1. James Taylor
  2. bx-python
  3. Issues
Issue #14 new

Getting Started: Indexing MAFs

chriskfuller
created an issue

Hi Guys,

Sorry for posting such a silly newbie question, but for the life of me, I can't figure out how to generate a MAF index file. Per your example, I need to run bzip-table, but neither this file nor the folder are part of my bx-python installation:

henduck% time ~/work/seek-bzip2/bzip-table < chrY.maf.bz2 > chrY.maf.bz2t

I've installed it on Mac OSX. Perhaps it didn't install correctly? Am I missing something? Any help is appreciated. Thank you.

Chris

Chris Fuller UCSF chris@genome.ucsf.edu

Comments (4)

  1. Neal McBurnett

    I found you while looking precisely for bzip2 random seeking, from http://stackoverflow.com/questions/12660028/reading-memory-mapped-bzip2-compressed-file

    Like the OP I also couldn't find bzip-table.

    Could you update the documentation at https://bitbucket.org/james_taylor/bx-python/wiki/IO/SeekingInBzip2Files to note the need for the extra repo?

    And maybe even add a README for seek-bzip2? with some nice keywords for google? :) And, for lots of extra points, a pip package with just the stuff (and just the stuff) needed for SeekingInBzip2Files?

    Or maybe there's a better bzip2-seek solution out there for python that you could recommend?

    And FWIW, note that when I check it out (via git-remote-hg) I get: "warning: remote HEAD refers to nonexistent ref, unable to checkout". But it works to use hg clone. After that, and running "make", it worked nicely!

    Thanks!

  2. Log in to comment