def test_overlapping_alignments_2(self):
"""Extraction of overlapping reads - with a non-default
minimal overlap.
"""
self._generate_bam_file(
self.example_data.sam_content_1, self._sam_bam_prefix)
self.gene_wise_quantification = GeneWiseQuantification()
self.gene_wise_quantification._min_overlap = 5
sam = pysam.Samfile(self._sam_bam_prefix + ".bam")
# 1 overlapping base in the 5' end of the reads => not enough
self.assertListEqual(self._mapping_ids(
self.gene_wise_quantification._overlapping_alignments(
sam, Gff3EntryMoc("chrom", 1, 10))), [])
# 4 overlapping base in the 5' end of the reads => not enough
self.assertListEqual(self._mapping_ids(
self.gene_wise_quantification._overlapping_alignments(
sam, Gff3EntryMoc("chrom", 1, 13))), [])
# 5 overlapping base in the 5' end of the reads => okay
self.assertListEqual(self._mapping_ids(
self.gene_wise_quantification._overlapping_alignments(
sam, Gff3EntryMoc("chrom", 1, 14))),
["myread:01", "myread:02", "myread:03", "myread:04", "myread:05"])
# 1 overlapping base in the 3' end of the reads => not enough
self.assertListEqual(self._mapping_ids(
self.gene_wise_quantification._overlapping_alignments(
sam, Gff3EntryMoc("chrom", 19, 23))), [])
# 4 overlapping base in the 3' end of the reads => not enough
self.assertListEqual(self._mapping_ids(
self.gene_wise_quantification._overlapping_alignments(
sam, Gff3EntryMoc("chrom", 16, 23))), [])
# 5 overlapping base in the 3' end of the reads => not enough
self.assertListEqual(self._mapping_ids(
self.gene_wise_quantification._overlapping_alignments(
sam, Gff3EntryMoc("chrom", 15, 23))),
["myread:01", "myread:02", "myread:03", "myread:04", "myread:05"])
def _quantify_gene_wise(
self, lib_name, read_alignment_path,
norm_by_alignment_freq, norm_by_overlap_freq,
annotation_files):
"""Perform the gene wise quantification for a given library."""
gene_quanti_paths = [
self._paths.gene_quanti_path(lib_name, annotation_file)
for annotation_file in annotation_files]
# Check if all output files for this library exist - if so
# skip their creation
if not any([self._file_needs_to_be_created(
gene_quanti_path, quiet=True)
for gene_quanti_path in gene_quanti_paths]):
sys.stderr.write(
"The file(s) %s exist(s). Skipping their/its generation.\n" %
", " .join(gene_quanti_paths))
return
gene_wise_quantification = GeneWiseQuantification(
min_overlap=self._args.min_overlap,
read_region=self._args.read_region,
clip_length=self._args.clip_length,
norm_by_alignment_freq=norm_by_alignment_freq,
norm_by_overlap_freq=norm_by_overlap_freq,
allowed_features_str=self._args.allowed_features,
skip_antisense=self._args.skip_antisense,
unique_only=self._args.unique_only)
gene_wise_quantification.calc_overlaps_per_alignment(
read_alignment_path, self._paths.annotation_paths)
for annotation_file, annotation_path in zip(
annotation_files, self._paths.annotation_paths):
gene_wise_quantification.quantify(
read_alignment_path, annotation_path,
self._paths.gene_quanti_path(
lib_name, annotation_file), self._args.pseudocounts)
def test_overlapping_alignments_1(self):
self._generate_bam_file(
self.example_data.sam_content_1, self._sam_bam_prefix)
self.gene_wise_quantification = GeneWiseQuantification()
sam = pysam.Samfile(self._sam_bam_prefix + ".bam")
# Overlap with all mappings
self.assertListEqual(self._mapping_ids(
self.gene_wise_quantification._overlapping_alignments(
sam, Gff3EntryMoc("chrom", 1, 100))),
["myread:01", "myread:02", "myread:03", "myread:04", "myread:05",
"myread:06", "myread:07", "myread:08", "myread:09", "myread:10"])
# Overlapping with no mapping
self.assertListEqual(self._mapping_ids(
self.gene_wise_quantification._overlapping_alignments(
sam, Gff3EntryMoc("chrom", 1, 5))), [])
