Rename file using partial match to another


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# 8  
I'm not sure I understand completly but in f1 the same IonCode may appear multiple times. However, the value in uniq is always unique and the each IonCode above each uniq unill the newline in f1 will be found in the data as a pair. That is in f1 IonCode_0404 but in data IonCode_0404.bam and IonCode_0404.bam.bai. In f1 IonCode_0402 but in data IonCode_0402.bam and IonCode_0402.bam.bai.
Both IonCode pairs are renamed with the $2 values from each matching IonCode above uniq with _test after it. Thank you very much Smilie.

Last edited by cmccabe; 10-24-2019 at 07:12 PM..
# 9  
Quote:
Originally Posted by cmccabe
I'm not sure I understand completly but in f1 the same IonCode may appear multiple times. However, the value in uniq is always unique
That is not the case in the demo f1 from post #1 red uniq is duplicated:

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_xx1-127-xxx_xxx_xxx_xxx_xx_xx_xx

This User Gave Thanks to Chubler_XL For This Post:
# 10  
My apologies, I have corected the typo in post 1 and here as well. All 3 uniq values in f1 will always be different I just transcribed them wrong. Line 3 (the duplicate) will never be there (computers make less mistakes) . Thank you Smilie.

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

# 11  
I put an echo "These are the files:" $file statement and the files in data before the script executes are:
Code:
These are the files: IonCode_0402_xxx.xxx_xxx.bam
These are the files: IonCode_0402_xxx.xxx_xxx.bam.bai
These are the files: IonCode_0404_xxx.xxx_xxx.bam
These are the files: IonCode_0404_xxx.xxx_xxx.bam.bai

after the script executes:
Code:
00-0000-xxx-xxx-xxx IonCode_0402 11-1111-yy-yy-yyy IonCode_0402 22-2222-zz-zzzz-zzz IonCode_0404 10-0000-aa-aa-aa IonCode_0412 55-1111-bb-bbb-bbb_test.bam
00-0000-xxx-xxx-xxx IonCode_0402 11-1111-yy-yy-yyy IonCode_0402 22-2222-zz-zzzz-zzz IonCode_0404 10-0000-aa-aa-aa IonCode_0412 55-1111-bb-bbb-bbb_test.bam.bai
IonCode_0402_xxx.xxx_xxx.bam
IonCode_0402_xxx.xxx_xxx.bam.bai

Thank you Smilie.
# 12  
Don't know what that "after the script executes" is showing. Are your filenames ending up with spaces in the etc. like shown above?

Here is the script I'm using:

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*.bam/${to}_test.bam}
          [ -f "$file" ] && [ "$newname" != "$file" ] && 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

And here is my test:
Code:
$ find /path/to/run -type f -print
/path/to/run/f1
/path/to/run/R_2019_00_00_00_00_00_xxxx_xx1-126-xxx_xxx_xxx_xxx_xx_xx_xx/data/IonCode_0402_xxx.xxx_xxx.bam
/path/to/run/R_2019_00_00_00_00_00_xxxx_xx1-126-xxx_xxx_xxx_xxx_xx_xx_xx/data/IonCode_0402_xxx.xxx_xxx.bam.bai
/path/to/run/R_2019_00_00_00_00_00_xxxx_xx1-127-xxx_xxx_xxx_xxx_xx_xx_xx/data/IonCode_0404_xxx.xxx_xxx.bam
/path/to/run/R_2019_00_00_00_00_00_xxxx_xx1-127-xxx_xxx_xxx_xxx_xx_xx_xx/data/IonCode_0404_xxx.xxx_xxx.bam.bai
$ ./cmccabe_rename 
$ find /path/to/run -type f -print
/path/to/run/f1
/path/to/run/R_2019_00_00_00_00_00_xxxx_xx1-126-xxx_xxx_xxx_xxx_xx_xx_xx/data/22-2222-zz-zzzz-zzz_test.bam
/path/to/run/R_2019_00_00_00_00_00_xxxx_xx1-126-xxx_xxx_xxx_xxx_xx_xx_xx/data/22-2222-zz-zzzz-zzz_test.bam.bai
/path/to/run/R_2019_00_00_00_00_00_xxxx_xx1-127-xxx_xxx_xxx_xxx_xx_xx_xx/data/00-0000-xxx-xxx-xxx_test.bam
/path/to/run/R_2019_00_00_00_00_00_xxxx_xx1-127-xxx_xxx_xxx_xxx_xx_xx_xx/data/00-0000-xxx-xxx-xxx_test.bam.bai

This User Gave Thanks to Chubler_XL For This Post:
# 13  
After the rename scripts runs then only one pair of the files is renamed with both values in it, with a space in between. This is shown in the above, but im not sure why. Your output looks good. Thank you Smilie.
# 14  
Here is what I get:


with echo mv
Code:
mv IonCode_0402_xxx.xxx_xxx.bam _test.bam
mv IonCode_0402_xxx.xxx_xxx.bam.bai _test.bam.bai
mv IonCode_0404_xxx.xxx_xxx.bam _test.bam
mv IonCode_0404_xxx.xxx_xxx.bam.bai _test.bam.bai

with mv
Code:
_test.bam
_test.bam.bai

Thank you Smilie.
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