egglib_sliding_windows.py

Python script to calculate ABBA BABA statistics, as well as pi and dXY from heliconius whole-genome data. It makes use of the EGGLIB library. Input was a "calls" format file, provided in Martin et al. 2013. Window size is specified with the -w flag, sliding increment with the -i flag and minimum number of sites with the -m flag. The latter is a hard cutoff, and windows with fewer sites are discarded. There is also a soft cutoff between 0 and 1, specified with --minimumExploitableData. The script will output a column called sitesOverMinExD. At a value of 0.5, this would report the number of sites in the window that had genotype calls for at least 50% of the individuals. To analyse autosomes and Z-linked scaffolds separately, the --include and --exclude flags were used, along with the file Hmel1-1_Zupdated_Zscafs.txt, which provides names of all Z-linked scaffolds provided in Martin et al. 2013. For the Z chromosome analysis, ploidy was specified using the --ploidy flag, because there were two females in the dataset of Martin et al. 2013.