Re^2: replace FASTA sequence headers

lines such as
%head_seqs = @headers_seqs;
make no sense.

It makes perfect sense. Copying values between lists, arrays and hashes is a normal idiom in Perl.

if ($line =~ /$key/) { $line =~ s/$key/$headers{$key}/; last; }
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Your $key values may contain regular expression meta-characters so you should use quotemeta on them.

Your loop exits on the first match but not necessarily the correct match. You should anchor the patterns.

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Re^3: replace FASTA sequence headers by Anonymous Monk on Jun 10, 2012 at 21:34 UTC
Thanks for your replies jwkrahn. Actually, EACH of my values in the hash of new / old headers have # character in them, some of them have other special characters such as _ etc I was under the impression that because my keys are all letter/number strings, that there should not be any problem with having special characters in the values, BUT not in the keys themselves Am I missing something here about needing "quotemeta" for the hash's values as well? I hope I am explaining the header pairs properly Here is an example below: cluster14621 \t Helitron#element_1	[reply]
Re^4: replace FASTA sequence headers by jwkrahn (Abbot) on Jun 11, 2012 at 01:26 UTC
Am I missing something here about needing "quotemeta" for the hash's values as well? I was suggesting quotemeta not because of the hash, but because of their use in a regular expression.	[reply]