AGP.py - working with AGP files¶
This module contains a parser for reading from agp formatted files.
Code¶
-
class
AGP.
AGP
¶ Bases:
object
Parser for AGP formatted files.
-
readFromFile
(infile)¶ read an agp file.
Example line:
scaffold_1 1 1199 1 W contig_13 1 1199 +
This method converts coordinates to zero-based coordinates using open/closed notation.
In AGP nomenclature (http://www.ncbi.nlm.nih.gov/genome/guide/Assembly/AGP_Specification.html) objects (obj) like scaffolds are assembled from components (com) like contigs.
Component types are:
- W
WGS sequence
- N
gap of specified length.
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mapLocation
(id, start, end)¶ map a genomic location.
- Raises
KeyError – If id is not present.
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