[Chicago] Perl Follow-up

[Jonathan Hayward]

EXTERIOR: DAGOBAH--DAY
           With Yoda strapped to his back, Luke climbs up one of the
        many thick vines that grow in the swamp until he reaches the
        Dagobah statistics lab. Panting heavily, he continues his
        exercises--grepping, installing new packages, logging in as
        root, and writing replacements for two-year-old shell scripts
        in Python.


YODA: Code!  Yes.  A programmer's strength flows from code maintainability.
      But beware of Perl.  Terse syntax... more than one way to do it...
      default variables.  The dark side of code maintainability are they.
      Easily they flow, quick to join you when code you write.  If once
      you start down the dark path, forever will it dominate your destiny,
      consume you it will.


LUKE: Is Perl better than Python?


YODA: No... no... no.  Quicker, easier, more seductive.


LUKE: But how will I know why Python is better than Perl?


YODA: You will know.  When your code you try to read six months from
      now.

[From rec.humor.funny, reprinted in an O'Reilly title]


On Fri, 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)
>>>>>
>>>> _______________________________________________
> Chicago mailing list
> Chicago at python.org
> http://mail.python.org/mailman/listinfo/chicago
>



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