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Rename file using partial match to another

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# 1  
Old 10-23-2019
Rename file using partial match to another
In the below I am trying to rename the contents within each data subfolder in a specific run, based on a partial match of the IonCode_0000_ in each file in the data subdirectory to $1 in f1. There will be multiple runs in f1 but each run in $uniq is unique and will be found in f1 and the rename values stored in $string. The below code is commented as to what I think is going on. Thank you Smilie.


f1
Code:
IonCode_0404 00-0000-xxx-xxx-xxx
IonCode_0402 11-1111-yy-yy-yyy
R_2019_00_00_00_00_00_xxxx_xx1-127-xxx_xxx_xxx_xxx_xx_xx_xx

IonCode_0402 22-2222-zz-zzzz-zzz
R_2019_00_00_00_00_00_xxxx_xx1-126-xxx_xxx_xxx_xxx_xx_xx_xx

IonCode_0404 10-0000-aa-aa-aa
IonCode_0412 55-1111-bb-bbb-bbb
R_2019_00_00_00_00_00_xxxx_xx1-120-xxx_xxx_xxx_xxx_xx_xx_xx

Code:
/path/to/run/R_2019_00_00_00_00_00_xxxx_xx1-127
      data   --- sub-folder ---
      IonCode_0402_xxx.xxx_xxx.bam
      IonCode_0402_xxx.xxx_xxx.bam.bai
      IonCode_0404_xxx.xxx_xxx.bam
      IonCode_0404_xxx.xxx_xxx.bam.bai

Code:
dir=/path/to/run/
for run in "$dir"/R_2019* ; do  ## # matching "R_2019*" to operate on desired directory and expand
  uniq=${run##*/}  ## store run with no path as s5
  cd "$dir"/"$uniq"/data  ## change directory to subfolder
   string=$(awk -F '\n' -v RS="" -v ref="$uniq" '$0 ~ ref {d=split($0, val, " "); for(i=2;i<d;i+=2) printf "%s ",val[i]; printf "\n"}' "$dir"/f1)  ## loop through f1 for unique run and store $2 in string
   for $f in "$dir"/"$s5"/data/*.bam* ; do sample_basename=$(basename "${f}") ;
     rename_file_path="$string" ## define rename string
     cmd=$(sed -n "/$f/,/IonCode_[0-9][0-9][0-9][0-9]_*/{s/\(.*\.bam\) \(.*\)/mv \1 \2/g}" $rename_file_path)  ## rename file in data subfolder matching IonCode_ to f1 and replacing with $2 of f1
  done
done

desired in data
Code:
11-1111-yy-yy-yyy_test.bam
11-1111-yy-yy-yyy_test.bam.bai
00-0000-xxx-xxx-xxx_test.bam
00-0000-xxx-xxx-xxx_test.bam.bai

Last edited by cmccabe; 10-24-2019 at 08:03 PM.. Reason: corrected typo
# 2  
Old 10-23-2019
You were pretty close on this. I used a here-string (<<<) piped into a while read block. As we want to change directories in the loop using a sub shell ensures the pwd is reset after each rename loop.

change echo mv in red below to mv if you are happy with what it's doing

Code:
dir=/path/to/run/
for run in "$dir"/R_2019* ; do  ## # matching "R_2019*" to operate on desired directory and expand
  uniq=${run##*/}  ## store run with no path as s5
  while read from to
  do
     (
       cd "$dir"/"$uniq"/data
       for file in *.bam*
       do
          newname=${file/$from/$to}
          [ -f "$file" ] && [ "$newname" != "$file" ] && echo mv "$file" "$newname"
       done
     )
  done <<<$(
     awk -F '\n' -v RS="" -v ref="$uniq" '
         $0 ~ ref {
             d=split($0, val);
             for(i=1;i<d;i++) print val[i];
          }' "$dir"/f1
  )  ## loop through f1 for unique run and populate from and to
done

This User Gave Thanks to Chubler_XL For This Post:
cmccabe
# 3  
Old 10-24-2019
Looks like the last file in the directory is getting renamed with both matching not the unique. Is another loop needed or all the values on one line instead of separate? Thank you Smilie.


