Fuck you perl! Why is this so hard?
I want to join an array composed of sequence that I split based on position within the array. I spent the last two hours figuring out how to do this, and this is all I came up with. It works, but Jesus:
#!/usr/bin/perl
use strict;
use warnings;
my $seq = qw(GGGCCGGCTCGCGGGCGCTGCCAGTCTCGGGCGGCGGTGTCCGGCGCG
CGGGCGGCCTGCTGGGCGGGCTGAAGGGTTAGCGGAGCACGGGCAAGGCG
GAGAGTGACGGAGTCGGCGAGCCCCCGCGGCGACAGGTTCTCTACTTAAAA
GACAATGACTACTGATGAAGGTGCCAAGAACAATGAAGAAAGCCCCACAGC
CACTGTTGCTGAGCAGGGAGAGGATATTACCTCCAAAAAAGACAGGGGAGT
ATTAAAGATTGTCAAAAGAGTGGGGAATGGTGAGGAAACGCCGATGATTGG
AGACAAAGTTTATGTCCATTACAAAGGAAAATTGTCAAATGGAAAGAAGTTT
GATTCCAGTCATGATAGAAATGAACCATTTGTCTTTAGTCTTGGCAAAGGCC
AAGTCATCAAGGCATGGGACATTGGGGTGGCTACCATGAAGAAAGGAGAGA
TATGCCATTTACTGTGCAAACCAGAATATGCATATGGCTCGGCTGGCAGTCT
CCCTAAAATTCCCTCGAATGCAACTCTCTTTTTTGAGATTGAGCTCCTTGATT
TCAAAGGAGAGGATTTATTTGAAGATGGAGGCATTATCCGGAGAACCAAACG
GAAAGGAGAGGGATATTCAAATCCAAACGAAGGAGCAACAGTAGAAATCCA
CCTGGAAGGCCGCTGTGGTGGAAGGATGTTTGACTGCAGAGATGTGGCATT
CACTGTGGGCGAAGGAGAAGACCACGACATTCCAATTGGAATTGACAAAGC
TCTGGAGAAAATGCAGCGGGAAGAACAATGTATTTTATATCTTGGACCAAGA
TATGGTTTTGGAGAGGCAGGGAAGCCTAAATTTGGCATTGAACCTAATGCTG
AGCTTATATATGAAGTTACACTTAAGAGCTTCGAAAAGGCCAAAGAATCCTG
GGAGATGGATACCAAAGAAAAATTGGAGCAGGCTGCCATTGTCAAAGAGAA
GGGAACCGTATACTTCAAGGGAGGCAAATACATGCAGGCGGTGATTCAGTAT
GGGAAGATAGTGTCCTGGTTAGAGATGGAATATGGTTTATCAGAAAAGGAAT
CGAAAGCTTCTGAATCATTTCTCCTTGCTGCCTTTCTGAACCTGGCCATGTGC
TACCTGAAGCTTAGAGAATACACCAAAGCTGTTGAATGCTGTGACAAGGCCC
TTGGACTGGACAGTGCCAATGAGAAAGGCTTGTATAGGAGGGGTGAAGCCC
AGCTGCTCATGAACGAGTTTGAGTCAGCCAAGGGTGACTTTGAGAAAGTGCT
GGAAGTAAACCCCCAGAATAAGGCTGCAAGACTGCAGATCTCCATGTGCCAG
AAAAAGGCCAAGGAGCACAACGAGCGGGACCGCAGGATATACGCCAACATG
TTCAAGAAGTTTGCAGAGCAGGATGCCAAGGAAGAGGCCAATAAAGCAATGG
GCAAGAAGACTTCAGAAGGGGTCACTAATGAAAAAGGAACAGACAGTCAAGC
AATGGAAGAAGAGAAACCTGAGGGCCACGTATGACGCCACGCCAAGGAGGG
AAGAGTCCCAGTGAACTCGGCCCCTCCTCAATGGGCTTTCCCCCAACTCAGG
ACAGAACAGTGTTTAATGTAAAGTTTGTTATAGTCTATGTGATTCTGGAAGCA
AATGGCAAAACCAGTAGCTTCCCAAAAACAGCCCCCCTGCTGCTGCCCGGAG
GGTTCACTGAGGGGTGGCACGGGACCACTCCAGGTGGAACAAACAGAAATGA
CTGTGGTGTGGAGGGAGTGAGCCAGCAGCTTAAGTCCAGCTCATTTCAGTTT
CTATCAACCTTCAAGTATCCAATTCAGGGTCCCTGGAGATCATCCTAACAATG
TGGGGCTGTTAGGTTTTACCTTTGAACTTTCATAGCACTGCAGAAACCTTTTA
AAAAAAAATGCTTCATGAATTTCTCCTTTCCTACAGTTGGGTAGGGTAGGGGA
AGGAGGATAAGCTTTTGTTTTTTAAATGACTGAAGTGCTATAAATGTAGTCTG
TTGCATTTTTAACCAACAGAACCCACAGTAGAGGGGTCTCATGTCTCCCCAGT
TCCACAGCAGTGTCACAGACGTGAAAGCCAGAACCTCAGAGGCCACTTGCTT
GCTGACTTAGCCTCCTCCCAAAGTCCCCCTCCTCAGCCAGCCTCCTTGTGAGA
GTGGCTTTCTACCACACACAGCCTGTCCCTGGGGGAGTAATTCTGTCATTCCT
AAAACACCCTTCAGCAATGATAATGAGCAGATGAGAGTTTCTGGATTAGCTTT
TCCTATTTTCGATGAAGTTCTGAGATACTGAAATGTGAAAAGAGCAATCAGAA
TTGTGCTTTTTCTCCCCTCCTCTATTCCTTTTAGGGAATAATATTCAATACACA
GTACTTCCTCCCAGCATTGCTACTGCTCAGCTTCTTCTTTCATTCTAATCCTTG
CTATTAAGAATTTAAGACTTGTGCTTACAATATTTTTGACCTGGAGTGGATCT
ATTTACATAGTCATTTAGGATCCATGCAGCTTTTTTTGTCTTTTTAAGATTATT
GGCTCATAAGCATATGTATACTGGTTTATGGAACTTTATTTACACTCCTCTATC
ATGCAAAAAAATTTTGACTTTTTAGTACTAAGCTTAATTTTTAAAAACAAAATC
TGTAGTGTTGACAAATAAATAGTTGCTCTTCTACACTAGGGGTTTCACCTGCA
