Login or Register to Ask a Question and Join Our Community


Shell Programming and Scripting

Bash to update file on prefix match in two directories

Login to Discuss or Reply to this Discussion in Our Community

 
Thread Tools Search this Thread
Top Forums Shell Programming and Scripting Bash to update file on prefix match in two directories
# 1  
Old 02-02-2020
Bash to update file on prefix match in two directories
I am trying to use bash to loop through a directory /path/to/data using a prefix match from /path/to/file. That match is obtained and works using the code below (in green)... what I can not seem to do is populate or update the corresponding prefix_file.txt in /path/to/data with the values in each of the data file in /path/to/data. The data file are always named the same way and have a single value in them.
I don't know if the portion in blue is helpful, but my thinking was on a prefix match each ${f}_file.txtis updated using the data file. Thank you Smilie.

/path/to/data
Code:
ID-5_xx.number.txt    ID-5_xx.diff.txt
67722024              180

ID-5_xx.test.txt      ID-5_xx.common.txt
59733                 92.249581%

AA-1_yy.number.txt    AA-1_yy.diff.txt
46722024              138

AA-1_yy.test.txt      AA-1_yy.common.txt
50033                 82.248581%

current /path/to/file
Code:
ID-5_xx_file.txt
number=
test=
diff=
common=

AA-1_yy_file.txt
number=
test=
diff=
common=

desired /path/to/file
Code:
ID-5_xx_file.txt
number=67722024
test=59733
diff=180
common=92.249581%

AA-1_yy_file.txt
number=46722024
test=50033
diff=138
common=82.248581%

bash
Code:
for f in /path/to/data ; do  # strat process loop for each sample
  file=$(printf '%s' ${f}.*.txt)
     fname=`basename $file` # strip of path
       prefix=$(echo $fname | cut -d. -f1) # remove after .
   if [[ $f = $prefix ]] # only execute file prefix match

    cd /path/to/file # change directory to where ${f}_file.txt is
    then [[ ${f}_file.txt == # update each ${f}_file.txt with values from /path/to/data
       number=${sample}.number.txt
       test=$qc_dir/extract/${sample}.test.txt
       diff=$qc_dir/extract/${sample}.diff.txt
       common=${sample}.common.txt ]]
fi
done

Last edited by cmccabe; 02-02-2020 at 10:01 AM.. Reason: fixed format
# 2  
Old 02-02-2020
How about getting your bash syntax right, first? What you post can't possibly run...

--- Post updated at 18:33 ---

OK, trying to guess what you're after, and making some assumptions, how about
Code:
TDIR="path/to/data"
for FN in ${TDIR}/*number*
  do    grep . ${FN%number*}* |
          awk ' {NFN = $0
                 sub (/\..*$/, "_file.txt", NFN)
                 sub (/^[^\.]*\./, "")
                 sub (/\.txt:/, "=")
                 print > NFN
                }'
   done




catfiles ${TDIR}/*file*
 
---------- data/AA-1_yy_file.txt: ----------

common=82.248581%
diff=138
number=46722024
test=50033

---------- data/ID-5_xx_file.txt: ----------

common=92.249581%
diff=180
number=67722024
test=59733

We assume a *number* file is always present, all files have a .txt suffix, and the order of entries being sorted by item is acceptable...
Last edited by RudiC; 02-02-2020 at 12:47 PM..
These 2 Users Gave Thanks to RudiC For This Post:
cmccabe vbe
# 3  
Old 02-04-2020
Thank you very much Smilie.
# 4  
Old 02-04-2020
That could even be condensed to



Code:
$ TDIR="path/to/data"
$ awk '
         {NFN = $0 = FILENAME ":" $0
         sub (/\..*$/, "_file.txt", NFN)
         sub (/^[^\.]*\./, "")
         sub (/\.txt:/, "=")
         print > NFN
        }' ${TDIR}/*

Be aware that for larger numbers of output files, you'd need to append to the files, and close them after each append.
Login or Register to Ask a Question

