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augur align: Ensure reference sequence is removed when no gaps are present #456

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augur align: Ensure reference sequence is removed when no gaps are present #456

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fcd03ea
Align: Ensure reference sequence is removed
Mar 16, 2020
f461134
Use better variable name
Mar 17, 2020
fb49e39
Add tests for strip_non_reference
Mar 22, 2020
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21 changes: 20 additions & 1 deletion augur/align.py
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Original file line number Diff line number Diff line change
Expand Up @@ -213,14 +213,33 @@ def strip_non_reference(alignment_fname, reference, keep_reference=False):
-------
list
list of trimmed sequences, effectively a multiple alignment

Tests
-----
>>> [s.name for s in strip_non_reference("tests/data/align/test_aligned_sequences.fasta", "with_gaps", keep_reference=False)]
Trimmed gaps in with_gaps from the alignment
['no_gaps', 'some_other_seq']
>>> [s.name for s in strip_non_reference("tests/data/align/test_aligned_sequences.fasta", "with_gaps", keep_reference=True)]
Trimmed gaps in with_gaps from the alignment
['with_gaps', 'no_gaps', 'some_other_seq']
>>> [s.name for s in strip_non_reference("tests/data/align/test_aligned_sequences.fasta", "no_gaps", keep_reference=True)]
No gaps in alignment to trim (with respect to the reference, no_gaps)
['with_gaps', 'no_gaps', 'some_other_seq']
>>> [s.name for s in strip_non_reference("tests/data/align/test_aligned_sequences.fasta", "no_gaps", keep_reference=False)]
No gaps in alignment to trim (with respect to the reference, no_gaps)
['with_gaps', 'some_other_seq']
>>> [s.name for s in strip_non_reference("tests/data/align/test_aligned_sequences.fasta", "missing", keep_reference=False)]
Traceback (most recent call last):
...
augur.align.AlignmentError: ERROR: reference missing not found in alignment
'''
aln = AlignIO.read(alignment_fname, 'fasta')
seqs = {s.name:s for s in aln}
if reference in seqs:
ref_array = np.array(seqs[reference])
if "-" not in ref_array:
print("No gaps in alignment to trim (with respect to the reference, %s)"%reference)
return aln
return [seq for seq in aln if (keep_reference or seq.name != reference)]
ungapped = ref_array!='-'
ref_aln_array = np.array(aln)[:,ungapped]
else:
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Binary file added tests/data/align/.test_aligned_sequences.fasta.swp
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6 changes: 6 additions & 0 deletions tests/data/align/test_aligned_sequences.fasta
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@@ -0,0 +1,6 @@
>with_gaps
---ATATA---
>no_gaps
GGGATATAGGG
>some_other_seq
--GATCTAGGG