-LastName-FirstName
+ for file in '"$DIR"/variants/*.vcf'
++ basename /home/cmccabe/f1/variants/19-0004-La-Fi.vcf
+ bname=19-0004-La-Fi.vcf
++ echo 19-0004-La-Fi.vcf
++ cut -d. -f1
+ VCF=19-0004-La-Fi
+ for f in '"$DIR"/file'
+ STRING=($(awk '{for(i=2; i<=NF; i++) print $i}' "$DIR"/file))
++ awk '{for(i=2; i<=NF; i++) print $i}' /home/cmccabe/f1/file
+ echo 'This is the string' 19-0000-LastName-FirstName
This is the string 19-0000-LastName-FirstName
+ for file in '"$DIR"/variants/*.vcf'
++ basename /home/cmccabe/f1/variants/19-0020-Las-Fir.vcf
+ bname=19-0020-Las-Fir.vcf
++ echo 19-0020-Las-Fir.vcf
++ cut -d. -f1
+ VCF=19-0020-Las-Fir
+ for f in '"$DIR"/file'
+ STRING=($(awk '{for(i=2; i<=NF; i++) print $i}' "$DIR"/file))
++ awk '{for(i=2; i<=NF; i++) print $i}' /home/cmccabe/f1/file
+ echo 'This is the string' 19-0000-LastName-FirstName
This is the string 19-0000-LastName-FirstName
+ for file in '"$DIR"/variants/*.vcf'
++ basename /home/cmccabe/f1/variants/190319-Control.vcf
+ bname=190319-Control.vcf
++ echo 190319-Control.vcf
++ cut -d. -f1
+ VCF=190319-Control
+ for f in '"$DIR"/file'
+ STRING=($(awk '{for(i=2; i<=NF; i++) print $i}' "$DIR"/file))
++ awk '{for(i=2; i<=NF; i++) print $i}' /home/cmccabe/f1/file
+ echo 'This is the string' 19-0000-LastName-FirstName
This is the string 19-0000-LastName-FirstName
+ for file in '"$DIR"/variants/*.vcf'
++ basename /home/cmccabe/f1/variants/190320-Control.vcf
+ bname=190320-Control.vcf
++ echo 190320-Control.vcf
++ cut -d. -f1
+ VCF=190320-Control
+ for f in '"$DIR"/file'
+ STRING=($(awk '{for(i=2; i<=NF; i++) print $i}' "$DIR"/file))
++ awk '{for(i=2; i<=NF; i++) print $i}' /home/cmccabe/f1/file
+ echo 'This is the string' 19-0000-LastName-FirstName
This is the string 19-0000-LastName-FirstName
My input:
File_1:
2000_t
g1110.b1
abb.1
2001_t
g1111.b1
abb.2
abb.2
g1112.b1
abb.3
2002_t
.
.
File_2:
2000_t Ali england 135
abb.1 Zoe british 150
2001_t Ali england 305
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03-27-2019
.I indented the code above but add comments to help me learn and help me in my logic. Thank you for your help