GGTTTGACACGCAGTTGCTCGCTTTTCCTGCCCTGTCAAGCTTCTCTGTTCTG
GCGTGAGTTGTGAAAGAGTTGAAGACAGCTTCCCATGCCGGTACACAGCCAG
TAGCCTAAATCTCCAGTACTTGAGCTGACCATTGAACTAGGGCAAGTCTTAAA
TGTGTACATGTAGTTGAATTTCAGTCCTTACGGGTAAACAGATTGAGCATGGC
TCTCTATTCCCTCAGCCTAAGAAACACTCATGGGAATGCATTTGGCAACCCAA
GGAACCATTTGCTTAAACCTGGAACATCTCACCTTTTTAAATCCTAAAAAACA
CTGGCAGTTATATTTTAAATTAGTTTTTATTTTTATGATGGTTTTATCAAAAGA
CTTTTATTATTAGATTGGGACCCCCTTCAAACCTAAAAATCAAGTTATTTCCTT
TTATAATACTTTTCTTCCCCATGGAACAAATGGGATCAATTTGTGAGTTTTTTC
CTTTAATGATAACTAAAATCCCTCTAATTTCTCATTTATGCTTTTGTCTTTTTTA
TGAAATATTTCTTTTAAAAGCCCCAGTCTCACCTACGAAATATGAAGAGCAAA
AGCTGATTTTGCTTACTTGCTAAACTGTTGGGAAAGCTCTGTAGAGCATGGTT
CCAGTGAGGCCAAGATTGAAATTTGATACTAAAAAGGCCACCTAGCTTTTTGC
AGATAACAAACAAGAAAGCTATTCCAAGACTCAGATGATGCCAGCTGTCTCCC
ACGTGTGTATTATGGTTCACCAGGGGGAACTGGCAAAAGTGTGTGTGGGGAG
GGGAAGGGTGTGTGAGTGGTTCTGAGCAAATAACTACAGGGTGCCCATTACC
ACTCAAGAAGACACTTCACGTATTCTTGTATCAAATTCAATAATCTTAAACAAT
TTGTGTAGAAGTCCACAGACATCTTTCAACCACCTTTTAGGCTGCATATGGAT
TGCCAAGTCAGCATATGAGGAATTAAAGACATTGTTTTTAAAAAAAAAAAATC
ATTTAGATGCACTTTTTTGTGTGTTCTTTAAATAAATCCAAAAAAAATGTGAAA
AAAAAAA);
my @x = split //, $seq;
my $exon_breaks= "0,133,257,402,545,660,817,908,992,1178,1418,3770";
my @y = split (/,/, $exon_breaks);
sub get_exon_sequence{
my @array = ($y[0]..$y[1]);
my $exon = join "", @x[@array];
print "$exon \n";
shift @y;
}
until($y[1] eq undef){&get_exon_sequence};
Monday, February 09, 2009
Wednesday, February 04, 2009
Lots of people that suck
So this semester I'm taking genomics, which is cool. But we have to learn perl. Which is also cool.
Except I have no programming experience, and this is a trial-by-fire if there ever was one.
Things are going well so far, I'm just so slow. Every day is an exercise in humility.
The good news? I'm talking to Alan a lot more. He's boss.
Here's a classical "alanism" from tonight:
I was happier than Nancy Grace after finding out that the Jon Benet Ramsey case was reopened.
Hvorostovsky did a program of Tchaikovsky, Medtner, and Rachmaninoff lied. I didn't really care for the Tchaikovsky, but the Medtner alone was worth the price of admission ($70).
His sublime legato made it seem like a ventriloquist was singing the consonants. A+.
Except I have no programming experience, and this is a trial-by-fire if there ever was one.
Things are going well so far, I'm just so slow. Every day is an exercise in humility.
The good news? I'm talking to Alan a lot more. He's boss.
Here's a classical "alanism" from tonight:
i'm starting to rethink that - the midwest has its perks,
like friends
normal life
green grass
lots of people that suck, so you look cooler.
****
I was happier than Nancy Grace after finding out that the Jon Benet Ramsey case was reopened.
Hvorostovsky did a program of Tchaikovsky, Medtner, and Rachmaninoff lied. I didn't really care for the Tchaikovsky, but the Medtner alone was worth the price of admission ($70).
His sublime legato made it seem like a ventriloquist was singing the consonants. A+.
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