Searching for a phrase in a text file
lukeaarond
lukeaarond at gmail.com
Wed Jul 6 00:07:47 CEST 2011
I have a text document with a lot of information in it, but I just need to
extract one sequence from it. Right before the sequence is always the phrase
'ncbi2na' and ends with an apostrophe, therefore, I want to search the whole
file for 'ncbi2na' and save the data until the end apostrophe. The text file
looks like the following:
....'junk'....
....'junk'....
....'junk'....
....'junk'....
....'junk'....
....'junk'....
ncbi2na ATTTGAATGCCAA'H
....'junk'....
....'junk'....
I am currently doing this by parsing each character until it sees the
characters n,c,b,i,2,n and a, next to eachother. As shown below:
fd=mopen(Filename,"r");
while ~meof(fd)
character(i)=mgetstr(1,fd)
//then various code to save information after ncbi2na and before the
apostrophe
end
mclose(fd)
However, since there is about 1000 rows of 'junk' before the sequence, it
takes a very long time to parse through and find the sequence.
Therefore, I was wondering if there is a quicker way? Perhaps a function or
method that allows me to "search" through the file until I find 'ncbi2na'
and start my parsing from there. Thank you in advance.
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