class ReadAligner(object):
"""An abstraction layer for different short read aligners."""
def __init__(self, segemehl_bin, show_progress):
self.segemehl = Segemehl(segemehl_bin, show_progress=show_progress)
def build_index(self, ref_seq_paths, index_path):
self.segemehl.build_index(ref_seq_paths, index_path)
def run_alignment(
self,
read_path_or_pair,
index_path,
ref_seq_path,
output_path,
nomatch_path,
threads,
accuracy,
evalue,
split,
paired_end=False,
):
self.segemehl.align_reads(
read_path_or_pair,
index_path,
ref_seq_path,
output_path,
nonmatch_file=nomatch_path,
threads=threads,
accuracy=accuracy,
evalue=evalue,
split=split,
paired_end=paired_end,
)
class ReadAligner(object):
"""An abstraction layer for different short read aligners."""
def __init__(self, segemehl_bin, show_progress):
self.segemehl = Segemehl(segemehl_bin, show_progress=show_progress)
def build_index(self, ref_seq_paths, index_path):
self.segemehl.build_index(ref_seq_paths, index_path)
def run_alignment(self, read_path_or_pair, index_path, ref_seq_path, output_path,
nomatch_path, threads, accuracy, evalue, split, paired_end=False):
self.segemehl.align_reads(read_path_or_pair, index_path, ref_seq_path,
output_path, nonmatch_file=nomatch_path,
threads=threads, accuracy=accuracy,
evalue=evalue, split=split, paired_end=paired_end)
def _align_paired_end_reads(self):
"""Manage the actual alignemnt of paired end reads."""
read_aligner = Segemehl(self._args.segemehl_bin, self._args.progress)
if self._helpers.file_needs_to_be_created(self._paths.index_path):
read_aligner.build_index(self._paths.ref_seq_paths,
self._paths.index_path)
for read_path_pair, output_path, nomatch_path, bam_path in zip(
self._paths.processed_read_path_pairs,
self._paths.primary_read_aligner_sam_paths,
self._paths.unaligned_reads_paths,
self._paths.primary_read_aligner_bam_paths):
if not self._helpers.file_needs_to_be_created(output_path):
continue
elif not self._helpers.file_needs_to_be_created(bam_path):
continue
read_aligner.run_alignment(read_path_pair,
self._paths.index_path,
self._paths.ref_seq_paths,
output_path,
int(self._args.processes),
nomatch_path,
int(self._args.hit_strategy),
int(self._args.segemehl_accuracy),
float(self._args.segemehl_evalue),
self._args.split,
paired_end=True)
def _align_single_end_reads(self):
"""Manage the actual alignment of single end reads."""
read_aligner = Segemehl(
self._args.segemehl_bin, self._args.progress)
if self._file_needs_to_be_created(self._paths.index_path):
read_aligner.build_index(
self._paths.ref_seq_paths, self._paths.index_path)
for read_path, output_path, nomatch_path, bam_path in zip(
self._paths.processed_read_paths,
self._paths.primary_read_aligner_sam_paths,
self._paths.unaligned_reads_paths,
self._paths.read_alignment_bam_paths):
if not self._file_needs_to_be_created(output_path):
continue
elif not self._file_needs_to_be_created(bam_path):
continue
read_aligner.run_alignment(
read_path, self._paths.index_path, self._paths.ref_seq_paths,
output_path, int(self._args.processes), nomatch_path,
int(self._args.hit_strategy),
int(self._args.segemehl_accuracy),
float(self._args.segemehl_evalue), self._args.split,
paired_end=False)
def data_segemehl():
fasta_file_path = "/tmp/test.fa"
index_file_path = "/tmp/test.idx"
