Created
May 30, 2009 21:44
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pmichaud@orange:~/rakudo$ cat k-nucleotide.p6.pl | |
# The Computer Language Benchmarks Game | |
# | |
# Based on the submission for Perl 5. | |
# contributed by Daniel carrera | |
# | |
# USAGE: perl6 k-nucleotide.p6.pl < k-nucleotide.input | |
# Read FASTA file from stdin and extract DNA sequence THREE. | |
my $sequence = ''; | |
my $lines; | |
while $*IN.get -> $line { | |
last if ($line.substr(0,6) eq '>THREE'); | |
} | |
while $*IN.get -> $line { | |
last if ($line.substr(0,1) eq '>'); | |
$sequence = $sequence ~ lc $line; | |
} | |
say $sequence; | |
exit; | |
# Count nucleotide sequences | |
my $len = $sequence.chars; | |
my (@keys,%table,$sum,$frame_size); | |
for 1..2 -> $frame_size { | |
%table = (); | |
update_hash($frame_size); | |
# Print. | |
$sum = $len - $frame_size + 1; | |
for %table.sort: {$^b.value <=> $^a.value||$^a.key leg $^b.key} { | |
printf "%s %.3f\n", .key, .value*100/$sum; | |
} | |
print "\n"; | |
} | |
for <ggt ggta ggtatt ggtattttaatt ggtattttaatttatagt> -> $seq { | |
%table = (); | |
update_hash($seq.chars); | |
printf "%3d\t$seq\n", (%table{$seq} || 0); | |
} | |
# Procedure to update a hashtable of k-nucleotide keys and count values | |
# for a particular reading-frame. | |
sub update_hash($frame_size) { | |
for 0..($len - $frame_size) -> $i { | |
%table{$sequence.substr($i,$frame_size)}++; | |
} | |
} | |
pmichaud@orange:~/rakudo$ ./perl6 k-nucleotide.p6.pl <k-nucleotide.input | |
agagagacgatgaaaattaatcgtcaatacgctggcgaacactgagggggacccaatgctcttctcggtctaaaaaggaatgtgtcagaaattggtcagttcaaaagtagaccggatctttgcggtattttaattggagaacaattcacggaacgtagcgttggctaccacacatcggattttcgccctctcccattatttattgtgttctcacatagaattattgtttagacatccctcgttgtatggagagttgcccgagcgtaaaggcataatccatataccgccgggtgagtgacctgaaattgtttttagttgggatttcgctatggattagcttacacgaagagattctaatggtactataggataattataatgctgcgtggcgcagtacaccgttacaaacgtcgttcgcatatgtggctaacacggtgaaaatacctacatcgtatttgcaatttcggtcgtttcatagagcgcattgaattactcaaaaattatatatgttgattatttgattagactgcgtggaaagaaggggtactcaagccatttgtaaaagctgcatctcgcttaagtttgagagcttacattagtgactaggtatacaaggtttttgagttcctttgaaatagttaactaatttaaaattaattaacgacatggaaatcacagaacctaatgctttgtaggagttatttatgctgtttactgcctctacaaccctaataaagcagtcctaagaatgaaacgcatcttttagttcagaaagtggtatccagggtggtggtcaatttaataaattcaacatcgggtctcaggatattcggtataattcaccgtaaggatgacgtcgaagctacaactgggtataatttaccatgcttccctgatgctgagtgcaatacactaagaatgagtttttaccccatatcaccagtatttgttctgttattgcgaagaaatggctatgctgagttggcgactaaagtcacccatcctttttattaggtaaccccctcccttaaactaactgatttgctggagctgccctgcatacatatactttatcatttatggacgtccgtgacgcttattatccaccatagtcgatatgctacacggattcattaatggatcgtaggagtttaagttatatttactaagatcggtctcggctactatcccgccttacccggcgctatttacggccatttttaatatattgacggtaattattcctatggtttcgaccgcacgtccttggacaagaaagaatggcaaaaaaaatgtaaaagaaaaaaaatattgagtccctaccatcatataaaaaatatgtgatgatgacgaaatgttagtggttattaaagaggtattctatctattacaccttttgttttctgtcgtagtatattaaagtctagaagccttacaggaggtaaatcagggttatacagccgatactccgcagcatgaatcaaggaggtgtcctaccatcgcgccttgtaatcttgtctgtgtatactgtatttagaccttttatacaaagtaaatatctcggctttatgtgattgggaggggcctactcaaacatgatgacttgacctaataatcactgtgcgggcgtcttatgactagctattccttgaaatccaccaccaaatggttaatatgtaaagacgatgaaacaaggggtattttaatttatagtggttgaatgtgtagttactttgcgtccattgcttgtaaaaccgtcaatcgcacacgttacttccataaaatttctacgaatacacccttcttaaaaaaaacgtaggaattcacgagtttaacaaacgataactgtataaagtggaagtccgaagaaagcagatgcccgaactggtattactcgaagatgtttcttaaccataggggcttcttaatggcccactacgcacattttgttcaagcccgagagggacatccccattacgggagtattactaaaactgttccgtaatacgttcagcaagggatgaaaaaggccactgctcaagttattgacgtgggagtattacatcggaagcctgaatcccacactatgatggtctgtacaggcctagggactgcgtctagacggtattaccggcttctaatcatacgatcgtgagtcttaacgggaagtaaggctcacacctaccccaaaccatttatctatgtaagtataaaattgtgcgtaagtgttcaaagtggacaataaagacgtggcaaaaacccccgcacataagccgctttagatttcacaaataccaatgcggttaaaaacatccttgagtcgtacatacaccatactcgcgttaaacggatataacagaagataataaatccggatgtggagtcggtgtaactatagaaagccaagtgaaataatgcttaccagtcatttagctatacggctttcatttcatgtcaagagggtggagtttgacctgtacagttgatggtatatcaccgatacttagaactcacctaaagaaattgctcgcagcgtgtaatccgcatattacaaacaatagatgggattcattatacataagacacgatgatctgctttttcaggttgcgagatgttgcctatcgtcaatcgagtcctgccttacaccacttaaacaaaagtattgacagggaacctattttcgaggtattatatagtccagcttgaatatcaatttgacagttaacctagtgaaaatcagtaagaggaaatacgccacattctccagtgaaattctacgggttatcgtctagtccaactatcaattataactcacgagatataagtaaattctcgtacttggcctgatttttattatactttggatccttagtaaacaggaagggagaaaccttcaacgaaaaacactggattttgttttactctcaaagctcttatatgacgcaagtcttaactttattacggtattttaatttagactaatgaaatgggcttggggtggccagaatcatagtacaatttagcggatacactattcggactttcctatcggctgtctggttggataagtatggggactaataggctagacatacctatacttaaactatacaggcgtcatctatctctgcaactttggagttccctgatgttctcccgccctttgggttcacatcttctataccgacacccctaataacgattagtttgtgggttagagtaaattaatacggttaatattaatgtatcgttgaaaagctggtgtcgccaataaggtaaccggctaggcagagtatatgtcacgaagtataactaccctaatgataagctgtaggaataaaattaatgctgtctctaagcgaagagatatttccgactctgttttaatgacgaatctcattacttctgacttgcaaatgttcaatatggcacggtttcacggcacctttgtgacgcatataatgaacttagaagattataacgacggaactttatatgataatccgttacgattaaagaatctgttaaatatcataatggcattcagttctagaccgtgcatcatggtaaacttactttctctgcatggcgacatacatttcgctattcaaattcgcgtgtggttacacccactcgcacctttggaatattaagagaagatgatcagaaaatccattcgctcaatttttctgacgtacgtctaatttatcctaggagacaaatcgttttatgtctctcacatttttgaagaaaggttcgagagacaatactcaggtcctgaactgctagaagatactcggtggagcgtggcaacaatgaaaaactcgtgacataaatgaatgatacttttccaagttcagttaagtgaatatgtttaacatacccggcttttcgatcttaagctgacgctggacgtgcgagtaatgtcagtctcttacatacactagtgactccaagtttcgtcaaaaacgccccctcccttctcgagcccactcacgctatgtattgacgcgaacttgttcgggatcagacttttcaggagttcggtcgcgtgtccctatgtgctaatatataagttagatcgcattagatgctaatctgaatacttatagacgaccttcaacgagaacgggtaccaccttgaggctagagttaggtgtgaaacgacaggtagggacatataaaatttgagtgcggctttagttaagggtttaattacctactcaaacatcacgctcgcgcccttcgtacgtaatcgaccatctagaggctaaggggactgtactaggtagtgattaatgatatcctagacgcacgtgccttagatcttcagactctgatggtccgcgatcaccgtaattgtagtcctccaactcgatcactttgttggcgtcaaagaaattacgatatctaaatacttataatacaataaccaaggatgagaatgactcatcgcgttggagttatattgcttgaagttctatggaatgaaagcacgttatctgccgtcccaatatctccagtgagctaattcattggacggtccactttgatcaatccccgaggagatgttcggacactttagtctgtaacacttagcgttgagaccacgaacaattgattactcagtcttgaaggtgttttccaaagttcattttaaataagactacgataggcctttcctattgatataaactacccggctctgttgttcgtgtgagtcgtacttctctgtgtttttctgattatagcaagattcgattcttagtgtaaacagcgatttttatttgacccgtcaatgagaagcgcataggatctaagcaaaattatcaagttgtgccacaaggtaagatctttccagttattgcaggtaggatgtatcccacgttgatagtatgaggtctgacgtcaactgtctaggagagttgaccgcgtgcgggtacaccggatttgcatcgatgttgagaacgcagaactcccactgtcgtggcggcgttcctgatatttagcaagaggcgttgataaagccctcatcatctagatctcgacctcatctgccctcttgctccatcattttctacacagactactttcctatctacgttagtataattgctttctatcttagtatcatttagagcttctccgtcaacaggttcgtgctattaaagttagtacgaaagggacaacttgtagcaacgcatttaatcggttttcgactacttcgcacaaaatcagataaagaagtttgtcattctattagacattgaattgcgcaattgacggtattttaatttatagtttgtaccacttatgatcgaacactgaataaatagacatgcggcctgcctccatattcaagtgtatcttaaaccaagtggttccaacgctcgcgctaaagaattaaagcctttatttcctccacggagtagcccgtaatccggttcgaaagagaccatcaaagcgctcttcaaccaagatatgattcatcctaacttcgatgaatgcgtctgtaacataaatatagaaggaatgattcggcgagttaattttcgccttctccaacatggcatccctacgttcgttataaggaccatacatgtaggttttaaaggtttgcggttaatcgatatttacatgagatacctttgcaattttt | |
pmichaud@orange:~/rakudo$ | |
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