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

[Brent Pedersen]

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
>
>
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