biotaphy.common.sequence

Module containing sequence class.

Module Contents

Classes

Sequence

Constructor for Sequence.
class biotaphy.common.sequence.Sequence(name='', seq='')[source]

Constructor for Sequence.

Parameters

  • name (str) – A name for this sequence.

  • seq (str) – A sequence string.

get_fasta(self)[source]

Get a fasta string.

Returns

str - A fasta string for the sequence.

get_fastq(self)[source]

Get a fastq string.

Returns

str - A fastq string for the sequence.

set_cont_values(self, values)[source]

Set the continuous values for the sequence.

Parameters

values (list) – A list of values.

set_qualarr(self, qual)[source]

Set the qualarr attribute.

Parameters

qual (list of int) – A list of code point integers.

Note

  • An offset of 33 is assumed.

set_qualstr(self, qual)[source]

Set the qualstr attribute.

Parameters

qual (str) – A new string to use for qualstr.

Note

  • An offset of 33 is assumed.