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Concatenate files by pairs

 
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# 1  
Old 06-11-2015
Concatenate files by pairs
Hi,
I would like to batch concatenate files by pairs. I have quite a few of them so I would not like to do that pair by pair separately.
the names of the file is of the type:

Code:
file1.fastq 
newfile1_new.fastq 
file2.fastq 
newfile2_new.fastq 
and so on...

I would like to concatenate file1 and newfile1 together etc...
Any idea how I could script that in shell commands?
Thanks a lot for your help!!
Last edited by Scrutinizer; 06-11-2015 at 07:41 AM.. Reason: code tags
# 2  
Old 06-11-2015
Please use code tags as required by forum rules!

That spec is utterly sparse. Please be aware that the better the spec the better the solutions.

For EXACTLY above sample structure, try
Code:
for i in ?????.fastq; do cat $i *${i%.*}_*; done

Redirect to taste.
These 2 Users Gave Thanks to RudiC For This Post:
jawad venky.b5
# 3  
Old 06-16-2015
Thanks a lot! After a few changes (it didnt have exactly this structure!...) it works perfectly!
Thanks again and sorry for not following the forum standards. I will do better next time!
Jawad
 
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