so, I need to extract the region from file 2 say, 52698648..52707224 for id-319, which begins from position 52704105 in gff file. And then search it in a file 1, for the sub-location of this gene, say, whether its in cDNA, mRNA etc. If its not fount the output should be:
else, if its found, output should be
'
please help me with the shell scripting or perl (or both)..I am new to this linux world.
sorry this was my first post, so I didn't have much idea.
Regarding problem:
It is a particular gene position in the whole genome, now this gene is madeup of CDS, mRNA, Introns etc..the information is right below it like:
etc..until the information of next gene comes..
like: (say gene2)
So I have file with these 'gene' location, now I need to extract its sub-location, like whether its in CDS, mRNA or Intron(in case no match found).
The location of gene(that we need to find) is in separate file:
I have to read it line by line, extract gene position, then search it in the main gene info. (gff) file. like:
note: '..' denotes FROM postion 52698648 TO 52707224.
Last edited by reena2305; 06-28-2011 at 01:32 AM..
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