I have an input file containing MANY records in this format:

 
>Record 1
AGTCTAGTCAT
CATCATAAGAT
CATCAATCACA
>Other Record
ATGAACAGCAG
ATGAAGAATGG
ATAG

[download]

Ah, yes. The ol' FASTA. IF you know that you have no repeats in the id/description info after the '>', the following "one liner" gets you a long way with a standard FASTA file: 

% perl -lne 's/>//?$s=$_:$s{$s}.=$_;\
> END{ <do smthng w/ %s> }' \
> huge.fasta massive.fasta humongo.fasta

[download]
The uniqueness condition mentioned above is crucial, otherwise this scriptlet will mess with your mind.

A generically useful specialization of the above is 

% perl -MStorable -lne 's/>//?$s=$_:$s{$s}.=$_;\
> END{ store \%s "for_later" }' \
> huge.fasta massive.fasta humongo.fasta

[download]
Then you can read the-hash-formerly-known-as-%s from any script whenever you please. See Storable. Keep in mind, however, that, if left unattended, Storable::store clobbers without remorse.

the lowliest monk

In reply to Re: Input record separator by tlm
in thread Input record separator by travisbickle34

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