Code:
mv IonCode_0404_xxx.xxx_xxx.bam 00-0000-xxx-xxx-xxx IonCode_0402 11-1111-yy-yy-yyy_xxx.xxx_xxx.bam
mv IonCode_0404_xxx.xxx_xxx.bam.bai 00-0000-xxx-xxx-xxx IonCode_0402 11-1111-yy-yy-yyy_xxx.xxx_xxx.bam.bai

desired
Code:
11-1111-yy-yy-yyy_test.bam   ---- this is IonCode_0402_xxx.xxx_xxx ---
11-1111-yy-yy-yyy_test.bam.bai   ---- this is IonCode_0402_xxx.xxx_xxx ---
00-0000-xxx-xxx-xxx_test.bam   ---- this is IonCode_0404_xxx.xxx_xxx ---
00-0000-xxx-xxx-xxx_test.bam.bai ---- this is IonCode_0404_xxx.xxx_xxx ---

Last edited by cmccabe; 10-24-2019 at 01:52 PM.. Reason: fixed format
# 4  
Old 10-24-2019
It looks a bit complicated.
Perhaps you want to do the following?
Code:
dir=/path/to/run
ind=0
while read a b c
do
  if [ -n "$b" ]
  then
    fsearch[ind]=$a
    mvto[ind]=$b
    ((ind++))
  elif [ -z "$a" ]
  then
    ind=0
  else
    while [ $ind -gt 0 ]
    do
      ((ind--))
      echo "In $dir/$a/data/ rename ${fsearch[ind]}*.bam* to ${mvto[ind]}_test.bam*" 
    done
  fi
done < $dir/f1

This User Gave Thanks to MadeInGermany For This Post:
cmccabe
# 5  
Old 10-24-2019
Quote:
Originally Posted by cmccabe
Looks like the last file in the directory is getting renamed with both matching not the unique. Is another loop needed or all the values on one line instead of separate? Thank you Smilie.
What do you want to happen here? f1 requires that IonCode_0404 in directory *127* be renamed to both 10-0000-aa-aa-aa and 00-0000-xxx-xxx-xxx. Is this a mistake in the data file or how should the script handle this?

Quote:
Originally Posted by cmccabe
desired
Code:
11-1111-yy-yy-yyy_test.bam   ---- this is IonCode_0402_xxx.xxx_xxx ---
11-1111-yy-yy-yyy_test.bam.bai   ---- this is IonCode_0402_xxx.xxx_xxx ---
00-0000-xxx-xxx-xxx_test.bam   ---- this is IonCode_0404_xxx.xxx_xxx ---
00-0000-xxx-xxx-xxx_test.bam.bai ---- this is IonCode_0404_xxx.xxx_xxx ---

Change the newname assignment to this newname=${file/$from*.bam/${to}_test.bam}
Last edited by Chubler_XL; 10-24-2019 at 05:15 PM..
This User Gave Thanks to Chubler_XL For This Post:
cmccabe
# 6  
Old 10-24-2019
Looks like only one pair gets renamed with both values: Thank you Smilie.


4 original files:
Code:
IonCode_0402_xxx.xxx_xxx.bam
IonCode_0402_xxx.xxx_xxx.bam.bai
IonCode_0404_xxx.xxx_xxx.bam
IonCode_0404_xxx.xxx_xxx.bam.bai

Current:
Code:
IonCode_0402_xxx.xxx_xxx.bam
IonCode_0402_xxx.xxx_xxx.bam.bai
00-0000-xxx-xxx-xxx IonCode_0402 11-1111-yy-yy-yyy_test.bam.bam
00-0000-xxx-xxx-xxx IonCode_0402 11-1111-yy-yy-yyy_test.bam.bam.bai

Desired after rename:
Code:
11-1111-yy-yy-yyy_test.bam   ---- this is IonCode_0402_xxx.xxx_xxx ---
11-1111-yy-yy-yyy_test.bam.bai   ---- this is IonCode_0402_xxx.xxx_xxx ---
00-0000-xxx-xxx-xxx_test.bam   ---- this is IonCode_0404_xxx.xxx_xxx ---
00-0000-xxx-xxx-xxx_test.bam.bai ---- this is IonCode_0404_xxx.xxx_xxx ---

# 7  
Old 10-24-2019
I further qualified my question (see #5 above) - this appears to be a problem with the data file.

If the actual renames were done instead of echo, only the first match would apply as the file would then have a different name and the 2nd rename would not be attempted. Red lines will not occur as file has already be renamed on lines 1 and 2:

Code:
$ ./cmccabe_rename 
mv IonCode_0404_xxx.xxx_xxx.bam 00-0000-xxx-xxx-xxx_test.bam
mv IonCode_0404_xxx.xxx_xxx.bam.bai 00-0000-xxx-xxx-xxx_test.bam.bai
mv IonCode_0402_xxx.xxx_xxx.bam 11-1111-yy-yy-yyy_test.bam
mv IonCode_0402_xxx.xxx_xxx.bam.bai 11-1111-yy-yy-yyy_test.bam.bai
mv IonCode_0404_xxx.xxx_xxx.bam 10-0000-aa-aa-aa_test.bam
mv IonCode_0404_xxx.xxx_xxx.bam.bai 10-0000-aa-aa-aa_test.bam.bai

Last edited by Chubler_XL; 10-24-2019 at 05:26 PM..
This User Gave Thanks to Chubler_XL For This Post:
cmccabe
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