merge files with similar substring

Question

I want to merge paired files that share similar start of the filesname. The output should be a unique name found in the corresponding input files. I am not sure how do do this, however, cat would do somehow.

107_MAE_E7_S11_L001_R1_001.fastq.gz
107_MAE_E7_S11_L002_R1_001.fastq.gz
108_IME_A8_S23_L001_R1_001.fastq.gz
108_IME_A8_S23_L002_R1_001.fastq.gz

out

107_MAE_E7_S11.fastq.gz
108_IME_A8_S23.fastq.gz

What do you mean by "share" ? They all start by `1`... So you could merge them all. Plus, you should start by providing your try code... :) — Amessihel, Feb 09 '16 at 10:16
Thanks for your edit. If I understand : you want to merge file1 ans 2 by the longuest prefix they share, if they share one ? — Amessihel, Feb 09 '16 at 10:25
Have a look [here](http://stackoverflow.com/questions/6973088/longest-common-prefix-of-two-strings-in-bash). Then, please start by providing a piece of your own code. — Amessihel, Feb 09 '16 at 10:31
Please edit your question and add the code you've already written. The StackOverflow community is only to happy to help you improve your code, but we are not short order programmers working for free. — ghoti, Feb 09 '16 at 14:26

score 0 · Answer 1 · answered Feb 09 '16 at 14:18

From your example (which is not clear if it is representative of all filenames), you can just cut out the middle of the file, and use uniq. What you key off of depends on whether all files really look like what you have above.

Example:

# cut -c1-14,27- myfilename | uniq
107_MAE_E7_S11.fastq.gz
108_IME_A8_S23.fastq.gz

merge files with similar substring

1 Answers1