Got wrong positions on chomped query maf subset about bx-python HOT 2 CLOSED

Usually reports like this are due to a user misunderstanding of the MAF format, for which treatment of the reverse strand is not necessarily obvious. See http://genome.ucsc.edu/FAQ/FAQformat#format5 . I'm pretty sure MAF originated at UCSC, so this should be considered as the formal specification of the format.

I haven't looked at the details of your post, so I'm not 100% positive this is what is happening. And I do appreciate that your post seems to be thorough. But your conclusion is consistent with the usual misunderstanding of MAF. I had similar problems in my own early encounters with MAF. Could you check to see whether this explains what you are seeing?

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@rsharris

Yes, you are right.

After another look at my MAF file, it turns out that the start postion of the query was always based on the positive line regardless of the strand. After changing to the reverse complement line based start position, everything just works fine !

Sorry for the bothering, and thank you for the help.

Best,

Songtao Gui

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