class Sequence

module sequence

The documentation is here.

This class is used to store sequence data, such as genomic or proteic sequences. It represents a succession of letters, such as

acagcaggcatagacaggatacagatttta.

Positions in a Sequence are numbered from 0 to length-1.

A Sequence can have a name, which is written on the first line in fasta format, after the ">".

Construction

__init__

Optional keyword fic allows construction by reading a file.

Sequence is implemented as a tabular in C++. For construction, the memory for a Sequence must be allocated by:

generate

generates an empty Sequence with a given length;

read_nf

reads a filename in specific or FASTA format; to recognize the formats, a filename in specific format must end with .seq, and a filename in FASTA format must end with .fa or .fst;

read_prop

builds or changes randomly from a Proportion; see Sequence generation.

Optional keywords:

deb=d

changes only after position d (>=0) included;

fin=f

changes only before position f (<len()) included;

long=lg

creates a new lg-length Sequence. In that case, deb and fin are not read;

read_Lprop

builds randomly from Lproportion and returns the resulting Partition; see Sequence generation.

Optional keywords:

deb=d

changes only after position d (>=0) included;

fin=f

changes only before position f (<len()) included;

long=lg

creates a new lg-length Sequence. In that case, deb and fin are not read;

etat_init=e

makes generation beginning with descriptor number e if it is valid. Otherwise, starts with a random descriptor of the Lproportion;

read_Part

builds randomly from a Partition and a Lproportion; each Segment of the Partition must have descriptors numbers, and each number must be the number of a Proportion of the Lproportion. At each position, the Proportion corresponding to the number is used to randomly generate a letter, as for a Sequence generation;

copy

copies deeply from another Sequence.

Handling

__len__

returns the length of the Sequence;

__getitem__ and __getslice__

are implemented, to get respectively characters and sub-sequences.
Beware: operator __getslice__ DOES NOT create a new Sequence object, but only a shallow copy, hence it must be used with care;

__setitem__

is used to change a letter in the Sequence.

__setslice__

is used to change a segment of the Sequence by the letters of a string or a Sequence. BEWARE: if the included part is of the same length as the replaced segment, the Sequence is modified in place, otherwise a new Sequence is built. Hence different behaviours can occur if the replacement is made inside a subsequence. See the example below.

For example:

alpha

returns the list of different letters in the Sequence;

shuffle

randomly shuffles the Sequence by (len*(log(len)+1)/2) random transpositions;

g_name

sets the name;

name

returns the name;

Input-Output

Specific format is:

__str__

outputs in specific format;

fasta

outputs in fasta format. The name of the Sequence is written on first line after ">";

Optional keyword:

lg=d

sets the length of the lines (default: 80). If null, returns the sequence in one line.

seq

outputs the mere sequence of letters as a string.