Gfapy
latest
Contents:
Introduction
Changelog
The Gfa class
Validation
Positional fields
Placeholders
Positions
Alignments
Tags
References
The Header
Custom records
Comments
Errors
Graph operations
rGFA
Gfapy
Docs
»
Gfapy documentation
Edit on GitHub
Gfapy documentation
¶
Contents:
Introduction
Requirements
Installation
Usage
Documentation
References
Changelog
The Gfa class
Collections of lines
Line identifiers
Identifiers of external sequences
Adding new lines
Editing the lines
Removing lines
Renaming lines
Validation
Manual validation
No validations
Validation when reading
Validation when writing
Continuous validation
Positional fields
Field names
Datatypes
Reading and writing positional fields
Validation
Aliases
Placeholders
Distinguishing placeholders
Compatibility methods
Positions
Last positions in GFA2
Alignments
Creating an alignment
Recognizing undefined alignments
Reading and editing CIGARs
Reading and editing traces
Query, reference and complement
Tags
Custom tags
Predefined tags
Datatypes
Validation
Reading and writing tags
Datatype of custom tags
Arrays of numerical values
Special cases: custom records, headers, comments and virtual lines.
References
Connecting a line to a Gfa object
References for each record type
Backreferences for each record type
Multiline group definitions
Induced set and captured path
Disconnecting a line from a Gfa object
Editing reference fields
Virtual lines
The Header
Multiple definitions of the predefined header tags
Multiple definitions of custom header tags
Reading multi-definitions tags
Setting tags
Modifying field array values
String representation of the header
Count the input header lines
Custom records
Retrieving, adding and deleting custom records
Interface without extensions
Extensions
Predefined datatypes for extensions
Custom datatypes for extensions
Comments
The comments collection
Accessing the comment content
Errors
Graph operations
rGFA
Indices and tables
¶
Index
Module Index
Search Page
Read the Docs
v: latest
Versions
latest
stable
Downloads
pdf
html
epub
On Read the Docs
Project Home
Builds
Free document hosting provided by
Read the Docs
.