pydna.contig

class pydna.contig.Contig(record, *args, graph=None, nodemap=None, **kwargs)[source]

Bases: Dseqrecord

This class holds information about a DNA assembly. This class is instantiated by the Assembly class and is not meant to be used directly.

classmethod from_string(record: str = '', *args, graph=None, nodemap=None, **kwargs)[source]: docstring.

classmethod from_SeqRecord(record, *args, graph=None, nodemap=None, **kwargs)[source]

reverse_complement()[source]

Reverse complement.

Examples

>>> from pydna.dseqrecord import Dseqrecord
>>> a=Dseqrecord("ggaatt")
>>> a
Dseqrecord(-6)
>>> a.seq
Dseq(-6)
ggaatt
ccttaa
>>> a.reverse_complement().seq
Dseq(-6)
aattcc
ttaagg
>>>

See also

pydna.dseq.Dseq.reverse_complement

detailed_figure()[source]

Returns a text representation of the assembled fragments.

Linear:

acgatgctatactgCCCCCtgtgctgtgctcta
                   TGTGCTGTGCTCTA
                   tgtgctgtgctctaTTTTTtattctggctgtatc

Circular:

||||||||||||||
acgatgctatactgCCCCCtgtgctgtgctcta
                   TGTGCTGTGCTCTA
                   tgtgctgtgctctaTTTTTtattctggctgtatc
                                      TATTCTGGCTGTATC
                                      tattctggctgtatcGGGGGtacgatgctatactg
                                                           ACGATGCTATACTG

figure()[source]

Compact ascii representation of the assembled fragments.

Each fragment is represented by:

Size of common 5' substring|Name and size of DNA fragment|
Size of common 5' substring

Linear:

frag20| 6
       \\/
       /\\
        6|frag23| 6
                 \\/
                 /\\
                  6|frag14

Circular:

 -|2577|61
|       \\/
|       /\\
|       61|5681|98
|               \\/
|               /\\
|               98|2389|557
|                       \\/
|                       /\\
|                       557-
|                          |
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