Rename file using partial match to another


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# 15  
Are you using bash shell? Can you post output with this additional debugging:

Code:
#!/bin/bash
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
       echo "Rename from:$from to:$to"
       for file in *.bam*
       do
          newname=${file/$from*.bam/${to}_test.bam}
          [ -f "$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

Here is how this looks with my setup:

Code:
$ ./cmccabe_rename 
Rename from:IonCode_0404 to:10-0000-aa-aa-aa
Rename from:IonCode_0412 to:55-1111-bb-bbb-bbb
Rename from:IonCode_0402 to:22-2222-zz-zzzz-zzz
mv IonCode_0402_xxx.xxx_xxx.bam 22-2222-zz-zzzz-zzz_test.bam
mv IonCode_0402_xxx.xxx_xxx.bam.bai 22-2222-zz-zzzz-zzz_test.bam.bai
Rename from:IonCode_0404 to:00-0000-xxx-xxx-xxx
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
Rename from:IonCode_0402 to:11-1111-yy-yy-yyy

This User Gave Thanks to Chubler_XL For This Post:
# 16  
Here is the output, yes I am using bash shell. Thank you Smilie.


Code:
 with echo
Rename from: to:
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

Files in directory to rename
Code:
ll
total 8
drwxr--r-- 2 cmccabe cmccabe 4096 Oct 28 09:59 ./
drwxr--r-- 3 cmccabe cmccabe 4096 Oct 28 08:12 ../
-rw-rw-r-- 1 cmccabe cmccabe    0 Oct 28 09:56 IonCode_0404_xxx_xxx_xxx.bam
-rw-rw-r-- 1 cmccabe cmccabe    0 Oct 28 09:58 IonCode_0404_xxx_xxx_xxx.bam.bai
-rw-rw-r-- 1 cmccabe cmccabe    0 Oct 28 09:50 IonCode_0402_xxx_xxx_xxx.bam
-rw-rw-r-- 1 cmccabe cmccabe    0 Oct 28 09:54 IonCode_0402_xxx_xxx_xxx.bam.bai

without echo in the code only one pair of files gets renamed with both values
Code:
ll
total 8
drwxr--r-- 2 cmccabe cmccabe 4096 Oct 28 09:59 ./
drwxr--r-- 3 cmccabe cmccabe 4096 Oct 28 08:12 ../
-rw-rw-r-- 1 cmccabe cmccabe    0 Oct 28 09:56 00-0000-xxx-xxx-xxx IonCode_0402 11-1111-yy-yy-yyy_test.bam
-rw-rw-r-- 1 cmccabe cmccabe    0 Oct 28 09:58 00-0000-xxx-xxx-xxx IonCode_0402 11-1111-yy-yy-yyy_test.bam.bai
-rw-rw-r-- 1 cmccabe cmccabe    0 Oct 28 09:50 IonCode_0402_xxx_xxx_xxx.bam
-rw-rw-r-- 1 cmccabe cmccabe    0 Oct 28 09:54 IonCode_0402_xxx_xxx_xxx.bam.bai


Last edited by cmccabe; 10-28-2019 at 01:18 PM..
# 17  
I suspect you have some corruption in the format of the f1 file. Perhaps it has been edited with a DOS editor or something like that.

Can you post here the output of od -c /path/to/run/f1
This User Gave Thanks to Chubler_XL For This Post:
# 18  
Here is the output ofod -c /path/to/f1. Thank you Smilie.

Code:
0000000   I   o   n   C   o   d   e   _   0   4   0   4       0   0   -
0000020   0   0   0   0   -   x   x   x   -   x   x   x   -   x   x   x
0000040  \n   I   o   n   C   o   d   e   _   0   4   0   2       1   1
0000060   -   1   1   1   1   -   y   y   -   y   y   -   y   y   y  \n
0000100   R   _   2   0   1   9   _   0   0   _   0   0   _   0   0   _
0000120   0   0   _   0   0   _   x   x   x   x   _   x   x   1   -   1
0000140   2   7   -   x   x   x   _   x   x   x   _   x   x   x   _   x
0000160   x   x   _   x   x   _   x   x   _   x   x  \n  \n   I   o   n
0000200   C   o   d   e   _   0   4   0   2       2   2   -   2   2   2
0000220   2   -   z   z   -   z   z   z   z   -   z   z   z  \n   R   _
0000240   2   0   1   9   _   0   0   _   0   0   _   0   0   _   0   0
0000260   _   0   0   _   x   x   x   x   _   x   x   1   -   1   2   6
0000300   -   x   x   x   _   x   x   x   _   x   x   x   _   x   x   x
0000320   _   x   x   _   x   x   _   x   x  \n  \n   I   o   n   C   o
0000340   d   e   _   0   4   0   4       1   0   -   0   0   0   0   -
0000360   a   a   -   a   a   -   a   a  \n   I   o   n   C   o   d   e
0000400   _   0   4   1   2       5   5   -   1   1   1   1   -   b   b
0000420   -   b   b   b   -   b   b   b  \n   R   _   2   0   1   9   _
0000440   0   0   _   0   0   _   0   0   _   0   0   _   0   0   _   x
0000460   x   x   x   _   x   x   1   -   1   2   0   -   x   x   x   _
0000500   x   x   x   _   x   x   x   _   x   x   x   _   x   x   _   x
0000520   x   _   x   x  \n

# 19  
Nothing wrong with the data file, it matches what I'm using here byte-for-byte. Can you post the script you are using?
This User Gave Thanks to Chubler_XL For This Post:
# 20  
I pass run_dir as an argument instead of hardcoding dir. I think that is the only difference. I made that change to make it easier for others. Thank you Smilie

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

# 21  
Running out of ideas on why this isn't working for you - Is they running on Solaris OS? Perhaps you need to user nawk instead of awk
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