[bip] mRNA lengths of all Human/Mouse refseqs (tutorial)

[Brandon King]

Hi Brent,

Your welcome.

What you have found in the SequenceUtils.py module was Chris Hart's code
for reverse complementing DNA sequence. And the short answer is I don't
know... He did some benchmarking if I remember correctly on why this was
faster... I've CC'ed Chris as he probably has a better answer. I think
that particular module was written pre-2002 and therefore was
benchmarked against an older version of Python. Chris?

Let me know if you have any other questions or request for documentation
and I'll see about writing some additional examples/tutorials.

-Brandon

P.S. Chris, you might want to check out http://bio.scipy.org/

Brent Pedersen wrote:
> hi, and thanks for making this available. i have immediate use for the
> fasta indexing.
> what's this in SequenceUtils.py? am i missing something or is
> [seq]*len(seq) uneccessary. what's the advantage over python's
> reversed?
>
>
> def reverse(seq):
>   """reverse a sequence"""
>   return(''.join(map(operator.getitem, [seq]*len(seq),
>                      xrange(len(seq)-1, -1, -1))))
>
>
>
> On Jan 16, 2008 3:29 PM, Brandon King <kingb at caltech.edu> wrote:
>   
>> Hi All,
>>
>> I recently needed to generate the sequence lengths for all Human and
>> Mouse refseqs mRNA's. I figured it was worth while to document how I did
>> it to try to get in the habit of making tutorials as I work on solving
>> specific problems.
>>
>> I used the bhutils.Fasta module (LGPL license) that Joe Roden and myself
>> wrote for the BioHub project for the purpose of being able handle
>> extracting sequence from chromosome sized Fasta files w/o using up a lot
>> of memory. It also needed to handle extracting sequence from Fasta files
>> with many fasta sequences in it.
>>
>> It is also very useful for selectively plucking sequences from multiple
>> fasta files w/ multiple sequences and combining them into a new
>> multi-sequence fasta file and it doesn't take much code to accomplish
>> these tasks. I will try to make tutorials for these as well.
>>
>> It might be useful if someone wants to post similar tutorials for how
>> these would be done with biopython, pygr, or other packages as well.
>>
>> bhutils is a collection of modules that were I found useful that could
>> easily be extracted from the BioHub project (making it a much lighter
>> weight package). http://woldlab.caltech.edu/html/bhutils/.
>>
>> The tutorial can be found here:
>> http://bio.scipy.org/wiki/index.php/Multisequence_fasta_sequence_lengths_with_bhutils
>>
>> -Brandon King
>>
>>
>> _______________________________________________
>> biology-in-python mailing list - bip at lists.idyll.org.
>>
>> See http://bio.scipy.org/ for our Wiki.
>>
>>     
>
>   
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