# Overlapping by 1 based - in the 5' end of the reads
self.assertListEqual(self._mapping_ids(
self.gene_wise_quantification._overlapping_alignments(
sam, Gff3EntryMoc("chrom", 1, 10))),
["myread:01", "myread:02", "myread:03", "myread:04", "myread:05"])
# No overlap - gene very close upstream of the reads
self.assertListEqual(self._mapping_ids(
self.gene_wise_quantification._overlapping_alignments(
sam, Gff3EntryMoc("chrom", 1, 9))), [])
# Overlapping by 1 based - in the 3' end of the reads
self.assertListEqual(self._mapping_ids(
self.gene_wise_quantification._overlapping_alignments(
sam, Gff3EntryMoc("chrom", 19, 23))),
["myread:01", "myread:02", "myread:03", "myread:04", "myread:05"])
# No overlap - very close downstream of the reads
self.assertListEqual(self._mapping_ids(
self.gene_wise_quantification._overlapping_alignments(
sam, Gff3EntryMoc("chrom", 20, 23))), [])
def test_overlapping_alignments_1(self):
self._generate_bam_file(self.example_data.sam_content_1,
self._sam_bam_prefix)
self.gene_wise_quantification = GeneWiseQuantification()
sam = pysam.Samfile(self._sam_bam_prefix + ".bam")
# Overlap with all mappings on the forward strand
self.assertListEqual(
self._mapping_ids(
self.gene_wise_quantification._overlapping_alignments(
sam, Gff3EntryMoc("chrom", 1, 100, "+"))),
["myread:01", "myread:02", "myread:03", "myread:04", "myread:05"])
# Overlapping with no mapping
self.assertListEqual(
self._mapping_ids(
self.gene_wise_quantification._overlapping_alignments(
sam, Gff3EntryMoc("chrom", 1, 5, "+"))), [])
# Overlapping by 1 based - in the 5' end of the reads
self.assertListEqual(
self._mapping_ids(
self.gene_wise_quantification._overlapping_alignments(
sam, Gff3EntryMoc("chrom", 1, 10, "+"))),
["myread:01", "myread:02", "myread:03", "myread:04", "myread:05"])
# No overlap - gene very close upstream of the reads
self.assertListEqual(
self._mapping_ids(
self.gene_wise_quantification._overlapping_alignments(
sam, Gff3EntryMoc("chrom", 1, 9, "+"))), [])
# Overlapping by 1 based - in the 3' end of the reads
self.assertListEqual(
self._mapping_ids(
self.gene_wise_quantification._overlapping_alignments(
sam, Gff3EntryMoc("chrom", 19, 23, "+"))),
["myread:01", "myread:02", "myread:03", "myread:04", "myread:05"])
# Overlapping by 1 based - in the 3' end of the reads but on the wrong strand
self.assertListEqual(
self._mapping_ids(
self.gene_wise_quantification._overlapping_alignments(
sam, Gff3EntryMoc("chrom", 19, 23, "-"))), [])
# No overlap - very close downstream of the reads
self.assertListEqual(
self._mapping_ids(
self.gene_wise_quantification._overlapping_alignments(
sam, Gff3EntryMoc("chrom", 20, 23, "+"))), [])
# Overlapping by 1 based - in the 3' end of the reads on the opposite strand, without strand specificity
self.gene_wise_quantification._strand_specific = False
self.assertListEqual(
self._mapping_ids(
self.gene_wise_quantification._overlapping_alignments(
sam, Gff3EntryMoc("chrom", 19, 23, "-"))),
["myread:01", "myread:02", "myread:03", "myread:04", "myread:05"])
# Overlapping by 1 based - in the 3' end of the reads on the opposite strand, with strand specificity
# only allowing antisense overlaps
self.gene_wise_quantification._strand_specific = True
self.gene_wise_quantification._antisense_only = True
self.assertListEqual(
self._mapping_ids(
self.gene_wise_quantification._overlapping_alignments(
sam, Gff3EntryMoc("chrom", 19, 100, "-"))),
["myread:01", "myread:02", "myread:03", "myread:04", "myread:05"])
def _quantify_gene_wise(
self, lib_name, read_alignment_path,
norm_by_alignment_freq, norm_by_overlap_freq,
annotation_files):
"""Perform the gene wise quantification for a given library."""
