Simple SAM parsing

Requiring no external dependencies (except a samtools installation for BAM reading)

Installation

pip install simplesam

Usage

For complete module documentation visit ReadTheDocs.

Quickstart

>>> from simplesam import Reader, Writer

Read from SAM/BAM files

# can also read BAM
>>> in_file = open('data/NA18510.sam', 'r')
>>> in_sam = Reader(in_file)

Access alignments using an iterator interface

>>> x = next(in_sam)
>>> type(x)
<class 'simplesam.Sam'>
>>> x
Sam(1:2:SRR011051.1022326)
>>> x.qname
'SRR011051.1022326'
>>> x.rname
'1'
>>> x.pos
2
>>> x.seq
'AACCCTAACCCCTAACCCTAACCCTAACCCTACCCCTAACCCTACCCCTCC'
>>> x.qual
'?<:;;=;>;<<<>96;<;;99;<=3;4<<:(;,<;;/;57<;%6,=:,((3'
>>> x.cigar
'8M1I42M'
>>> x.cigars
((8, 'M'), (1, 'I'), (42, 'M'))
>>> x.gapped('seq')
'AACCCTAACCCTAACCCTAACCCTAACCCTACCCCTAACCCTACCCCTCC'
>>> len(x)
50
>>> x.flag
35
>>> x.mapped
True
>>> x.paired
True
>>> x.duplicate
False
>>> x.secondary
False
>>> x.coords
[2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]
>>> x.tags
{'H1': 0, 'UQ': 33, 'RG': 'SRR011051', 'H0': 0, 'MF': 130, 'Aq': 25, 'NM': 2}
>>> str(x)
'SRR011051.1022326\t35\t1\t2\t255\t8M1I42M\t*\t0\t0\tAACCCTAACCCCTAACCCTAACCCTAACCCTACCCCTAACCCTACCCCTCC\t?<:;;=;>;<<<>96;<;;99;<=3;4<<:(;,<;;/;57<;%6,=:,((3\tAq:i:25\tH0:i:0\tH1:i:0\tMF:i:130\tNM:i:2\tRG:Z:SRR011051\tUQ:i:33\n'

Read the SAM sequence header structure

>>> from pprint import pprint
>>> pprint(in_sam.header)
{'@HD': OrderedDict([('VN:1.0', ['GO:none', 'SO:coordinate'])]),
 '@SQ': {'SN:1': ['LN:247249719'],
         'SN:2': ['LN:242951149'],
         'SN:3': ['LN:199501827'],
         'SN:4': ['LN:191273063'],
         'SN:5': ['LN:180857866'],
         'SN:6': ['LN:170899992'],
         'SN:7': ['LN:158821424'],
         'SN:8': ['LN:146274826'],
         ...
 '@RG': {'ID:SRR011049': ['PL:ILLUMINA',
                           'PU:BI.PE.080626_SL-XAN_0002_FC304CDAAXX.080630_SL-XAN_0007_FC304CDAAXX.5',
                           'LB:Solexa-5112',
                           'PI:330',
                           'SM:NA18510',
                           'CN:BI'],
          'ID:SRR011050': ['PL:ILLUMINA',
                           'PU:BI.PE.080626_SL-XAN_0002_FC304CDAAXX.080630_SL-XAN_0007_FC304CDAAXX.6',
                           'LB:Solexa-5112',
                           'PI:330',
                           'SM:NA18510',
                           'CN:BI'],
         ...}
         }
}

Write SAM files from Sam objects

# Reader and Writer can also use the context handler (with: statement)
>>> out_file = open('test.sam', 'w')
>>> out_sam = Writer(out_file, in_sam.header)
>>> out_sam.write(x)
>>> out_sam.close()

Write SAM files from Sam objects to stdout (allows samtools view compression)

>>> from sys import stdout
>>> stdout_sam = Writer(stdout, in_sam.header)
>>> stdout_sam.write(x)
>>> stdout_sam.close()

$ python my_script_that_uses_simplesam.py | samtools view -hbo test.bam