Fix incorrect trimming of reverse reads. (86399bbc) · Commits · ILVO / GBprocesS

gbprocess/operations/trimming.py

+2 −2

Original line number	Diff line number	Diff line
		@@ -177,7 +177,7 @@ class CutadaptPositionalTrimmer(CommandLineWrapper, Trimmer):
		# Will be needed if we handle spacers!
		]
		if len(output_files) == 2:
		args.extend(["-U", len(self._common_side_cutsite_remnant) + 1])
		args.extend(["-U", len(self._common_side_cutsite_remnant)])

		args.extend(output_file_arg)
		args.extend(files)
		@@ -406,7 +406,7 @@ class CutadaptPatternTrimmer(CommandLineWrapper, Trimmer):

		def _build_patterns(self, barcode):
		result = []
		result.append(self._reverse_complement(self._common_side_cutsite_remnant + self._common_adapter_sequence))
		result.append(self._reverse_complement(self._common_adapter_sequence + self._common_side_cutsite_remnant))
		if self._barcode_adapter_sequence:
		result.append(self._barcode_side_cutsite_remnant + \
		self._reverse_complement(barcode) + \

test/test_operations.py

+89 −16

Original line number	Diff line number	Diff line
		@@ -12,7 +12,7 @@ from gbprocess.operations.filtering import (AverageQualityFilter, LengthFilter,
		MaxNFilter, SlidingWindowQualityFilter)
		from gbprocess.operations.merging import FastqJoinMerger
		from gbprocess.pipeline import SerialPipeline
		from gbprocess.operations.trimming import CutadaptPatternTrimmer
		from gbprocess.operations.trimming import CutadaptPatternTrimmer, CutadaptPositionalTrimmer
		from utils import CustomTestCase

		from data import barcodes, fastq_forward, fastq_reverse, fastq_forward_no_at, fastq_reverse_no_at, invalid_fastq_content
		@@ -624,13 +624,86 @@ class TestSlidingWindowQualityFilter(CustomOperationTestCase):
		extension = self.single_end_fastq.extension
		self.assertEqual(str(forward.name), f'{run}{extension}')

		class TestCutadaptPositionalTrimmer(CustomOperationTestCase):
		def setUp(self):
		super().setUp()
		barcode = dedent(
		"""
		>barcode1
		ATCCCCGG
		""").strip()
		with open(self.tempdir.name + "/barcodes.fasta", 'w+') as barcodes_file:
		barcodes_file.write(barcode)
		barcodes_file.flush()
		self.barcodes = self.tempdir.name + "/barcodes.fasta"
		self.paired_fastq.sample_name = "barcode1"
		self.single_end_fastq.sample_name = "barcode1"

		self.forward_result = dedent("""
		@EU861894-140/1
		TCGGCCTGCCCGGGGATCTCAAACNCTGGTAAGCTTCTCCGGTTAGTGACGAATCACTGTACCTGCTCCACCGCTTGTGCGGGCCCTCGTCA
		+
		HHAH#III#I:IHJIJG#JIJJI?3IIJ0JJ#G3JGHG#I90?HIJG9JEIIBD#C#G@#C=)I@#BHBBCDCD;ACDCB;??CD>#D#:DA
		@EU861894-138/1
		TCCACATGTGGTCCCCCGCTTCGGGGCAGGTTGCCCACGTGTTACGCGACCGTTCGCCATTAACCAC
		+
		HHG?BAJJG0BII#GI8;FJIBFBHGJI>+EC=BECBDCHDEAAD#=E6DDFF=9CD#A#8H@@>#D
		""").strip()

		self.reverse_result = dedent("""
		@EU861894-140/2
		GAATTGACAGGGGCACGCATAAGCGGTGCGGTATGTGCATTAATTCGTCACTAACTGAAGAACCTCACCAGGCTTTGAAACCCACGGAGAGCGGGAG
		+
		F1FFEFFA#AGGJB!EHDI434:J?GJI##B#)BJIICJJGEBFIBJ>GGDJIGI#)II<H6=ID#E?CD4##CDEFB#C#CA#-<#?#FCE#!DC'
		@EU861894-138/2
		CGGGGGTGGTTAGGCAACCCCCCCCGAAGCGGGGGACAACAGCCTTAAACGGTTCCTAATACCGCATGGTGA
		+
		FB2@FHB2HFJGFFHJ?8=##JDGHDEIBH?H#HI)EFFEF#C#B#HE?#D?#;#DDCA#:DD>BCB###D'
		""").strip()

		def test_trim_single(self):
		trim_op = CutadaptPositionalTrimmer(barcode_side_cutsite_remnant="",
		common_side_cutsite_remnant="GCG",
		barcodes=self.barcodes,
		output_file_name_template="{run}_{extension}",
		output_directory=self.tempdir.name)
		result = trim_op.perform(self.single_end_fastq)
		fastq_result = list(result)
		self.assertTrue(len(fastq_result) == 1)
		fastq, = fastq_result.pop().files
		self.assertFileContentEquals(fastq, self.forward_result)

