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#!parrot
# Copyright (C) 2005-2010, Parrot Foundation.
# Reads from stdin a file in the format made by fasta.pir
# ./parrot -R jit
# N = 2500000 for fasta
# 2.2 s on AMD@2000/512K cache
# Original by Joshua Isom, heavily hacked by Leopold Toetsch
# create tr table at compile-time
# tr{wsatugcyrkmbdhvnATUGCYRKMBDHVN}
# {WSTAACGRYMKVHDBNTAACGRYMKVHDBN};
.sub tr_00_init :immediate
.local pmc tr_array
tr_array = new 'FixedIntegerArray' # Todo char array
tr_array = 256 # Python compat ;)
.local string from, to
from = 'wsatugcyrkmbdhvnATUGCYRKMBDHVN'
to = 'WSTAACGRYMKVHDBNTAACGRYMKVHDBN'
.local int i, ch, r, len
len = length from
null i
loop:
ch = ord from, i
r = ord to, i
tr_array[ch] = r
inc i
if i < len goto loop
.return(tr_array)
.end
.sub main :main
.local pmc stdin, stdout
.local string line, seq
$P0 = getinterp
stdin = $P0.'stdin_handle'()
stdout = $P0.'stdout_handle'()
# stdout is linebuffered per default - make it block buffered
stdout.'buffer_size'(8192)
seq = ''
beginwhile:
line = stdin.'readline'()
unless line goto endwhile
$I0 = ord line
unless $I0 == 62 goto else # '>'
if seq == '' goto no_rev
print_revcomp(seq)
seq = ''
no_rev:
print line
goto endif
else:
line = chopn line, 1
seq .= line
endif:
goto beginwhile
endwhile:
if seq == '' goto done
print_revcomp(seq)
done:
.end
.sub print_revcomp
.param string line
.local int i, linelen, ch
.local string revline
linelen = length line
$P0 = new 'String'
# $P0.'reverse'(line)
# reverse is no longer available so
i = linelen
revline = ''
rev_loop:
i -= 1
$S0 = substr line, i, 1
revline .= $S0
if i > 0 goto rev_loop
#
$P0 = revline
#
# line was reversed in-place so we need
line = revline
#
.const 'Sub' tr_00 = 'tr_00_init'
line = $P0.'trans'(line, tr_00)
i = 0
$S0 = 'x'
print_loop:
$S0 = substr line, i, 60
print $S0
print "\n"
i += 60
if i >= linelen goto done
goto print_loop
done:
$S0 = ''
.end
# Local Variables:
# mode: pir
# fill-column: 100
# End:
# vim: expandtab shiftwidth=4 ft=pir:
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