You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
Want to add two new metrics to describe alignment quality:
average sequence length
stddev of sequence lengths
Detail
The cath-align-summary script provides some metrics to describe a (FunFam) sequence alignment: number of sequences, alignment length, dops score, gap positions, total positions.
This summary information for each alignment is currently stored in the cathpy.core.util.AlignmentSummary class:
Overview
Want to add two new metrics to describe alignment quality:
Detail
The
cath-align-summary
script provides some metrics to describe a (FunFam) sequence alignment: number of sequences, alignment length, dops score, gap positions, total positions.This summary information for each alignment is currently stored in the
cathpy.core.util.AlignmentSummary
class:cathpy/cathpy/core/util.py
Lines 527 to 536 in 9e24388
This could be changed to include attributes that store
average_domain_length
andstddev_domain_length
.These
AlignmentSummary
objects are created byAlignmentSummaryRunner
(ie a process that generates an alignment summary for eachSTOCKHOLM
alignment).We would need to calculate these values and add them to the summary object within that runner:
cathpy/cathpy/core/util.py
Line 612 in 9e24388
Making changes
General approach to making changes:
feature/new_alignment_metrics
)cathpy/tests/util_test.py
Lines 36 to 48 in 9e24388
pytest
)master
branchcathpy
:)The text was updated successfully, but these errors were encountered: