Create an index file¶

Use peasel.create_ssi to build a sequence index:

>>> import peasel
>>> peasel.create_ssi('my_big_sequence_file.fasta') # creates my_big_sequence_file.fasta.ssi
2 # Number of sequences indexed

Retrieving sequences from an index¶

Sequence-indexes support dict-like behavior:

>>> import peasel
>>> # Open the index
>>> index = peasel.open_ssi('my_big_sequence_file.fasta')
>>> index['sequence1']
<EaselSequence 0x7f38735b80f0 [name="sequence1";description="";length=5]>
>>> index.get('sequence1')
<EaselSequence 0x7f38735b8108 [name="sequence1";description="";length=5]>
>>> print index.get('missing_sequence')
None

Using a temporary index¶

If you’d prefer not to litter the filesystem with .ssi files, use the temp_ssi context manager:

>>> import peasel
>>> with peasel.temp_ssi('my_big_sequence_file.fasta') as index:
...     index['sequence1']
...
<EaselSequence 0x7ff15065a0f0 [name="sequence1";description="";length=5]>

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 to file_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 to file_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