#PHASESPERM A program to phase sperm.

##Before you start This python script requires scipy and numpy. If you do not have these installed you can type:

sudo apt-get install python-scipy
sudo apt-get install python-numpy

phasesperm.py expects data to be in a tab delimited file with 3 columns containing the scaffold, position and consensus information, and then one column for each sperm sequenced. The symbol '-' is used for missing data. For example, if 4 sperm were sequenced, then a few lines of this file might look like:

scaffold_49     1043    T       -       -       A	T
scaffold_49     2240    T       T       -       T	A
scaffold_49     2363    G       G       -       -	C

If you want to generate test data in this format, type:

simulatesperm.py

Pipeline:

• trimsnp.py test.txt 10 > test-min10.txt
• phasesperm.py test-min10.txt
• cd MST/
• make
• ./MST.exe ../MST-data.txt ../MST-out.txt
• cd ../
• addmarkers.py MST-out.txt > MST-out-wmakers.txt
• trimtopairs.py outR.csv > pairs.txt
• mltrack.py pairs.txt
• Rscipt graphoutR.R