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Top Forums Shell Programming and Scripting Rename portion of file based on another file Post 302583070 by anjulka on Monday 19th of December 2011 01:07:58 PM
Old 12-19-2011
Rename portion of file based on another file

Hello,

I've been searching and reading, but I can't figure out how to solve this problem with my newbie skills.

In my directory, I have a list of files (see dirlist.txt attachment) that I need to merge and rename. I have part of the code of the code figured out (see below). However, I have no idea how to replace the barcode sequence (6 letter combination in the center) with the barcode number based on barcodekey.txt. awk seems like the command I need, but I can't figure out how.

Code:
find *gz | while IFS="_" read name lanename date sequence lane readpair number
do
    if [ ! -f "${lanename}_${sequence}_${readpair}.fastq.gz"]; then
        cat *_${lanename}_*_${sequence}_*_${readpair}* > ${lanename}_${sequence}_${readpair}.fastq.gz
    fi
done
unset IFS

Could you please help and explain how it works (that way I don't have to come back again for a minor change; eg, when we decide to change CRC1_bc05 to AA_01_T in 6 mo)?

As a bonus, is there a way to change CRC (in the lanename) to ColonTrio while leaving the 1 and not messing up the merge [ ! -f ...] part? Would you recommend doing it before the merge and change what the [!-f is looking for] Or should I just do sed at the very end after done?

Thank you so much,
anjulka
 

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GIT-MERGE-INDEX(1)						    Git Manual							GIT-MERGE-INDEX(1)

NAME
git-merge-index - Run a merge for files needing merging SYNOPSIS
git merge-index [-o] [-q] <merge-program> (-a | [--] <file>*) DESCRIPTION
This looks up the <file>(s) in the index and, if there are any merge entries, passes the SHA1 hash for those files as arguments 1, 2, 3 (empty argument if no file), and <file> as argument 4. File modes for the three files are passed as arguments 5, 6 and 7. OPTIONS
-- Do not interpret any more arguments as options. -a Run merge against all files in the index that need merging. -o Instead of stopping at the first failed merge, do all of them in one shot - continue with merging even when previous merges returned errors, and only return the error code after all the merges. -q Do not complain about a failed merge program (a merge program failure usually indicates conflicts during the merge). This is for porcelains which might want to emit custom messages. If git merge-index is called with multiple <file>s (or -a) then it processes them in turn only stopping if merge returns a non-zero exit code. Typically this is run with a script calling git's imitation of the merge command from the RCS package. A sample script called git merge-one-file is included in the distribution. ALERT ALERT ALERT! The git "merge object order" is different from the RCS merge program merge object order. In the above ordering, the original is first. But the argument order to the 3-way merge program merge is to have the original in the middle. Don't ask me why. Examples: torvalds@ppc970:~/merge-test> git merge-index cat MM This is MM from the original tree. # original This is modified MM in the branch A. # merge1 This is modified MM in the branch B. # merge2 This is modified MM in the branch B. # current contents or torvalds@ppc970:~/merge-test> git merge-index cat AA MM cat: : No such file or directory This is added AA in the branch A. This is added AA in the branch B. This is added AA in the branch B. fatal: merge program failed where the latter example shows how git merge-index will stop trying to merge once anything has returned an error (i.e., cat returned an error for the AA file, because it didn't exist in the original, and thus git merge-index didn't even try to merge the MM thing). GIT
Part of the git(1) suite Git 1.7.10.4 11/24/2012 GIT-MERGE-INDEX(1)
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