gene_quanti_paths = [
self._paths.gene_quanti_path(lib_name, annotation_file)
for annotation_file in annotation_files]
# Check if all output files for this library exist - if so
# skip their creation
if not any([self._file_needs_to_be_created(
gene_quanti_path, quiet=True)
for gene_quanti_path in gene_quanti_paths]):
sys.stderr.write(
"The file(s) %s exist(s). Skipping their/its generation.\n" %
", " .join(gene_quanti_paths))
return
gene_wise_quantification = GeneWiseQuantification(
min_overlap=self._args.min_overlap,
read_region=self._args.read_region,
clip_length=self._args.clip_length,
norm_by_alignment_freq=norm_by_alignment_freq,
norm_by_overlap_freq=norm_by_overlap_freq,
allowed_features_str=self._args.allowed_features,
skip_antisense=self._args.skip_antisense,
unique_only=self._args.unique_only)
if norm_by_overlap_freq:
gene_wise_quantification.calc_overlaps_per_alignment(
read_alignment_path, self._paths.annotation_paths)
for annotation_file, annotation_path in zip(
annotation_files, self._paths.annotation_paths):
gene_wise_quantification.quantify(
read_alignment_path, annotation_path,
self._paths.gene_quanti_path(
lib_name, annotation_file), self._args.pseudocounts)
def data_gene_wise_quanti():
gene_wise_quantification = GeneWiseQuantification()
sam_bam_prefix = "dummy"
sam_content = """@HD VN:1.0
@SQ SN:chrom LN:1500
@SQ SN:plasmid1 LN:100
@SQ SN:plasmid2 LN:200
myread:01 0 chrom 10 255 10M * 0 0 GTGGACAACC * NM:i:1 MD:Z:11T3 NH:i:1 XI:i:1 XA:Z:Q
myread:02 0 chrom 10 255 10M * 0 0 GTGGACAACC * NM:i:1 MD:Z:11T3 NH:i:1 XI:i:1 XA:Z:Q
myread:03 0 chrom 10 255 10M * 0 0 GTGGACAACC * NM:i:1 MD:Z:11T3 NH:i:1 XI:i:1 XA:Z:Q
myread:04 0 chrom 10 255 10M * 0 0 GTGGACAACC * NM:i:1 MD:Z:11T3 NH:i:1 XI:i:1 XA:Z:Q
myread:05 0 chrom 10 255 10M * 0 0 GTGGACAACC * NM:i:1 MD:Z:11T3 NH:i:1 XI:i:1 XA:Z:Q
myread:06 16 chrom 35 255 10M * 0 0 GTGGACAACC * NM:i:1 MD:Z:11T3 NH:i:1 XI:i:1 XA:Z:Q
myread:07 16 chrom 35 255 10M * 0 0 GTGGACAACC * NM:i:1 MD:Z:11T3 NH:i:1 XI:i:1 XA:Z:Q
myread:08 16 chrom 35 255 10M * 0 0 GTGGACAACC * NM:i:1 MD:Z:11T3 NH:i:1 XI:i:1 XA:Z:Q
myread:09 16 chrom 35 255 10M * 0 0 GTGGACAACC * NM:i:1 MD:Z:11T3 NH:i:1 XI:i:1 XA:Z:Q
myread:10 16 chrom 35 255 10M * 0 0 GTGGACAACC * NM:i:1 MD:Z:11T3 NH:i:1 XI:i:1 XA:Z:Q
"""
global gene_wise_quantification
global sam_bam_prefix
global sam_content
def setUp(self):
self.example_data = ExampleData()
self._sam_bam_prefix = "dummy"
self.gene_wise_quantification = GeneWiseQuantification()
class TestGeneWiseQuantification(unittest.TestCase):
def setUp(self):
self.example_data = ExampleData()
self._sam_bam_prefix = "dummy"
self.gene_wise_quantification = GeneWiseQuantification()
def tearDown(self):
for suffix in [".sam", ".bam", ".bam.bai"]:
os.remove(self._sam_bam_prefix + suffix)
def test_overlapping_alignments_1(self):
self._generate_bam_file(self.example_data.sam_content_1,
self._sam_bam_prefix)
self.gene_wise_quantification = GeneWiseQuantification()
sam = pysam.Samfile(self._sam_bam_prefix + ".bam")
# Overlap with all mappings
self.assertListEqual(
self._mapping_ids(
self.gene_wise_quantification._overlapping_alignments(
sam, Gff3EntryMoc("chrom", 1, 100))), [
"myread:01", "myread:02", "myread:03", "myread:04",
"myread:05", "myread:06", "myread:07", "myread:08",
"myread:09", "myread:10"
])
# Overlapping with no mapping
self.assertListEqual(
self._mapping_ids(
self.gene_wise_quantification._overlapping_alignments(
sam, Gff3EntryMoc("chrom", 1, 5))), [])
