platform: | Unix |
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synopsis: | Create the class HIT which represents a TFBS hit. |
Define the representation of a TFBS hit.
Create an instance of the HIT.
Parameters: |
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Warning: | start and end are 1-based. |
Warning: | The seq_record attribute is not the actual sequence of the hit but the whole sequence containing the hit. |
Todo: | Raise an error when the strand is wrong. |
Give the length of the TFBS hit.
Returns: | The length of the TFBS hit. |
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Return type: | int |
Get the start and end positions of a TFBS hit given its end position on the positive strand.
Parameters: |
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Returns: | The start and end positions and the strand. |
Return type: | tuple(int, int, str) |
Note: | The strand is ‘+’ if the hit is on the positive strand and ‘-‘ otherwise. |
Warning: | The input position is given 0-based as extracted from TFFM computations but the output start and end are 1-based since it is a more conventionnal way to print the TFBS hit positions. |
Module author: Anthony Mathelier <amathelier@cmmt.ubc.ca>