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huguesrichard / Allopipe

AlloPipe is a computational method to assess the alloreactivity expected from a donor/recipient transplantation pair
MIT License
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when are bedmerged used #14

Closed huguesrichard closed 2 months ago

huguesrichard commented 3 months ago

The whole for loop at this position relies on a set of bed_merged files. When are those evaluated? Under which conditions?

https://github.com/huguesrichard/Allopipe/blob/bf4e2ac4427669c5215e2f4fe9d9e941d19df9bc/src/build_peptides.py#L339

PierreLaville commented 2 months ago

In the current version, build_peptides.py isn't called in any other script. It seems that most of its functions have been included in aams_helpers.py.

The for loop doesn't exist in the current version : https://github.com/huguesrichard/Allopipe/blob/8fa66335bccfe66b8695b757d066953ff848eea0/src/tools/aams_helpers.py#L334 The merged file can now be added with an argument: https://github.com/huguesrichard/Allopipe/blob/8fa66335bccfe66b8695b757d066953ff848eea0/src/tools/netmhc_arguments.py#L108

As a result, build_peptides.py script has been deleted there (unmerged yet).

huguesrichard commented 2 months ago

sounds good