Add metrics to alignment summary (average + std dev length of sequences)

[sillitoe]

Overview

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:

cathpy/cathpy/core/util.py

Lines 527 to 536 in 9e24388

	class AlignmentSummary(object):
	"""Stores summary information about an alignment."""
	def __init__(self, *, path, dops, aln_length, seq_count, gap_count, total_positions):
	self.path = path
	self.dops = float(dops) if dops is not None else None
	self.aln_length = int(aln_length)
	self.seq_count = int(seq_count)
	self.gap_count = int(gap_count)
	self.total_positions = int(total_positions)

This could be changed to include attributes that store average_domain_length and stddev_domain_length.

These AlignmentSummary objects are created by AlignmentSummaryRunner (ie a process that generates an alignment summary for each STOCKHOLM 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

def run(self):

Making changes

General approach to making changes:

1. clone this repo
2. create a new branch (eg called feature/new_alignment_metrics)
3. add a test to check that your feature is working
   

   cathpy/tests/util_test.py

   Lines 36 to 48 in 9e24388

   	def test_alignment_summary_file(self):
   	runner = AlignmentSummaryRunner(
   	aln_file=self.merge_sto_file)
   	entries = runner.run()
   	self.assertEqual(len(entries), 1)
   	summary = entries[0]
   	self.assertEqual(summary.aln_length, 92)
   	self.assertEqual(summary.dops, 88.422)
   	self.assertEqual(summary.gap_count, 25228)
   	self.assertEqual(summary.total_positions, 64492)
   	self.assertEqual(summary.seq_count, 701)
   	self.assertEqual(round(summary.gap_per, 2), round(39.12, 2))

4. add the code to make your new test pass
5. make sure your changes have not broken anything else (ie run pytest)
6. commit your changes, push back to origin (GitHub)
7. make sure your changes have not broken anything else
8. create a pull request (PR)
9. someone else (me) reviews the code
10. code is merged into master branch
11. we add your name as an official contributor to cathpy :)