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I have a text file like this 

sp|QBWMM1-2|PDCI_Mouse(741-770) 8864=mil (25/2.20/2.50) sp|Pm345|Hisf_Mouse(613-640) 776=mil (25/2.20/2.50) sp|P0065-2|Hila_Mouse(344-393)6543=mil (25/2.20/2.50) sp|Q90081|Rira_Mouse(47-72) 7365=mil (25/2.20/2.50) sp|QQQQQ1|Ubs_Mouse(162-190) 22=mil (25/2.20/2.50)

I have another text file like this

sp|QBWMM1-2|PDCI_Mouse complex subunit alpha OS=Mouse OX=90009 PE=1 SV=1 sp|Pm345|Hisf_Mouse Heat shock 70 kDa protein 1A OS=Mouse OX=90009 PE=1 SV=1 sp|O15012|SCCC_Mouse Protein transport protein Sec16A OS=MOUSE OX=90009 PE=1 SV=4 sp|P0065-2|Hila_Mouse Filamin-A OS=MOUSE OX=90009 PE=1 SV=4 sp|Q90081|Rira_Mouse Alpha-actin OS=Mouse OX=90009 PE=1 SV=2 sp|QQQQQ1|Ubs_Mouse Tubulin alpha8 chain OS=Mouse OX=90009 PE=1 SV=1 sp|QQQQQ2|Ubs_Mouse Plasta-3 OS=Mouse OX=90009 PE=1 SV=4

I want to merge them together keep the similar part and put the rest together. So for example, in text 1 and text 2, the following are similar:

sp|QBWMM1-2|PDCI_Mouse(741-770) 8864=mil (25/2.20/2.50) sp|QBWMM1-2|PDCI_Mouse complex subunit alpha OS=Mouse OX=90009 PE=1 SV=1

the first part is the most important. they are considered similar because they have similar strings sp|QBWMM1-2|PDCI_Mouse

then I want to put them togther and it becomes 

sp|QBWMM1-2|PDCI_Mouse complex subunit alpha OS=Mouse OX=90009 PE=1 SV=1 (741-770) 8864=mil (25/2.20/2.50)

So the output could be like this:

sp|QBWMM1-2|PDCI_Mouse complex subunit alpha OS=Mouse OX=90009 PE=1 SV=1 (741-770) 8864=mil (25/2.20/2.50) sp|Pm345|Hisf_Mouse Heat shock 70 kDa protein 1A OS=Mouse OX=90009 PE=1 SV=1 (613-640) 776=mil (25/2.20/2.50)) sp|O15012|SCCC_Mouse Protein transport protein Sec16A OS=MOUSE OX=90009 PE=1 SV=4 sp|P0065-2|Hila_Mouse Filamin-A OS=MOUSE OX=90009 PE=1 SV=4 (344-393)6543=mil (25/2.20/2.50) sp|Q90081|Rira_Mouse Alpha-actin OS=Mouse OX=90009 PE=1 SV=2 47-72) 7365=mil (25/2.20/2.50) sp|QQQQQ1|Ubs_Mouse Tubulin alpha8 chain OS=Mouse OX=90009 PE=1 SV=1 (162-190) 22=mil (25/2.20/2.50) sp|QQQQQ2|Ubs_Mouse Plasta-3 OS=Mouse OX=90009 PE=1 SV=4
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  • 1
    What is sublime? Sublime Text? Then why the bash tag? I don't know "sublime", but probably you want to search for a tutorial on regular expressions. Commented Jan 4, 2019 at 2:46
  • @Sparhawk you are right, I updated my question to make it more comprehensive Commented Jan 4, 2019 at 3:05
  • 2
    You have totally changed the question with that edit! But the answer is using join. Hopefully you can use that to search for a tutorial, but it's fairly straightforward. Good luck. Commented Jan 4, 2019 at 3:07
  • join -a 1 text1.txt text2.txt does not give me the answer but thanks for your point Commented Jan 4, 2019 at 3:19

1 Answer 1

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If file1 is your first text file, and file2 is your second text file, this should work in Bash:

join -a 1 <(sort -k1,1 file2) <(sed -E -e 's/([^\s])\(/\1 (/' file1 | sort -k1,1)

Join is called with two files as arguments, which two files (anonymous pipes or FIFOs actually) are the result of two process substitutions that take the form <(...)in the above command.

The second argument file contains a modified version of file1, having a space inserted before the first ( on each line so as to create a proper space-delimited join field; this modification is done by sed. The contents of both argument files are sorted based on the join field (i.e. field 1), as required by join. The -a 1 option ensures that non-pairable lines in file2 (i.e. the first argument file) are also output.

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