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View Code? Open in Web Editor NEWA python package to compute clusters of sequence feature variant types (SFVTs) based upon user-selected subsequence.
License: Creative Commons Zero v1.0 Universal
A python package to compute clusters of sequence feature variant types (SFVTs) based upon user-selected subsequence.
License: Creative Commons Zero v1.0 Universal
if you input two linear sections for the alignments(12-13,14-15) or if you input between 2 and infinity non linear sections and 0 linear sections for the reference sequence and the alignments (so something like 100,105,110 wouldn't work but 100,105,110-11 would work).
Give users the option to plot the top X number of plots or only plots with more then Y sequences in them
Save a report of the number data behind the plots
Check to make sure that the os.read function works for all operating systems
Add ability to report or not report "N"s in variant types
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Add a function to natively read IEDB epitope format; such as "H25, H45, V46, N47, L496, S306, L307, P308, T333"
NOTE: Further enhance to allow for epitopes to be pasted that are discontinuous peptides on multi chains such as: "A: H25, H45, V46, N47, L496, S306, L307, P308, T333; B: D363, G364, W365, Q382, T385, Q386, I389, D390, T393, V396, N397, I400;"
Basically strip off the characters or better yet extract the characters and use them to find the reference sequence
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