makeDesignFiles.py

[leajessop]

I'm trying to use the python script to create the needed design files. I'm getting the following error

Creating .npb and .poe files... Looping through baits... Traceback (most recent call last): File "makeDesignFiles.py", line 227, in <module> n[d/binsize] += 1 IndexError: list index out of range

Any suggestions are much appreciated. Lea

[leajessop]

calling python makeDesignFiles.py --designDir=/CHiC/CHiCago/binSize1300 --rmapfile=/CHiC/CHiCago/binSize1300/MboIhg19.rmap --baitmapfile=/CHiC/CHiCago/binSize1300/baitmap.baitmap --outfilePrefix=/CHiC/CHiCago/bs1300 --minFragLen=150 --maxFragLen=40000 --maxLBrownEst=1500000 --binsize=1300 --removeb2b=True --removeAdjacent=True

[Mikhail Spivakov]

Thanks for your report. I've never seen this before, but I suppose the obvious reason would be if d/binsize is zero, where d is the distance between two fragments. Could it be by any chance that it's zero in some cases (e.g., duplicated fragments or something like that)?

[Mikhail Spivakov]

If you're not comfortable debugging the python code step by step, feel free to share your rmap and baitmap files with me (via ftp) and I can have a go.

[leajessop]

Thank you. It's odd because a few months ago I used the same baitmap and rmap files with slightly different settings and it worked fine. I can share the files with you thru Dropbox. OK to use your babraham e-mail account?

Lea

[Mikhail Spivakov]

Thanks for reporting this issue, which was caused by a rounding error. We'll post the updated version to the repo soon.

[Mikhail Spivakov]

Basically, you've provided the first use example whereby maxLBrownEst is not a multiple of binsize. Previously, there was never the need to perform any rounding, so we didn't spot an issue there. Thanks!