Sponsored Content
Top Forums Shell Programming and Scripting Rename file using partial match to another Post 303040446 by Chubler_XL on Tuesday 29th of October 2019 02:47:56 PM
Old 10-29-2019
OK I've found the issue - you have a folder that wasn't in the f1 file and so from and to were not populated this should correct it:

Code:
run_dir=$1
for run in "$run_dir" ; do  ## # grab run to operate on desired directory
   uniq=${run_dir##*/}  ## store run with no path as uniq
while read from to
  do
     [ -z "$to" ] ||
     (
       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

This User Gave Thanks to Chubler_XL For This Post:
 

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

awk partial match and filter records

Hi, I am having file which contains around 15 columns, i need to fetch column 3,12,14 based on the condition that column 3 starts with 40464 this is the sample data how to achieve that (3 Replies)
Discussion started by: aemunathan
3 Replies

2. Shell Programming and Scripting

Using grep returns partial matches, I need to get an exact match or nothing

I’m trying to modify someone perl script to fix a bug. The piece of code checks that the zone name you want to add is unique. However, when the code runs, it finds a partial match using grep, and decides it already exists, so the “create” command exits. $cstatus = `${ZADM} list -vic | grep... (3 Replies)
Discussion started by: TKD
3 Replies

3. UNIX for Dummies Questions & Answers

Partial match in two files then substitute

Hi, I was trying to figure this out but failed so I hope someone here can help me, thank you in advance. I have two files. file1: aa M bb N cc O dd P ee Q file2: aa A_87_P254063 cc A_87_P016532 bb A_87_P104793 dd A_87_P055331 ee A_87_P059706 aa A_87_P071636 ee A_87_P028302... (2 Replies)
Discussion started by: yuejian
2 Replies

4. UNIX for Dummies Questions & Answers

How to substitute for the partial match?

Hi I have a question and hope I can get answer here. Thank you in advance. I have two files: file1: aa X bb Y cc Z file2: cc A bb B dd C aa D bb E If the 1st column match in both file1 and file2, the 2nd column in file2 will be replaced by the 2nd column in file1. If there is no... (2 Replies)
Discussion started by: yuejian
2 Replies

5. Shell Programming and Scripting

Match partial text

I posted the incorrect files yesterday and apologize. I also modified the awk script but with no luck. There are two text files in the zip (name.txt and output.txt). I am trying to match $2 in name.txt with $1 in output.txt and if they match then $1 of name.txt is copied to $7 of output.txt. ... (7 Replies)
Discussion started by: cmccabe
7 Replies

6. Shell Programming and Scripting

Rename specific file extension in directory with match to another file in bash

I have a specific set (all ending with .bam) of downloaded files in a directory /home/cmccabe/Desktop/NGS/API/2-15-2016. What I am trying to do is use a match to $2 in name to rename the downloaded files. To make things a more involved the date of the folder is unique and in the header of name... (1 Reply)
Discussion started by: cmccabe
1 Replies

7. Shell Programming and Scripting

Rename files to match file list pattern

Hi All, I have 100 folders with the first delimiter has a unique name i.e (123_hello and 575_hello) and each folder have atlist 1000 plus files with naming convention i.e (575_hello_1.iso ... 575_hello_1000.iso). 575_hello/575_hello_1.iso 575_hello/575_hello_2.iso 575_hello/575_hello_3.iso... (8 Replies)
Discussion started by: lxdorney
8 Replies

8. Shell Programming and Scripting

Partial Match and Replace

Hi, I have a tab delimited text file like this one. I need to do a partial match of a particular cell and then replace matches with an empty cell. So here is a sample: Smith FordMustang ChevroletCamaro Miller FordFiesta Jones KiaSorrento Davis ChevroletCamaro Johnson ToyotaHighlander I... (4 Replies)
Discussion started by: mikey11415
4 Replies

9. 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

10. Shell Programming and Scripting

Bash to rename portion of file using match to another

In the portion of bash below I am using rename to match the $id variable to $file and when a match (there will alwsys be one) is found then the $id is removed from each bam and bam.bai in $file and _test is added to thee file name before the extension. Each of the variables is set correctly but... (3 Replies)
Discussion started by: cmccabe
3 Replies
ALTER 
TABLESPACE(7) SQL Commands ALTER TABLESPACE(7) NAME
ALTER TABLESPACE - change the definition of a tablespace SYNOPSIS
ALTER TABLESPACE name RENAME TO newname ALTER TABLESPACE name OWNER TO newowner DESCRIPTION
ALTER TABLESPACE changes the definition of a tablespace. You must own the tablespace to use ALTER TABLESPACE. To alter the owner, you must also be a direct or indirect member of the new owning role. (Note that superusers have these privileges automatically.) PARAMETERS
name The name of an existing tablespace. newname The new name of the tablespace. The new name cannot begin with pg_, as such names are reserved for system tablespaces. newowner The new owner of the tablespace. EXAMPLES
Rename tablespace index_space to fast_raid: ALTER TABLESPACE index_space RENAME TO fast_raid; Change the owner of tablespace index_space: ALTER TABLESPACE index_space OWNER TO mary; COMPATIBILITY
There is no ALTER TABLESPACE statement in the SQL standard. SEE ALSO
CREATE TABLESPACE [create_tablespace(7)], DROP TABLESPACE [drop_tablespace(7)] SQL - Language Statements 2010-05-14 ALTER TABLESPACE(7)
All times are GMT -4. The time now is 07:17 PM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy