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Support EMBOSS needle/water alignments to the reverse strand (#4142)
* update * update * update * update * update * update * add tests
This commit is contained in:
mdehoon
GitHub
@ -11,7 +11,7 @@ for example from the needle, water, and stretcher tools.
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"""
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from Bio.Align import Alignment
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from Bio.Align import interfaces
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from Bio.Seq import Seq
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from Bio.Seq import Seq, reverse_complement
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from Bio.SeqRecord import SeqRecord
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@ -99,6 +99,7 @@ class AlignmentIterator(interfaces.AlignmentIterator):
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aligned_sequences = [""] * number_of_sequences
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consensus = ""
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starts = [0] * number_of_sequences
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ends = [0] * number_of_sequences
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column = 0
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index = 0
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continue
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@ -171,14 +172,19 @@ class AlignmentIterator(interfaces.AlignmentIterator):
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n = len(sequences)
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for i in range(n):
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start = starts[i]
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if start == 0:
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sequence = Seq(sequences[i])
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else:
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end = ends[i]
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if start < end:
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coordinates[i, :] += start
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data = sequences[i]
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else:
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start, end = end, start
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coordinates[i, :] = end - coordinates[i, :]
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data = reverse_complement(sequences[i])
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if start == 0:
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sequence = Seq(data)
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else:
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# create a partially defined sequence
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length = start + len(sequences[i])
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data = {start: sequences[i]}
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sequence = Seq(data, length=length)
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sequence = Seq({start: data}, length=end)
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record = SeqRecord(sequence, identifiers[i])
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records.append(record)
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alignment = Alignment(records, coordinates)
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@ -198,21 +204,43 @@ class AlignmentIterator(interfaces.AlignmentIterator):
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identifier, start = prefix.split(None, 1)
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assert identifiers[index].startswith(identifier)
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aligned_sequence, end = line[21:].split(None, 1)
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start = int(start) - 1 # Python counting
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start = int(start)
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end = int(end)
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length = len(sequences[index])
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sequence = aligned_sequence.replace("-", "")
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if length == 0 and len(sequence) > 0:
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if start < end:
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start -= 1 # Python counting
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assert end == start + len(sequence)
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else:
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end -= 1 # Python counting
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assert end == start - len(sequence)
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# Record the start
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starts[index] = start
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else:
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if starts[index] <= ends[index]:
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# forward strand
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if (
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self.metadata["Align_format"] == "srspair"
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and len(sequence) == 0
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):
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assert start == ends[index]
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assert end == start
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else:
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start -= 1
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assert end == start + len(sequence)
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else:
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if (
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self.metadata["Align_format"] == "srspair"
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and len(sequence) == 0
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):
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start += 1
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assert start == starts[index] + length
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assert end == start + len(sequence)
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assert start - 1 == ends[index]
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assert end == start
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else:
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end -= 1
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assert end == start - len(sequence)
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# Record the end
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ends[index] = end
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sequences[index] += sequence
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aligned_sequences[index] += aligned_sequence
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if index == 0:
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47
Tests/Emboss/water_reverse1.txt
Normal file
47
Tests/Emboss/water_reverse1.txt
Normal file
@ -0,0 +1,47 @@
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########################################
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# Program: water
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# Rundate: Sat 22 Oct 2022 23:47:41
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# Commandline: water
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# -asequence seqA.fa
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# -bsequence seqB.fa
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# -gapopen 0.001
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# -gapextend 0.001
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# -sreverse1
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# -outfile water_reverse1.txt
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# Align_format: srspair
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# Report_file: water_reverse1.txt
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########################################
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#=======================================
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#
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# Aligned_sequences: 2
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# 1: seqA
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# 2: seqB
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# Matrix: EDNAFULL
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# Gap_penalty: 0.001
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# Extend_penalty: 0.001
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#
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# Length: 121
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# Identity: 32/121 (26.4%)
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# Similarity: 32/121 (26.4%)
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# Gaps: 89/121 (73.6%)
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# Score: 159.911
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#
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#
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#=======================================
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seqA 121 GGGGGGGGGGGGGGGGGGGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 72
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seqB 1 GGGGGGGGGGGGGGGGGGG------------------------------- 19
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seqA 71 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 22
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seqB 19 -------------------------------------------------- 19
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seqA 21 TTTTTTTTCCCCCCCCCCCCC 1
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seqB 20 --------CCCCCCCCCCCCC 32
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#---------------------------------------
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#---------------------------------------
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47
Tests/Emboss/water_reverse2.txt
Normal file
47
Tests/Emboss/water_reverse2.txt
Normal file
@ -0,0 +1,47 @@
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########################################
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# Program: water
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# Rundate: Sun 23 Oct 2022 00:06:18
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# Commandline: water
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# -asequence seqA.fa
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# -bsequence seqB.fa
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# -gapopen 0.001
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# -gapextend 0.001
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# -sreverse2
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# -outfile water_reverse2.txt
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# Align_format: srspair
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# Report_file: water_reverse2.txt
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########################################
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#=======================================
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#
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# Aligned_sequences: 2
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# 1: seqA
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# 2: seqB
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# Matrix: EDNAFULL
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# Gap_penalty: 0.001
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# Extend_penalty: 0.001
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#
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# Length: 121
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# Identity: 32/121 (26.4%)
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# Similarity: 32/121 (26.4%)
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# Gaps: 89/121 (73.6%)
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# Score: 159.911
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#
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#
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#=======================================
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seqA 1 GGGGGGGGGGGGGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50
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seqB 32 GGGGGGGGGGGGG------------------------------------- 20
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seqA 51 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 100
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seqB 20 -------------------------------------------------- 20
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seqA 101 AACCCCCCCCCCCCCCCCCCC 121
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seqB 19 --CCCCCCCCCCCCCCCCCCC 1
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#---------------------------------------
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#---------------------------------------
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39
Tests/Emboss/water_reverse3.txt
Normal file
39
Tests/Emboss/water_reverse3.txt
Normal file
@ -0,0 +1,39 @@
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########################################
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# Program: water
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# Rundate: Sat 22 Oct 2022 22:56:03
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# Commandline: water
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# -asequence seqA.fa
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# -bsequence seqB.fa
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# -gapopen 1
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# -gapextend 0.5
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# -sreverse1
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# -outfile water_reverse3.txt
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# Align_format: srspair
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# Report_file: water_reverse3.txt
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########################################
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#=======================================
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#
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# Aligned_sequences: 2
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# 1: seqA
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# 2: seqB
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# Matrix: EDNAFULL
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# Gap_penalty: 1.0
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# Extend_penalty: 0.5
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#
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# Length: 19
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# Identity: 16/19 (84.2%)
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# Similarity: 16/19 (84.2%)
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# Gaps: 3/19 (15.8%)
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# Score: 77.5
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#
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#
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#=======================================
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seqA 20 TTTTTTTAAA-CCGGGCCC 3
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seqB 3 TTTTTTT--ACCCGGGCCC 19
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#---------------------------------------
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#---------------------------------------
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39
Tests/Emboss/water_reverse4.txt
Normal file
39
Tests/Emboss/water_reverse4.txt
Normal file
@ -0,0 +1,39 @@
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########################################
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# Program: water
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# Rundate: Sat 22 Oct 2022 22:56:15
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# Commandline: water
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# -asequence seqA.fa
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# -bsequence seqB.fa
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# -gapopen 1
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# -gapextend 0.5
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# -sreverse2
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# -outfile water_reverse4.txt
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# Align_format: srspair
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# Report_file: water_reverse4.txt
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########################################
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#=======================================
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#
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# Aligned_sequences: 2
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# 1: seqA
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# 2: seqB
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# Matrix: EDNAFULL
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# Gap_penalty: 1.0
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# Extend_penalty: 0.5
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#
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# Length: 19
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# Identity: 16/19 (84.2%)
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# Similarity: 16/19 (84.2%)
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# Gaps: 3/19 (15.8%)
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# Score: 77.5
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#
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#
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#=======================================
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seqA 3 GGGCCCGGTT-TAAAAAAA 20
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seqB 19 GGGCCCGG--GTAAAAAAA 3
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#---------------------------------------
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#---------------------------------------
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@ -1214,6 +1214,223 @@ numpy.array([['K', 'I', 'L', 'I', 'V', 'D', 'D', 'Q', 'Y', 'G', 'I', 'R', 'I',
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with self.assertRaises(StopIteration):
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next(alignments)
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def test_water_reverse1(self):
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# water -asequence seqA.fa -bsequence seqB.fa -gapopen 10 -gapextend 0.5 -sreverse1 -outfile water_reverse1.txt
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path = "Emboss/water_reverse1.txt"
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alignments = Align.parse(path, "emboss")
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self.assertEqual(alignments.metadata["Program"], "water")
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self.assertEqual(alignments.metadata["Rundate"], "Sat 22 Oct 2022 23:47:41")
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self.assertEqual(
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alignments.metadata["Command line"],
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"water -asequence seqA.fa -bsequence seqB.fa -gapopen 0.001 -gapextend 0.001 -sreverse1 -outfile water_reverse1.txt",
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)
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self.assertEqual(alignments.metadata["Align_format"], "srspair")
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self.assertEqual(alignments.metadata["Report_file"], "water_reverse1.txt")
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alignment = next(alignments)
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self.assertEqual(alignment.annotations["Matrix"], "EDNAFULL")
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self.assertAlmostEqual(alignment.annotations["Gap_penalty"], 0.001)
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self.assertAlmostEqual(alignment.annotations["Extend_penalty"], 0.001)
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self.assertEqual(alignment.annotations["Identity"], 32)
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self.assertEqual(alignment.annotations["Similarity"], 32)
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self.assertEqual(alignment.annotations["Gaps"], 89)
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self.assertAlmostEqual(alignment.annotations["Score"], 159.911)
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self.assertEqual(len(alignment), 2)
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self.assertEqual(alignment.shape, (2, 121))
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self.assertEqual(alignment.sequences[0].id, "seqA")
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self.assertEqual(alignment.sequences[1].id, "seqB")
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self.assertEqual(
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alignment.sequences[0].seq,
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"GGGGGGGGGGGGGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCC",
