SeqBox

seq process tools box

install

pip

pip install SeqBox

Attributes

• name: sequence name, If not defined, the default is ‘name’

• seq: base sequence

• stype: ‘DNA’ or ‘RNA’

• dict_base: The principle of complementary base pairing of DNA and RNA.

  • dict_base_DNA = {“A”:”T”, “C”:”G”, “T”:”A”, “G”:”C”, “a”:”t”, “c”:”g”, “t”:”a”, “g”:”c”};
  • dict_base_RNA = {“A”:”U”, “C”:”G”, “U”:”A”, “G”:”C”, “a”:”u”, “c”:”g”, “u”:”a”, “g”:”c”}

more info: the three parameters are all optional and can be defined later when using the function.

functions

• generator: sequence generator
  • random：randomly generated sequence, possible repetitions.
  • norepeat：randomly generate non-repeating sequences.
  • distance：randomly generate sequences with edit distances between sequences greater than a fixed value.
• variation：random transformation of sequences, including deletions, additions and mutations.