Metadata-Version: 2.1
Name: Mikado
Version: 1.2.2
Summary: A Python3 annotation program to select the best gene model in each locus
Home-page: https://github.com/lucventurini/mikado
Author: Luca Venturini
Author-email: luca.venturini@earlham.ac.uk
License: GPL3
Description: Mikado is a lightweight Python3 pipeline whose purpose is to facilitate the identification
        of expressed loci from RNA-Seq data * and to select the best models in each locus.
        
        The logic of the pipeline is as follows:
        
        1. In a first step, the annotation (provided in GTF/GFF3 format) is parsed to locate *superloci* of overlapping features on the **same strand**.
        2. The superloci are divided into different *subloci*, each of which is defined as follows:
        
            * For multiexonic transcripts, to belong to the same sublocus they must share at least a splicing junction (i.e. an intron)
            * For monoexonic transcripts, they must overlap for at least one base pair
            * All subloci must contain either only multiexonic or only monoexonic transcripts
        3. In each sublocus, the pipeline selects the best transcript according to a user-defined prioritization scheme.
        4. The resulting *monosubloci* are merged together, if applicable, into *monosubloci_holders*
        5. The best non-overlapping transcripts are selected, in order to define the *loci* contained inside the superlocus.
        
            * At this stage, monoexonic and multiexonic transcript are checked for overlaps
            * Moreover, two multiexonic transcripts are considered to belong to the same locus if they share a splice *site* (not junction)
            
        6. Once the loci have been defined, the program backtracks and looks for transcripts which can be assigned unambiguously to a single locus and constitute valid alternative splicing isoforms of the main transcripts. 
        
        The criteria used to select the "*best*" transcript are left to the user's discretion, using specific configuration files.
Keywords: rna-seq annotation genomics transcriptomics
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: GNU Lesser General Public License v3 or later (LGPLv3+)
Classifier: Operating System :: POSIX :: Linux
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Provides-Extra: mysql
Provides-Extra: postgresql
Provides-Extra: bam