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)
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self.assertEqual(
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alignment.sequences[1].seq,
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"GGGGGGGGGGGGGGGGGGGCCCCCCCCCCCCC",
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)
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self.assertTrue(
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numpy.array_equal(
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alignment.coordinates,
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# fmt: off
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# flake8: noqa
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numpy.array([[121, 102, 13, 0],
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[ 0, 19, 19, 32]])
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# fmt: on
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)
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)
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self.assertEqual(
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alignment[0],
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"GGGGGGGGGGGGGGGGGGGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCCCCCCCCCCCCC",
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)
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self.assertEqual(
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alignment[1],
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"GGGGGGGGGGGGGGGGGGG-----------------------------------------------------------------------------------------CCCCCCCCCCCCC",
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)
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self.assertEqual(
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alignment.column_annotations["emboss_consensus"],
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"||||||||||||||||||| |||||||||||||",
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)
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with self.assertRaises(StopIteration):
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next(alignments)
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def test_water_reverse2(self):
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# water -asequence seqA.fa -bsequence seqB.fa -gapopen 10 -gapextend 0.5 -sreverse2 -outfile water_reverse2.txt
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path = "Emboss/water_reverse2.txt"
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alignments = Align.parse(path, "emboss")
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self.assertEqual(alignments.metadata["Program"], "water")
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self.assertEqual(alignments.metadata["Rundate"], "Sun 23 Oct 2022 00:06:18")
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self.assertEqual(
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alignments.metadata["Command line"],
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"water -asequence seqA.fa -bsequence seqB.fa -gapopen 0.001 -gapextend 0.001 -sreverse2 -outfile water_reverse2.txt",
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)
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self.assertEqual(alignments.metadata["Align_format"], "srspair")
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self.assertEqual(alignments.metadata["Report_file"], "water_reverse2.txt")
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alignment = next(alignments)
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self.assertEqual(alignment.annotations["Matrix"], "EDNAFULL")
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self.assertAlmostEqual(alignment.annotations["Gap_penalty"], 0.001)
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self.assertAlmostEqual(alignment.annotations["Extend_penalty"], 0.001)
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self.assertEqual(alignment.annotations["Identity"], 32)
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self.assertEqual(alignment.annotations["Similarity"], 32)
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self.assertEqual(alignment.annotations["Gaps"], 89)
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self.assertAlmostEqual(alignment.annotations["Score"], 159.911)
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self.assertEqual(len(alignment), 2)
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self.assertEqual(alignment.shape, (2, 121))
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self.assertEqual(alignment.sequences[0].id, "seqA")
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self.assertEqual(alignment.sequences[1].id, "seqB")
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self.assertEqual(
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alignment.sequences[0].seq,
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"GGGGGGGGGGGGGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCC",
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)
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self.assertEqual(
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alignment.sequences[1].seq,
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"GGGGGGGGGGGGGGGGGGGCCCCCCCCCCCCC",
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)
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self.assertTrue(
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numpy.array_equal(
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alignment.coordinates,
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# fmt: off
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numpy.array([[ 0, 13, 102, 121],
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[32, 19, 19, 0]])
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# fmt: on
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)
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)
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self.assertEqual(
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alignment[0],
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"GGGGGGGGGGGGGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCC",
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)
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self.assertEqual(
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alignment[1],
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"GGGGGGGGGGGGG-----------------------------------------------------------------------------------------CCCCCCCCCCCCCCCCCCC",
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)
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self.assertEqual(
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alignment.column_annotations["emboss_consensus"],
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"||||||||||||| |||||||||||||||||||",
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)
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with self.assertRaises(StopIteration):
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next(alignments)
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def test_water_reverse3(self):
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# water -asequence seqA.fa -bsequence seqB.fa -gapopen 10 -gapextend 0.5 -sreverse1 -outfile water_reverse3.txt
