[H-GEN] one for an awk guru

[Anthony Towns]

-----BEGIN PGP SIGNED MESSAGE-----


>    nawk ' BEGIN {i=1;m=1}
>    $1 ~ /SSBOND/{cysteine[i] = $4;i++;cysteine[i] = $6;i++}
>    END {for (m in cysteine)
>                    printf "%s\n",cysteine[m]}
>    ' $1


#!/usr/bin/perl
while(<>) {                                  # $_ = next line
    if ( /^SSBOND\b/ ) {                     # is the 1st word SSBOND?
        push( @cysteine, (split ' ')[3,5] ); # push the 4th and 6th
    }
}
foreach (@cysteine) { print $_, "\n" }       # print out in order added


FWIW, the Perl version takes about 10 seconds on an 80,000 line file
(about 1.3MB) while the gawk version takes just under a minute.
They're about equal at 1,000 lines.  Awk seems to end up swapping,
curiously -- ie it's using up about 20MB just to cope with a 1.3MB
file. 

Rewriting both so they just print the output as they receive it puts
gawk at about 2 seconds for the 80k line file, while Perl remains
about 7 seconds. 

Using awk, mawk, or nawk in place of gawk, yields similar times for
the on the fly output, and equal or slightly better times than Perl
for the original program.

Cheers,
aj, who is learning a new language

- --
Anthony Towns <aj at humbug.org.au> <http://azure.humbug.org.au/~aj/>
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