IMP logo
IMP Reference Guide  develop.cb469e0f11,2024/05/28
The Integrative Modeling Platform
IMP.pmi.topology.Sequences Class Reference

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

Inherits object.

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 1009 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_fnsequence file
name_mapdictionary mapping the FASTA name to final stored name

Definition at line 1020 of file pmi/topology/__init__.py.


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