pluaron
2024-05-29

SeqBox

seq process tools box

install

pip

1
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.