IMP.pmi.topology.Sequences Class Reference

A dictionary-like wrapper for reading and storing sequence data. More...

Detailed Description

A dictionary-like wrapper for reading and storing sequence data.

Keys are FASTA sequence names, and each value a string of one-letter codes.

The FASTA header may contain multiple fields split by pipe (|) characters. If so, the FASTA sequence name is the first field and the second field (if present) is the UniProt accession. For example, ">cop9|Q13098" yields a FASTA sequence name of "cop9" and UniProt accession of "Q13098".

Note

This class is only available in Python.

Definition at line 1011 of file pmi/topology/__init__.py.

Public Member Functions
def	__init__
	Read a FASTA file and extract all the requested sequences. More...

Constructor & Destructor Documentation

def IMP.pmi.topology.Sequences.__init__	(		self,
			fasta_fn,
			name_map = None
	)

Read a FASTA file and extract all the requested sequences.

Parameters

fasta_fn	sequence file
name_map	dictionary mapping the FASTA name to final stored name

Definition at line 1022 of file pmi/topology/__init__.py.

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The documentation for this class was generated from the following file:

• pmi/topology/__init__.py