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Wednesday, May 15, 2013

Transform fastPHASE Output to Haploview Input

After successfully phasing with fastPHASE, I wanted to view the resulting haplotypes in Haploview.  Since I couldn't find any scripts online to convert the hapguess_switch.out file from fastPHASE into the .haps file that Haploview requires, I wrote a brief Python script to do the heavy lifting.

This script is run from the command line by typing python make_haploview_input.py hapguess_switch.out and will produce a hapguess_switch.haps file.  Because of the use of generators, this will only work on Python 2.6 or higher.  You will also need to create a .info file to match the .haps file.  The .info file has the marker loci in the same order as the .haps file and consists of two columns; the first being the marker name and the second being the marker position.


  1. Hi,

    I've copied your code exactly as displayed but I am getting indentation error messages :

    "elif genotypes=="TRUE":
    IndentationError: unindent does not match any outer indentation level"

    I've tried deleting the spaces and re-inserting them but no success.

    1. Sorry about that Danica. Looks like there was an error with formatting when I pasted the code into GitHub. I reformatted things and have updated the above code. Thanks for pointing this out.

  2. Hi there
    I have used this code to haps file, could you tell me this haps file belong to which format? there are 6 kinds of format in Haploview.