read_fasta_file_path = "/tmp/test_reads.fa"
aligning_result_path = "/tmp/test_aligning_results.sam"
unmapped_reads_path = "/tmp/test_unmapped_reads.fa"
segemehl = Segemehl(segemehl_bin="segemehl.x")
maxDiff = None
genome_fasta_lower = """>SL1344 genome sequence
agagattacgtctggttgcaagagatcatgacagggggaattggttgaaaataaatatat
cgccagcagcacatgaacaagtttcggaatgtgatcaatttaaaaatttattgacttagg
cgggcagatactttaaccaatataggaatacaagacagacaaataaaaatgacagagtac
acaacatccatgaaccgcatcagcaccaccaccattaccaccatcaccattaccacaggt
aacggtgcgggctgacgcgtacaggaaacacagaaaaaagcccgcacctgaacagtgcgg
gcttttttttcgaccagagatcacgaggtaacaaccatgcgagtgttgaagttcggcggt
acatcagtggcaaatgcagaacgttttctgcgtgttgccgatattctggaaagcaatgcc
aggcaagggcaggtagcgaccgtactttccgcccccgcgaaaattaccaaccatctggtg
gcaatgattgaaaaaactatcggcggccaggatgctttgccgaatatcagcgatgcagaa
cgtattttttctgacctgctcgcaggacttgccagcgcgcagccgggattcccgcttgca
cggttgaaaatggttgtcgaacaagaattcgctcagatcaaacatgttctgcatggtatc
agcctgctgggtcagtgcccggatagcatcaacgccgcgctgatttgccgtggcgaaaaa
atgtcgatcgcgattatggcgggacttctggaggcgcgtgggcatcgcgtcacggtgatc
gatccggtagaaaaattgctggcggtgggccattaccttgaatctaccgtcgatatcgcg
gaatcgactcgccgtatcgccgccagccagatcccggccgatcacatgatcctgatggcg
ggctttaccgccggtaatgaaaagggtgaactggtggtgctgggccgtaatggttccgac
"""
genome_fasta_upper = """>SL1344 genome sequence
AGAGATTACGTCTGGTTGCAAGAGATCATGACAGGGGGAATTGGTTGAAAATAAATATAT
CGCCAGCAGCACATGAACAAGTTTCGGAATGTGATCAATTTAAAAATTTATTGACTTAGG
CGGGCAGATACTTTAACCAATATAGGAATACAAGACAGACAAATAAAAATGACAGAGTAC
ACAACATCCATGAACCGCATCAGCACCACCACCATTACCACCATCACCATTACCACAGGT
AACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGAACAGTGCGG
GCTTTTTTTTCGACCAGAGATCACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGT
ACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCC
AGGCAAGGGCAGGTAGCGACCGTACTTTCCGCCCCCGCGAAAATTACCAACCATCTGGTG
GCAATGATTGAAAAAACTATCGGCGGCCAGGATGCTTTGCCGAATATCAGCGATGCAGAA
CGTATTTTTTCTGACCTGCTCGCAGGACTTGCCAGCGCGCAGCCGGGATTCCCGCTTGCA
CGGTTGAAAATGGTTGTCGAACAAGAATTCGCTCAGATCAAACATGTTCTGCATGGTATC
AGCCTGCTGGGTCAGTGCCCGGATAGCATCAACGCCGCGCTGATTTGCCGTGGCGAAAAA
ATGTCGATCGCGATTATGGCGGGACTTCTGGAGGCGCGTGGGCATCGCGTCACGGTGATC
GATCCGGTAGAAAAATTGCTGGCGGTGGGCCATTACCTTGAATCTACCGTCGATATCGCG
GAATCGACTCGCCGTATCGCCGCCAGCCAGATCCCGGCCGATCACATGATCCTGATGGCG
GGCTTTACCGCCGGTAATGAAAAGGGTGAACTGGTGGTGCTGGGCCGTAATGGTTCCGAC
"""
sam_result_aligned_1 = """
read_01 0 SL1344 181 255 60M * 0 0 ACAACATCCATGAACCGCATCAGCACCACCACCATTACCACCATCACCATTACCACAGGT * NM:i:0 MD:Z:60 NH:i:1 XI:i:0 XA:Z:Q
"""
sam_result_aligned_2 = """
read_03 0 SL1344 301 255 20M * 0 0 GCTTTTTTTTCGACCAGACA * NM:i:1 MD:Z:18G1 NH:i:1 XI:i:0 XA:Z:Q
"""
sam_result_aligned_3 = """
read_05 0 SL1344 301 255 20M * 0 0 GCTTTTTTTTCGACCAGTCA * NM:i:2 MD:Z:17A0G1 NH:i:1 XI:i:0 XA:Z:Q
"""
sam_result_no_aligned = """
"""
global fasta_file_path
global index_file_path
global read_fasta_file_path
global aligning_result_path
global unmapped_reads_path
global segemehl
global maxDiff
global genome_fasta_lower
global genome_fasta_upper
global sam_result_aligned_1
global sam_result_aligned_2
global sam_result_aligned_3
global sam_result_no_aligned
def setUp(self):
self.segemehl = Segemehl(segemehl_bin="segemehl.x")
self.example_data = ExampleData()
self.maxDiff = None
def __init__(self, segemehl_bin, show_progress):
self.segemehl = Segemehl(segemehl_bin, show_progress=show_progress)