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.
Hi,
ReplyDeleteI'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.
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.
DeleteHi there
ReplyDeleteI 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.
regards
John