Hi all,
I am having trouble with combining data from several files, and I can't even figure out how to get started. So, I am NOT asking for any code (though pseudo-code is ok) as I would like to try figuring this problem out myself. So, if anyone can give me any references or hints that would be great.
So, here is what I am trying to do:
I have say 2 files (I'd like to do this to as many files as the user needs):
***FILE 1*** >cat atacta--gat--acgt- ac-ac-ggttta-ca--
>dog atgcgtatgc-atcgat-ac--ac-a-ac-a-cac
>mouse acagctagc-atgca-- ----acgtatgctacg--atg- ***end file 1***
***FILE 2***
>mouse aatctgatcgc-atgca-- ----acgtaaggctagg-
>cat atacta--gat--acgt- ac-acacagcta--ca--
>dog atgcgtatgc-atcgat -ac--ac-a-ac-a-cac ***end file 2***
Basically, I would like to concatenate the sequence of each corresponding animal so that the various input files would be out put to a file like so:
***output*** >cat atacta--gat--acgt-ac-ac-ggttta-ca--atacta--gat--acgt-ac-acacagcta--ca--
>dog atgcgtatgc-atcgat-ac--ac-a-ac-a-cacatgcgtatgc-atcgat-ac--ac-a-ac-a-cac
>mouse
acagctagc-atgca------acgtatgctacg--atg-aatctgatcgc-atgca------ acgtaaggctagg-
***output end***
Notice that in the two files the data are not in the same order. So, I am trying to figure out how to have the script figure out what the first organism is in FILE 1( say "cat" in this case) and find the corresponding "cat" in the other input files. Then take the sequence data (all the cat data) from FILE 2 and concatenate it to the cat sequence data in FILE 1 to an output file. Then it should go on to the next organism in FILE 1 and search for that next organism in the other files (in this case FILE 2). I do not care about the order of the data, only that the "like" data is concatenated together.
Again, I do NOT want this solved for me (unless I am totally lost). Otherwise, I'll never learn. I would just like either hints / suggestions / pseudo code / even links to books or sites that discuss this particular topic. Meanwhile, I am eagerly awaiting my "PERL Cookbook" and I'll keep searching the web.
-Thanks! -Mike
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