[Chicago] Perl Follow-up

[Brian Herman]

Nice job


___________________________________

Cowards die many times before their deaths,
The valiant never taste of death but once."
--From Julius Caesar (II, ii, 32-37)


On Mar 12, 2010, at 11:45 PM, Clyde Forrester
<clydeforrester at gmail.com> wrote:

> And the results are in. I have a Perl program and a Python program,
> each of which read a 60MB human Y chromosome, and compute the
> reverse complement. The Perl program takes about 15 seconds, and the
> Python program does it in about 3 seconds. The Python program also
> tends to be slightly more compact.
>
>> # revcomp.py
>> import string
>> chrY_line_list = []
>> for line in open('chrY.fa','r'):
>>  if line[0] == '>':
>>    continue
>>  else:
>>    chrY_line_list.append(line.strip('\n'))
>> chrY_string = ''.join(chrY_line_list)
>> print len(chrY_string)
>> print chrY_string[10000:10020]
>> chrY_revcomp = chrY_string[::-1]
>> trans = string.maketrans("ACGTacgt", "TGCAtgca")
>> chrY_revcomp = chrY_revcomp.translate(trans)
>> print len(chrY_revcomp)
>> print chrY_revcomp[-10020:-10000]
>
>> # revcomp.pl
>> use strict;
>> use warnings;
>> my $infile = 'chrY.fa';
>> open (my $in,'<',$infile) or die "Can't read $infile: $!\n";
>> chomp(my @dna = <$in>);
>> close ($in);
>> while(substr($dna[0],0,1) eq '>') {
>>  shift(@dna);
>> }
>> my $dna = join('', at dna);
>> my $length = length($dna);
>> print "DNA length: $length\n";
>> my $substr = substr($dna,10000,20);
>> print "$substr\n";
>> my $revcomp = reverse $dna;
>> $revcomp =~ tr/ACGTacgt/TGCAtgca/;
>> $length = length($revcomp);
>> print "revcomp length: $length\n";
>> $substr = substr($revcomp,-10020,20);
>> print "$substr\n";
>
>
> Alex Gaynor wrote:
>> On Fri, Mar 12, 2010 at 12:54 PM, Clyde Forrester
>> <clydeforrester at gmail.com> wrote:
>>> I raised some issues about Perl vs. Python, and I'd like to invite
>>> some
>>> comment and advice.
>>>
>>> First, can anyone recommend a properly Pythonic way of doing
>>> translations?
>>>
>>> One example of such translations would be complementing DNA
>>> sequences.
>>> Translating T to A, A to T, C to G, and G to C.
>>>
>>>>> import string
>>>>> trans = string.maketrans("TACG", "ATGC")
>>>>> my_dna = "agtcaagta".upper()
>>>>> my_dna.translate(trans)
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