API documentation¶
peasel
Module¶
peasel
- class
peasel.
EaselSequence
¶Wrapper for the Easel ESL_SQ object
__len__
(self)¶x.__len__() <==> len(x)
Length of the sequence
__getitem__
(self, s)¶Slice the sequence
Parameters: s (slice) – Slice to get, e.g. s[1:3]
Returns: EaselSequence
sliced to the specified residues.
create
(name, residues, accession, description)¶Create a sequence
Parameters:
- name (str) – Sequence name
- seq (str) – Sequence residues
- acc (str) – Sequence accession number
- desc (str) – Sequence description
Returns: A new
EaselSequence
name
¶Sequence identifier
seq
¶Sequence
-
peasel.
create_ssi
(file_path, ssi_name=None, sq_format=SQFILE_UNKNOWN)¶ Create a Simple Sequence Index for a file.
Parameters: - file_path – Path to the sequence file
- ssi_path – Path to the sequence SSI file. If not given,
.ssi
is appended tofile_path
. - sq_format – File format.
-
peasel.
open_ssi
(file_path, ssi_path=None, sq_format=SQFILE_UNKNOWN)¶ Open a simple sequence index for a file.
Parameters: - file_path (str) – Path to the sequence file
- ssi_path (str) – Path to the sequence SSI file. If not given,
.ssi
is appended tofile_path
. - sq_format – File format.
-
peasel.
read_fasta
(path)¶ Read sequences in FASTA format from a file.
Parameters: path (str) – Path to file containing sequences in FASTA format. Returns: A generator of EaselSequence
objects.
-
peasel.
read_seq_file
(path, sq_format=SQFILE_UNKNOWN)¶ Read sequences from
path
. This is a generator function.Parameters: path (str) – Path to sequence file Returns: Generator of EaselSequence
objects.
-
peasel.
write_fasta
(sequences, fp)¶ Writes sequences to the open file handle fp
Parameters: - sequences – Iterable of
EaselSequence
objects - fp – Open file-like object
- sequences – Iterable of