		def test_trim_paired(self):
		trim_op = CutadaptPositionalTrimmer(barcode_side_cutsite_remnant="",
		common_side_cutsite_remnant="GCG",
		barcodes=self.barcodes,
		output_file_name_template="{run}_{orientation}{extension}",
		output_directory=self.tempdir.name)
		output_seq_data = trim_op.perform(self.paired_fastq)
		fastq, = output_seq_data
		forward, reverse = fastq.files
		# Check output file contents
		self.assertFileContentEquals(forward, self.forward_result)
		self.assertFileContentEquals(reverse, self.reverse_result)

		# Check output directory
		self.assertEqual(forward.parent, reverse.parent)
		self.assertEqual(self.tempdir.name, str(forward.parent))

		# Check output name
		run = self.single_end_fastq.run
		extension = self.single_end_fastq.extension
		self.assertEqual(forward.name, f"{run}_1{extension}")
		self.assertEqual(reverse.name, f"{run}_2{extension}")


		class TestCutadaptPatternTrimmer(CustomOperationTestCase):
		def setUp(self):
		super().setUp()
		barcode = dedent(
		"""
		>barcode1
		ATCCCCGGG
		CCGCTT
		""").strip()
		with open(self.tempdir.name + "/barcodes.fasta", 'w+') as barcodes_file:
		barcodes_file.write(barcode)
		@@ -640,9 +713,9 @@ class TestCutadaptPatternTrimmer(CustomOperationTestCase):
		self.single_end_fastq.sample_name = "barcode1"
		self.forward_result = dedent("""
		@EU861894-140/1
		CCGATCTCTCGGCCTGCCCGGGGATCTCAAACNCTGGTAAGCTTCTCCGGTTAGTGACGAATCACT
		CCGATCTCTCGGCCTGCCCGGGGATCTCAAACNCTGGTAAGCTTCTCCGGTTAGTGACGAATC
		+
		??CFFF?;HHAH#III#I:IHJIJG#JIJJI?3IIJ0JJ#G3JGHG#I90?HIJG9JEIIBD#C#G
		??CFFF?;HHAH#III#I:IHJIJG#JIJJI?3IIJ0JJ#G3JGHG#I90?HIJG9JEIIBD#
		@EU861894-138/1
		AGAGCGCATCCACATGTGGTCCCCCGCTTCGGGGCAGGTTGCCCACGTGTTACGCGACCGTTCGCCATTAACCAC
		+
		@@ -651,9 +724,9 @@ class TestCutadaptPatternTrimmer(CustomOperationTestCase):

		self.reverse_result = dedent("""
		@EU861894-140/2
		AAGGAATTGACAGGGGCACGCATAAGCGGTGCGGTATGTGCATTAATTCGTCACTAACTGAAGAACCTCACCAGGCTTTGAAACCCACGGAGAGCGGGAG
		AAGGAATTGACAGGGGCACG
		+
		@1@F1FFEFFA#AGGJB!EHDI434:J?GJI##B#)BJIICJJGEBFIBJ>GGDJIGI#)II<H6=ID#E?CD4##CDEFB#C#CA#-<#?#FCE#!DC'
		@1@F1FFEFFA#AGGJB!EH
		@EU861894-138/2
		CTTCGGGGGTGGTTAGGCAACCCCCCCCGAAGCGGGGGACAACAGCCTTAAACGGTTCCTAATACCGCATGGTGA
		+
		@@ -663,7 +736,7 @@ class TestCutadaptPatternTrimmer(CustomOperationTestCase):
		def test_trim_single(self):
		trim_op = CutadaptPatternTrimmer(common_adapter_sequence="GTGGAGCAGGTAC",
		barcode_adapter_sequence="",
		common_side_cutsite_remnant="GCG",
		common_side_cutsite_remnant="AGT",
		barcode_side_cutsite_remnant="",
		barcodes=self.barcodes,
		minimum_length=1,
		@@ -678,9 +751,9 @@ class TestCutadaptPatternTrimmer(CustomOperationTestCase):

		def test_trim_paired(self):
		trim_op = CutadaptPatternTrimmer(common_adapter_sequence="GTGGAGCAGGTAC",
		barcode_adapter_sequence="",
		common_side_cutsite_remnant="GCG",
		barcode_side_cutsite_remnant="",
		barcode_adapter_sequence="ACATACCGCA",
		common_side_cutsite_remnant="AGT",
		barcode_side_cutsite_remnant="CAT",
		barcodes=self.barcodes,
		minimum_length=1,
		error_rate=0,