In [1]:

    

import pysam


    

In [2]:

    

samfile = pysam.AlignmentFile("bam_0.bam")


    

In [11]:

    

for aligned_segment in samfile.fetch('chr22', 46929962, 46929966):
    print(aligned_segment)


    

    




HISEQ:142:C5822ANXX:3:2116:16538:101199	83	22	46929962	60	100M	22	46929716	100	CATGATCTGGGCATTAGGGCCTTCATCAGGGTCGTTAGCACGAATCTTTGCCACCACCGACCCCACTGGGTTGTTCTCCTCAACAAACAGCTCCAGTTCG	array('B', [33, 26, 28, 30, 26, 30, 34, 29, 32, 31, 33, 34, 27, 30, 27, 30, 32, 32, 33, 33, 34, 30, 29, 33, 27, 29, 33, 30, 32, 32, 32, 29, 27, 32, 30, 27, 30, 33, 33, 27, 27, 32, 28, 28, 29, 34, 30, 30, 29, 33, 33, 33, 27, 33, 33, 27, 33, 27, 32, 27, 33, 33, 33, 33, 27, 34, 29, 32, 32, 32, 30, 29, 32, 30, 29, 34, 29, 33, 34, 29, 33, 28, 27, 33, 28, 28, 27, 33, 30, 33, 34, 29, 33, 33, 30, 31, 29, 27, 26, 29])	[('BD', 'MLLMPNQNJNNNKJLLHLLMJJLMLLMKHLLMLJIKLMIKLJILKJBJMLLIKLIKKLMKHHLIMNLHLJJIIJJJJLJKIIHIBJIMLNLLNONNJMII'), ('PG', 'MarkDuplicates'), ('RG', 'FAKE_Normal_Exome'), ('BI', 'OPOOSRSRNQRQOMPQKOPNMMPOOPPPKONNNLKNQOLOMLKNMLELOONLONLOMMOOJJNLNNNINLLLLKLLMLLNLKKLDKKNPPMNNPONMOMM'), ('NM', 0), ('BQ', '@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@'), ('MQ', 60), ('OQ', 'FGGGGFGGGDGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGBCBBB'), ('AS', 100), ('XS', 0)]
HISEQ:142:C5822ANXX:3:1106:18985:32932	147	22	46929964	60	100M	22	46929901	100	TGATCTGGGCATTAGGGCCTTCATCAGGGTCGTTAGCACGAATCTTTGCCACCACCGACCCCACTGGGTTGTTCTCCTCAACAAACAGCTCCAGTTCGTC	array('B', [28, 30, 25, 27, 33, 29, 32, 32, 33, 33, 27, 30, 27, 30, 32, 32, 33, 33, 34, 30, 29, 33, 27, 29, 33, 30, 32, 32, 32, 29, 27, 32, 29, 27, 30, 33, 33, 27, 27, 32, 28, 27, 29, 34, 30, 30, 29, 33, 33, 33, 27, 33, 33, 27, 33, 27, 32, 27, 33, 33, 33, 33, 27, 34, 29, 32, 31, 31, 30, 28, 31, 30, 28, 33, 28, 32, 33, 28, 32, 27, 27, 32, 27, 27, 26, 32, 29, 32, 33, 28, 32, 32, 29, 31, 29, 27, 25, 28, 28, 29])	[('BD', 'LMLKROKNONKJLLHLLMJJLMLLMKHLLMLJIKLMIKKIHKJIAILKKHJKHJJKLJGGKHLMKGKIIHIIJJJLJKIIHIBIHLKMJKLMLLLPLLII'), ('PG', 'MarkDuplicates'), ('RG', 'FAKE_Normal_Exome'), ('BI', 'OOONTSORSRPNQQLPQOMMPOOPPPKONOOMLORPMPNMKNMLELOONLONLOMMOOJJNLNONJNLLLLLMMNMLNLKKLDKKNPOMNNOOMMPONMM'), ('NM', 0), ('BQ', '@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@'), ('MQ', 60), ('OQ', 'GGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGCGGGFGGGGGGGGGGGGGGGGEGGGGGGGGGGGGGGGGGFGGGGGGGGFGGGGGGGGGGGGGGCCCCC'), ('AS', 100), ('XS', 0)]

In [12]:

    

dir(aligned_segment)


    

    
Out[12]:





['__class__',
 '__copy__',
 '__deepcopy__',
 '__delattr__',
 '__dir__',
 '__doc__',
 '__eq__',
 '__format__',
 '__ge__',
 '__getattribute__',
 '__gt__',
 '__hash__',
 '__init__',
 '__init_subclass__',
 '__le__',
 '__lt__',
 '__ne__',
 '__new__',
 '__pyx_vtable__',
 '__reduce__',
 '__reduce_ex__',
 '__repr__',
 '__setattr__',
 '__sizeof__',
 '__str__',
 '__subclasshook__',
 'aend',
 'alen',
 'aligned_pairs',
 'bin',
 'blocks',
 'cigar',
 'cigarstring',
 'cigartuples',
 'compare',
 'flag',
 'get_aligned_pairs',
 'get_blocks',
 'get_overlap',
 'get_reference_positions',
 'get_reference_sequence',
 'get_tag',
 'get_tags',
 'has_tag',
 'infer_query_length',
 'inferred_length',
 'is_duplicate',
 'is_paired',
 'is_proper_pair',
 'is_qcfail',
 'is_read1',
 'is_read2',
 'is_reverse',
 'is_secondary',
 'is_supplementary',
 'is_unmapped',
 'isize',
 'mapping_quality',
 'mapq',
 'mate_is_reverse',
 'mate_is_unmapped',
 'mpos',
 'mrnm',
 'next_reference_id',
 'next_reference_name',
 'next_reference_start',
 'opt',
 'overlap',
 'pnext',
 'pos',
 'positions',
 'qend',
 'qlen',
 'qname',
 'qqual',
 'qstart',
 'qual',
 'query',
 'query_alignment_end',
 'query_alignment_length',
 'query_alignment_qualities',
 'query_alignment_sequence',
 'query_alignment_start',
 'query_length',
 'query_name',
 'query_qualities',
 'query_sequence',
 'reference_end',
 'reference_id',
 'reference_length',
 'reference_name',
 'reference_start',
 'rlen',
 'rname',
 'rnext',
 'seq',
 'setTag',
 'set_tag',
 'set_tags',
 'tags',
 'template_length',
 'tid',
 'tlen',
 'tostring']

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