[Bioperl-l] Now very OT: removing duplicate fasta records

[Sam Griffiths-Jones]

On Wed, 18 Dec 2002, Ewan Birney wrote:

> Much to the horror of the person who left this for me I replaced the
> whole thing in Perl and moved from a directory of UNIX files to a
> directory of RCS files in UNIX (I hadn't met relational databases
> then and I thought those were only for "professional" software
> engineers, and I stayed clear of them. Stupid in retrospect). It did
> provide marginally better data recovery at the very least. (I don't
> think Erik has ever forgiven me for not using his beloved gawk
> 5-liners). Looking back on it, I am not that proud of what I wrote,
> but it did work,

And still does!

> and it is still used in areas of Pfam today (a scary thought),
> though Kevin might have gutted most of my code by now.
>

pfam [scripts]103% find . -name '*.p[lm]' | xargs grep -i ewan

<big snips>

./pfamrcs/pfkill.pl:  die("Badly - could not remove $family from
current! Please talk to ewan asap as database is in a bad state\n");

./pfamrcs/pfupdate.pl:  print ("PFUPDATE: Problem - we could not copy
the files from the current set. <sigh>. Please talk to ewan\n");

./pfamrcs/pfmove.pl:  print "I am really sorry. Currently this will
exit the program to prevent hanging scripts (try again in a couple of
minutes?).  If the lock is not being free'd, talk to ewan\n";


Recognise these?  :)

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Sam Griffiths-Jones                              sgj@sanger.ac.uk
http://www.sanger.ac.uk/Users/sgj                +44 (0)1223 834244

Wisdom #2179: You can't hide a piece of broccoli in a glass of
milk.
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