Fastq module

In [20]:

    

%matplotlib inline
from sequana import *


    

In [21]:

    

f = FastQ(sequana_data('test.fastq', 'testing'))


    

In [22]:

    

f.count_reads()


    

    
Out[22]:





250

In [23]:

    

f.identifier


    

    
Out[23]:





Identifier (Illumina_1.8+)

In [24]:

    

f.next()


    

    
Out[24]:





{'identifier': b'@HISEQ:426:C5T65ACXX:5:2302:1943:2127 1:N:0:GTGAAA',
 'quality': b'BCCFFFFFHHHHHIIJJJJJJIIJJJJJJJJFHIHIJJJIJIIIIGHFFFFFFEEEEEEEDDDDDFDDDDDDDDD>CDDEDEEDDDDDDCCDDDDDDDDCD',
 'sequence': b'CTTACCTTCGCATCAAGAGGTACCAACATGGAGGATGAGGCGGACCAATACTTTTCACATGATGATCCAATTAGTAGTGATCAATCCAGGTTCGGATGGTT'}

In [25]:

    

fq = FastQC(sequana_data('test.fastq', 'testing'))


    

In [26]:

    

fq.boxplot_quality()


    

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