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path = "Emboss/water_reverse3.txt"
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alignments = Align.parse(path, "emboss")
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self.assertEqual(alignments.metadata["Program"], "water")
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self.assertEqual(alignments.metadata["Rundate"], "Sat 22 Oct 2022 22:56:03")
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self.assertEqual(
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alignments.metadata["Command line"],
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"water -asequence seqA.fa -bsequence seqB.fa -gapopen 1 -gapextend 0.5 -sreverse1 -outfile water_reverse3.txt",
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)
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self.assertEqual(alignments.metadata["Align_format"], "srspair")
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self.assertEqual(alignments.metadata["Report_file"], "water_reverse3.txt")
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alignment = next(alignments)
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self.assertEqual(alignment.annotations["Matrix"], "EDNAFULL")
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self.assertAlmostEqual(alignment.annotations["Gap_penalty"], 1.0)
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self.assertAlmostEqual(alignment.annotations["Extend_penalty"], 0.5)
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self.assertEqual(alignment.annotations["Identity"], 16)
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self.assertEqual(alignment.annotations["Similarity"], 16)
|
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self.assertEqual(alignment.annotations["Gaps"], 3)
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self.assertAlmostEqual(alignment.annotations["Score"], 77.5)
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self.assertEqual(len(alignment), 2)
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self.assertEqual(alignment.shape, (2, 19))
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self.assertEqual(alignment.sequences[0].id, "seqA")
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self.assertEqual(alignment.sequences[1].id, "seqB")
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self.assertEqual(
|
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repr(alignment.sequences[0].seq),
|
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"Seq({2: 'GGGCCCGGTTTAAAAAAA'}, length=20)",
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)
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self.assertEqual(
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repr(alignment.sequences[1].seq),
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"Seq({2: 'TTTTTTTACCCGGGCCC'}, length=19)",
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)
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self.assertTrue(
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numpy.array_equal(
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alignment.coordinates,
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# fmt: off
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# flake8: noqa
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numpy.array([[20, 13, 11, 10, 10, 2],
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[ 2, 9, 9, 10, 11, 19]])
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# fmt: on
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)
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)
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self.assertEqual(alignment[0], "TTTTTTTAAA-CCGGGCCC")
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self.assertEqual(alignment[1], "TTTTTTT--ACCCGGGCCC")
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self.assertEqual(
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alignment.column_annotations["emboss_consensus"],
|
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"||||||| | ||||||||",
|
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)
|
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with self.assertRaises(StopIteration):
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next(alignments)
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|
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def test_water_reverse4(self):
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# water -asequence seqA.fa -bsequence seqB.fa -gapopen 10 -gapextend 0.5 -sreverse2 -outfile water_reverse4.txt
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path = "Emboss/water_reverse4.txt"
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alignments = Align.parse(path, "emboss")
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self.assertEqual(alignments.metadata["Program"], "water")
|
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self.assertEqual(alignments.metadata["Rundate"], "Sat 22 Oct 2022 22:56:15")
|
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self.assertEqual(
|
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alignments.metadata["Command line"],
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"water -asequence seqA.fa -bsequence seqB.fa -gapopen 1 -gapextend 0.5 -sreverse2 -outfile water_reverse4.txt",
|
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)
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self.assertEqual(alignments.metadata["Align_format"], "srspair")
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self.assertEqual(alignments.metadata["Report_file"], "water_reverse4.txt")
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alignment = next(alignments)
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||||
self.assertEqual(alignment.annotations["Matrix"], "EDNAFULL")
|
||||
self.assertAlmostEqual(alignment.annotations["Gap_penalty"], 1.0)
|
||||
self.assertAlmostEqual(alignment.annotations["Extend_penalty"], 0.5)
|
||||
self.assertEqual(alignment.annotations["Identity"], 16)
|
||||
self.assertEqual(alignment.annotations["Similarity"], 16)
|
||||
self.assertEqual(alignment.annotations["Gaps"], 3)
|
||||
self.assertAlmostEqual(alignment.annotations["Score"], 77.5)
|
||||
self.assertEqual(len(alignment), 2)
|
||||
self.assertEqual(alignment.shape, (2, 19))
|
||||
self.assertEqual(alignment.sequences[0].id, "seqA")
|
||||
self.assertEqual(alignment.sequences[1].id, "seqB")
|
||||
self.assertEqual(
|
||||
repr(alignment.sequences[0].seq),
|
||||
"Seq({2: 'GGGCCCGGTTTAAAAAAA'}, length=20)",
|
||||
)
|
||||
self.assertEqual(
|
||||
repr(alignment.sequences[1].seq),
|
||||
"Seq({2: 'TTTTTTTACCCGGGCCC'}, length=19)",
|
||||
)
|
||||
self.assertTrue(
|
||||
numpy.array_equal(
|
||||
alignment.coordinates,
|
||||
# fmt: off
|
||||
# flake8: noqa
|
||||
numpy.array([[ 2, 10, 12, 12, 20],
|
||||
[19, 11, 11, 10, 2]])
|
||||
# fmt: on
|
||||
)
|
||||
)
|
||||
self.assertEqual(alignment[0], "GGGCCCGGTT-TAAAAAAA")
|
||||
self.assertEqual(alignment[1], "GGGCCCGG--GTAAAAAAA")
|
||||
self.assertEqual(
|
||||
alignment.column_annotations["emboss_consensus"],
|
||||
"|||||||| ||||||||",
|
||||
)
|
||||
with self.assertRaises(StopIteration):
|
||||
next(alignments)
|
||||
|
||||
def test_pair_aln_full_blank_line(self):
|
||||
path = "Emboss/emboss_pair_aln_full_blank_line.txt"
|
||||
alignments = Align.parse(path, "emboss")
|
||||
|
||||
Reference in New Issue
Block a user