def test_bam(tmpdir):
datatest = sequana_data("test.bam", "testing")
s = BAM(datatest)
assert len(s) == 1000
assert s.is_sorted is True
df = s.get_df_concordance()
assert s.is_paired is True
assert int(df.length.sum()) == 67938
assert int(df.M.sum()) == 67788
df = s.get_df()
# call this here before other computations on purpose
with TempFile(suffix=".json") as fh:
s.bam_analysis_to_json(fh.name)
assert s.get_read_names()
s.get_mapped_read_length()
s.get_stats()
s.get_stats_full()
s.get_samtools_stats_as_df()
with TempFile() as fh:
s.to_fastq(fh.name)
from sequana import FastQ
ff = FastQ(fh.name)
len(ff) == len(s)
# plotting
with TempFile(suffix='.png') as fh:
s.plot_bar_flags(filename=fh.name, logy=True)
s.plot_bar_flags(filename=fh.name)
with TempFile(suffix='.png') as fh:
s.plot_bar_mapq(filename=fh.name)
s.get_gc_content()
s.get_length_count()
s.plot_gc_content()
s.boxplot_qualities()
s.boxplot_qualities(max_sample=50)
try:
s.plot_gc_content(bins=[1, 2, 10])
assert False
except:
assert True
def test_bam(tmpdir):
datatest = sequana_data("test.bam", "testing")
s = BAM(datatest)
assert len(s) == 1000
assert s.is_sorted is True
df = s.get_df_concordance()
assert s.is_paired is True
assert int(df.length.sum()) == 67938
assert int(df.M.sum()) == 67788
# call this here before other computations on purpose
with TempFile(suffix=".json") as fh:
s.bam_analysis_to_json(fh.name)
assert s.get_read_names()
s.get_mapped_read_length()
s.get_stats()
s.get_full_stats_as_df()
with TempFile() as fh:
s.to_fastq(fh.name)
from sequana import FastQ
ff = FastQ(fh.name)
len(ff) == len(s)
# plotting
with TempFile(suffix='.png') as fh:
s.plot_bar_flags(filename=fh.name, logy=True)
s.plot_bar_flags(filename=fh.name)
with TempFile(suffix='.png') as fh:
s.plot_bar_mapq(filename=fh.name)
s.get_gc_content()
s.get_length_count()
s.plot_gc_content()
s.boxplot_qualities()
s.boxplot_qualities(max_sample=50)
try:
s.plot_gc_content(bins=[1,2,10])
assert False
except:
assert True
def test_bam(tmpdir):
s = BAM(datatest)
assert len(s) == 1000
assert s.is_sorted is True
assert len(list(s.iter_unmapped_reads())) == 2
s.reset()
assert len(list(s.iter_mapped_reads())) == 998
s.reset()
# call this here before other computations on purpose
with TempFile(suffix=".json") as fh:
s.bam_analysis_to_json(fh.name)
assert s.get_read_names()
s.get_mapped_read_length()
s.get_stats()
s.get_full_stats_as_df()
with TempFile(suffix='.png') as fh:
s.plot_bar_flags(filename=fh.name, logy=True)
s.plot_bar_flags(filename=fh.name)
with TempFile(suffix='.png') as fh:
s.plot_bar_mapq(filename=fh.name)
with TempFile() as fh:
s.to_fastq(fh.name)
from sequana import FastQ
ff = FastQ(fh.name)
len(ff) == len(s)
s.get_gc_content()
s.get_length_count()
s.plot_gc_content()
try:
s.plot_gc_content(bins=[1, 2, 10])
assert False
except:
assert True