A python wrapper for the gene prediction program geneid.
To use PyWrap_geneid, an installed or built geneid with any version, preferably, geneid_v1.4.4.Jan_13_2011 is required. Using Ubuntu, geneid can be installed as follows.
Visit https://genome.crg.es/software/geneid/ and download a tar.gz file of desired version.
Unzip the file. Type:
tar -zxvf geneid(version).tar.gz
More information can be found on the geneid GitHub page (https://github.com/guigolab/geneid).
The geneid distribution contains the following files and directories:
*bin/ compiled binaries *CVS/ Entries, Repository, Root *docs/ documentation: a short handbook. *include/ geneid.h: The geneid header file. *objects/ object files after compiling the source code. *param/ Parameter files for several species. *samples/ Test sequences. *src/ source code of geneid program. *GNULicense This software is registered under GNU license. *Makefile This file is required to build geneid binary file. *README This file.
Move into the geneid directory.
Type:
make
This will generate the geneid executable file within the bin/ subdirectory.
Type:
geneid -h
to test the binary file has been correctly created.
To run PyWrap_geneid properly it is necessary that the geneid compilation is successful.
Ensure Execution Permission
Type:
chmod +x /path/to/geneid
For PyWrap_geneid Python version 3.6 or higher is required.
PyWrap_geneid can be installed from PyPi as follows.
pip install pywrapgeneid
PyWrap_geneid supports prediction of acceptor sites, exons, genes etc. The general sequence file format is fasta format but gff format can also be used for the same.
To run a prediction geneid can be executed on the input file as usual or the input file can be split
import pywrapgeneid
Download example.py to run the job using the module.