Search text file for records in another text file and pull extra data over to new
 

Hey guys,

I'm a massive newbie to the whole Linux scene but am enjoying the flexibility offered so far.

However, I have searched for a while and cannot work out how to tackle this problem.

I basically have two files: file_1.txt and file_2.txt

file_1.txt contains a list of genes, with each line containing a new gene e.g.:
CDS.002
CDS.005
CDS.035
etc.

file_2.txt contains the original gene data in the following format:
>CDS.001
MSENGNKNIAIVEAFSETDKKTGEVVTLVPNTNNTVQPVALMRLGLFVPTLKSTSRGR
>CDS.002
MALTLAGLEIEKTSGYWRAKGFKQPGILERLE
>CDS.003
MKAIPFALLFLSSIVVADTTVYQCEMSVADVKNGALTDVIKAPYGAMVVDSGDQFYVVRDDRVLSSPYLTNRNGKLTGVGEDHFVYNKYKGFYGVHASQQ SYLFDDCKEVG
etc.

Basically I want to search file_2.txt for all of the genes in file_1.txt. If found, I then want to put both the gene name (e.g. >CDS.002) AND the gene sequence (e.g. MALTLAGLEIEKTSGYWRAKGFKQPGILERLE) from file_2.txt into a new text file. I want all of the results in the final text file.

So, I'd end up with a text file similar to this:
>CDS.002
MSENGNKIAIVEAFSETDKKTGEVVTLVPNTNNTVQPVALMRLGLFVPTLKSTSRGR
>CDS.005
MALTLAGLEIEKTSGYWRAKGFKQPGILERLEYVVRDDRVLSSPYLTNRNGKLTGVGEDHFVYN
>CDS.035
MKAIPFALLFLSSIVVADTTVYQCEMSVADVKNGALTDVIKAPYGAMVVDSGDQFKYKGFYGVHASQQSYLFDDCKEVGFSETDKKTGEVVTLVPAGLEI EKTSGYWRAKGFKQPGILERLEYVVRDD
etc.

Now I have no idea how complicated this is for someone that knows their stuff! But for me, it's a little over my head at this stage. I'm very new to using the Terminal, and am only just starting out learning Perl.

Any assistance would be greeted with a thousand thanks :)

Thanks for any help!
Adzrules

this probably can be done in perl but i dont know how. you can probably bash it out with a while loop and grep (check the man page for the -A option).

Nice! I didn't even know of the grep -A option...
To add my 2 cents, with the grep -f option, you don't even need the loop

Thanks for the replies guys. No problem if you don't want to, but could you give me an example of how fgrep would work in this instance? Having trouble finding the relevant info online in a format that I can understand!

^ it is hard to correct your mistake since you dont post what you tried and what error you are getting.

My apologies. I'm using this website here: http://kb.iu.edu/data/afiy.html to help me get to terms with things.

So I've just used the following: for i in `cat file_1.txt`; do grep $i file_2.txt; done

Which shows the correct genes, but how can I modify that to make it pull the gene sequence that is present on the lines below, but not the next gene name???? Any help is MUCH appreciated!

combining mine and millgate's suggestions, this should work:

Thanks, but that just seems to write nothing to a text file. The file gets created and no errors are reported but the text file output is blank!

can you post this diagnostic info:

Sure, here's what I get:

in your first post you explain that file_1.txt contains a list of stuff like:but it really looks like:so according to the above the string "CDS.015 HCM2.0015c" doesnt exist in file_2.txt.

Apologies, I selected the wrong file (I renamed them to file_1.txt etc. for the benefit of your viewing). This is what it really is:

^ is there still a typo ?

i dont see how for example the string "HCM2.0015c" exists in file_2.txt ?

I just created a mock similar test and this works:

Oh for goodness sake! Again, I'm being retarded, wrong file AGAIN! Sorry.

That's what it actually looks like. Definitely this time!

That doesn't seem to work for me. Again, it just creates a blank text file!