Previous Thread | Next Thread

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

awk to update file based on match in 3 fields

Trying to use awk to store the value of $5 in file1 in array x. That array x is then used to search $4 of file1 to find aa match (I use x to skip the header in file1). Since $4 can have multiple strings in it seperated by a , (comma), I split them and iterate througn each split looking for a match.... (2 Replies)
Discussion started by: cmccabe
2 Replies

2. Shell Programming and Scripting

awk move select fields to match file prefix in two directories

In the awk below I am trying to use the file1 as a match to file2. In file2 the contents of $5,&6,and $7 (always tab-delimited) and are copied to the output under the header Quality metrics. The below executes but the output is empty. I have added comments to help and show my thinking. Thank you... (0 Replies)
Discussion started by: cmccabe
0 Replies

3. Shell Programming and Scripting

Bash to extract file prefix and from input to use in output

In the bash below which does execute I am trying to extract the contents of ${id} is 1234, as ${id} stores the variable that changes each time. After the path is removed the contents of ${id} are stored in pref, so they can be used in the output. Currently I am not able to extract the 1234 in the... (6 Replies)
Discussion started by: cmccabe
6 Replies

4. Shell Programming and Scripting

awk to update value based on pattern match in another file

In the awk, thanks you @RavinderSingh13, for the help in below, hopefully it is close as I am trying to update the value in $12 of the tab-delimeted file2 with the matching value in $1 of the space delimeted file1. I have added comments for each line as well. Thank you :). awk awk '$12 ==... (10 Replies)
Discussion started by: cmccabe
10 Replies

5. Shell Programming and Scripting

Perl to update field in file based of match to another file

In the perl below I am trying to set/update the value of $14 (last field) in file2, using the matching NM_ in $12 or $9 in file2 with the NM_ in $2 of file1. The lengths of $9 and $12 can be variable but what is consistent is the start pattern will always be NM_ and the end pattern is always ;... (4 Replies)
Discussion started by: cmccabe
4 Replies

6. Shell Programming and Scripting

awk to update file based on partial match in field1 and exact match in field2

I am trying to create a cronjob that will run on startup that will look at a list.txt file to see if there is a later version of a database using database.txt as the source. The matching lines are written to output. $1 in database.txt will be in list.txt as a partial match. $2 of database.txt... (2 Replies)
Discussion started by: cmccabe
2 Replies

7. Shell Programming and Scripting

Match and store numerical prefix to update files

In the bash below the unique headers of each vcf.gz are stored in a text file with the same name. That is if 16-0000-file.vcf.gz was used the header text file would be 16-0000-file_header.txt. There can be multiple vcf.gz in a directory, usually 3, that I need to fix the header in each file before... (6 Replies)
Discussion started by: cmccabe
6 Replies

8. Shell Programming and Scripting

awk match to update contents of file

I am trying to match $1 in file1 with $2 in file2. If a match is found then $3 and $4 of file2 are copied to file1. Both files are tab-delimeted and I am getting a syntax error and would also like to update file1 in-place without creating a new file, but am not sure how. Thank you :). file1 ... (19 Replies)
Discussion started by: cmccabe
19 Replies

9. Shell Programming and Scripting

awk to update field file based on match

If $1 in file1 matches $2 in file2. Then the value in $2 of file2 is updated to $1"."$2 of file2. The awk seems to only match the two files but not update. Thank you :). awk awk 'NR==FNR{A ; next} $1 in A { $2 = a }1' file1 file2 file1 name version NM_000593 5 NM_001257406... (3 Replies)
Discussion started by: cmccabe
3 Replies

10. Shell Programming and Scripting

how to extract paragraphs from file in BASH script followed by prefix ! , !! and !!!

I]hi all i am in confusion since last 2 days :( i posted thraed yesterday and some friends did help but still i couldnt get solution to my problem let it be very clear i have a long log file of alkatel switch and i have to seperate the minor major and critical alarms shown by ! , !! and !!!... (6 Replies)
Discussion started by: nabmufti
6 Replies
Login or Register to Ask a Question