Hi Graff I was going over your code and I think there are few issues in the begining that you might suggest a way out of.

 
$methrange{$bgn}{$end} = $_;

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Here you are using begin and end as keys of the HOH %methrange but there are some CDS in the file which can have same start and end but belong to different gene ids how can we account for such anomalies using your code. Also I tried running your code for about half an hour it did not produce any result thus efficiency is still an issue here. What'd you guys say about trying DBDsqlite or mysql for this task would the overhead be more or less??

In reply to Re^2: Comparing and getting information from two large files and appending it in a new file by perlkhan77
in thread Comparing and getting information from two large files and appending it in a new file by perlkhan77

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