# Overlapping by 1 based - in the 5' end of the reads
self.assertListEqual(
self._mapping_ids(
self.gene_wise_quantification._overlapping_alignments(
sam, Gff3EntryMoc("chrom", 1, 10))),
["myread:01", "myread:02", "myread:03", "myread:04", "myread:05"])
# No overlap - gene very close upstream of the reads
self.assertListEqual(
self._mapping_ids(
self.gene_wise_quantification._overlapping_alignments(
sam, Gff3EntryMoc("chrom", 1, 9))), [])
# Overlapping by 1 based - in the 3' end of the reads
self.assertListEqual(
self._mapping_ids(
self.gene_wise_quantification._overlapping_alignments(
sam, Gff3EntryMoc("chrom", 19, 23))),
["myread:01", "myread:02", "myread:03", "myread:04", "myread:05"])
# No overlap - very close downstream of the reads
self.assertListEqual(
self._mapping_ids(
self.gene_wise_quantification._overlapping_alignments(
sam, Gff3EntryMoc("chrom", 20, 23))), [])
def test_overlapping_alignments_2(self):
"""Extraction of overlapping reads - with a non-default
minimal overlap.
"""
self._generate_bam_file(self.example_data.sam_content_1,
self._sam_bam_prefix)
self.gene_wise_quantification = GeneWiseQuantification()
self.gene_wise_quantification._min_overlap = 5
sam = pysam.Samfile(self._sam_bam_prefix + ".bam")
# 1 overlapping base in the 5' end of the reads => not enough
self.assertListEqual(
self._mapping_ids(
self.gene_wise_quantification._overlapping_alignments(
sam, Gff3EntryMoc("chrom", 1, 10))), [])
# 4 overlapping base in the 5' end of the reads => not enough
self.assertListEqual(
self._mapping_ids(
self.gene_wise_quantification._overlapping_alignments(
sam, Gff3EntryMoc("chrom", 1, 13))), [])
# 5 overlapping base in the 5' end of the reads => okay
self.assertListEqual(
self._mapping_ids(
self.gene_wise_quantification._overlapping_alignments(
sam, Gff3EntryMoc("chrom", 1, 14))),
["myread:01", "myread:02", "myread:03", "myread:04", "myread:05"])
# 1 overlapping base in the 3' end of the reads => not enough
self.assertListEqual(
self._mapping_ids(
self.gene_wise_quantification._overlapping_alignments(
sam, Gff3EntryMoc("chrom", 19, 23))), [])
# 4 overlapping base in the 3' end of the reads => not enough
self.assertListEqual(
self._mapping_ids(
self.gene_wise_quantification._overlapping_alignments(
sam, Gff3EntryMoc("chrom", 16, 23))), [])
# 5 overlapping base in the 3' end of the reads => not enough
self.assertListEqual(
self._mapping_ids(
self.gene_wise_quantification._overlapping_alignments(
sam, Gff3EntryMoc("chrom", 15, 23))),
["myread:01", "myread:02", "myread:03", "myread:04", "myread:05"])
def _mapping_ids(self, mappings):
return [mapping.qname for mapping in mappings]
def _generate_bam_file(self, sam_content, file_prefix):
sam_file = "{}.sam".format(file_prefix)
bam_file = "{}.bam".format(file_prefix)
sam_fh = open(sam_file, "w")
sam_fh.write(sam_content)
sam_fh.close()
pysam.view("-Sb",
"-o{}".format(bam_file),
sam_file,
catch_stdout=False)
pysam.index(bam_file)
def setUp(self):
self.example_data = ExampleData()
self._sam_bam_prefix = "dummy"
self.gene_wise_quantification = GeneWiseQuantification()
class TestGeneWiseQuantification(unittest.TestCase):
def setUp(self):
self.example_data = ExampleData()
self._sam_bam_prefix = "dummy"
self.gene_wise_quantification = GeneWiseQuantification()
def tearDown(self):
for suffix in [".sam", ".bam", ".bam.bai"]:
os.remove(self._sam_bam_prefix + suffix)
def test_overlapping_alignments_1(self):
self._generate_bam_file(
self.example_data.sam_content_1, self._sam_bam_prefix)
