def test_pacbio(): b = PacbioSubreads(sequana_data("test_pacbio_subreads.bam")) assert len(b) == 130 b.df #assert b.nb_pass[1] == 130 with TempFile() as fh: b.filter_length(fh.name, threshold_min=500) print(b) # check length assert b.stats['mean_GC'] > 62.46 assert b.stats['mean_GC'] < 65.47 b.summary() b = PacbioSubreads(sequana_data("test_pacbio_subreads.bam")) # test hist_snr from scratch b._df = None b.hist_snr() # test hist_len from scratch b._df = None b.hist_read_length() b.hist_nb_passes() b.get_mean_nb_passes() # test from scratch b._df = None b.hist_GC() # test from scratch b._df = None b.plot_GC_read_len() # test from scratch b._df = None with TempFile() as fh: b.to_fasta(fh.name, threads=1) with TempFile() as fh: b.to_fastq(fh.name, threads=1) with TempFile() as fh: b.save_summary(fh.name)
""" read length histograms pacbio data ===================================== QC pacbio example """ ######################################## # First, let us get a data set example. # Note the .bam extension from sequana import sequana_data dataset = sequana_data("test_pacbio_subreads.bam") ############################################# # Create a :class:`sequana.pacbio.BAMPacbio` instance from sequana.pacbio import PacbioSubreads qc = PacbioSubreads(dataset) ######################################### # plot the histogram of read length qc.hist_read_length() ################################################# # plot the histogram of the SNRs for each base qc.hist_snr()