self.gene_wise_quantification = GeneWiseQuantification()
sam = pysam.Samfile(self._sam_bam_prefix + ".bam")
# Overlap with all mappings
self.assertListEqual(self._mapping_ids(
self.gene_wise_quantification._overlapping_alignments(
sam, Gff3EntryMoc("chrom", 1, 100))),
["myread:01", "myread:02", "myread:03", "myread:04", "myread:05",
"myread:06", "myread:07", "myread:08", "myread:09", "myread:10"])
# Overlapping with no mapping
self.assertListEqual(self._mapping_ids(
self.gene_wise_quantification._overlapping_alignments(
sam, Gff3EntryMoc("chrom", 1, 5))), [])
# Overlapping by 1 based - in the 5' end of the reads
self.assertListEqual(self._mapping_ids(
self.gene_wise_quantification._overlapping_alignments(
sam, Gff3EntryMoc("chrom", 1, 10))),
["myread:01", "myread:02", "myread:03", "myread:04", "myread:05"])
# No overlap - gene very close upstream of the reads
self.assertListEqual(self._mapping_ids(
self.gene_wise_quantification._overlapping_alignments(
sam, Gff3EntryMoc("chrom", 1, 9))), [])
# Overlapping by 1 based - in the 3' end of the reads
self.assertListEqual(self._mapping_ids(
self.gene_wise_quantification._overlapping_alignments(
sam, Gff3EntryMoc("chrom", 19, 23))),
["myread:01", "myread:02", "myread:03", "myread:04", "myread:05"])
# No overlap - very close downstream of the reads
self.assertListEqual(self._mapping_ids(
self.gene_wise_quantification._overlapping_alignments(
sam, Gff3EntryMoc("chrom", 20, 23))), [])
def test_overlapping_alignments_2(self):
"""Extraction of overlapping reads - with a non-default
minimal overlap.
"""
self._generate_bam_file(
self.example_data.sam_content_1, self._sam_bam_prefix)
self.gene_wise_quantification = GeneWiseQuantification()
self.gene_wise_quantification._min_overlap = 5
sam = pysam.Samfile(self._sam_bam_prefix + ".bam")
# 1 overlapping base in the 5' end of the reads => not enough
self.assertListEqual(self._mapping_ids(
self.gene_wise_quantification._overlapping_alignments(
sam, Gff3EntryMoc("chrom", 1, 10))), [])
# 4 overlapping base in the 5' end of the reads => not enough
self.assertListEqual(self._mapping_ids(
self.gene_wise_quantification._overlapping_alignments(
sam, Gff3EntryMoc("chrom", 1, 13))), [])
# 5 overlapping base in the 5' end of the reads => okay
self.assertListEqual(self._mapping_ids(
self.gene_wise_quantification._overlapping_alignments(
sam, Gff3EntryMoc("chrom", 1, 14))),
["myread:01", "myread:02", "myread:03", "myread:04", "myread:05"])
# 1 overlapping base in the 3' end of the reads => not enough
self.assertListEqual(self._mapping_ids(
self.gene_wise_quantification._overlapping_alignments(
sam, Gff3EntryMoc("chrom", 19, 23))), [])
# 4 overlapping base in the 3' end of the reads => not enough
self.assertListEqual(self._mapping_ids(
self.gene_wise_quantification._overlapping_alignments(
sam, Gff3EntryMoc("chrom", 16, 23))), [])
# 5 overlapping base in the 3' end of the reads => not enough
self.assertListEqual(self._mapping_ids(
self.gene_wise_quantification._overlapping_alignments(
sam, Gff3EntryMoc("chrom", 15, 23))),
["myread:01", "myread:02", "myread:03", "myread:04", "myread:05"])
def _mapping_ids(self, mappings):
return [mapping.qname for mapping in mappings]
def _generate_bam_file(self, sam_content, file_prefix):
sam_file = "%s.sam" % file_prefix
bam_file = "%s.bam" % file_prefix
sam_fh = open(sam_file, "w")
sam_fh.write(sam_content)
sam_fh.close()
pysam.view("-Sb", "-o%s" % bam_file, sam_file)
pysam.index(bam_file)
