Metadata-Version: 2.1
Name: mhcgnomes
Version: 1.2.0
Summary: Python library for parsing MHC nomenclature in the wild
Home-page: https://github.com/til-unc/mhcgnomes
Author: Alex Rubinsteyn
Author-email: alex.rubinsteyn@unc.edu
License: http://www.apache.org/licenses/LICENSE-2.0.html
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        ![](https://raw.githubusercontent.com/til-unc/mhcgnomes/main/gnome-red-text.png) 
        
        # mhcgnomes: Parsing MHC nomenclature in the wild
        
        MHCgnomes is a parsing library for multi-species MHC nomenclature which
        aims to correctly parse every name in [IEDB](http://www.iedb.org/), [IMGT/HLA](https://www.ebi.ac.uk/ipd/imgt/hla/), [IPD/MHC](https://www.ebi.ac.uk/ipd/mhc/), and the allele lists for both [NetMHCpan](https://services.healthtech.dtu.dk/service.php?NetMHCpan-4.1) and [NetMHCIIpan](https://services.healthtech.dtu.dk/service.php?NetMHCIIpan-4.0) predictors. This allows for standardization between immune databases and tools, which often use different naming conventions.
        
        ## Usage example
        
        ```python
        
        In [1]: mhcgnomes.parse("HLA-A0201")
        Out[1]: Allele(
            gene=Gene(
                species=Species(name="Homo sapiens', prefix="HLA"), 
                name="A"), 
            allele_fields=("02", "01"), 
            annotations=(), 
            mutations=())
        
        In [2]: mhcgnomes.parse("HLA-A0201").to_string()
        Out[2]: 'HLA-A*02:01'
        
        In [3]: mhcgnomes.parse("HLA-A0201").compact_string()
        Out[3]: 'A0201'
        
        ```
        
        ## The problem: MHC nomenclature is nuts
        
        Despite the valiant efforts of groups such as the [Comparative MHC Nomenclature Committee](https://www.ebi.ac.uk/ipd/mhc/committee/), the names of MHC alleles you might encounter in different datasets (or accepted by immunoinformatics tools) are frustratingly ill specified. It's not uncommon to see dozens of different forms for the same allele.
        
        For example, these all refer to the same MHC protein sequence:
        
        * "HLA-A\*02:01"
        * "HLA-A02:01"
        * "HLA-A:02:01"
        * "HLA-A0201"
        
        
        Additionally, for human alleles, the species prefix is often omitted:
        
        * "A\*02:01"
        * "A\*0201"
        * "A02:01"
        * "A:02:01"
        * "A0201"
        
        Originally alleles for many genes were numbered with two digits:
        
        * "HLA-MICB*01"
        
        But as the number of identified alleles increased, the number of
        fields specifying a distinct protein increase to two. This became 
        conventionally called a "four digit" format, since each field has two
        digits. Yet, as the number of identified alleles continued to increase, then 
        the number of digits per field has often increased from two to three: 
        
        * "MICB\*002:01"
        * "HLA-A00201"
        * "A:002:01"
        * "A\*00201"
        
        These are not always currently treated as equivalent to allele strings with two digits in their first field, but that feature is in the works.
        
        We might also encounter "6 digit" and "8 digit" MHC alleles, which specify 
        synonymous differences in the coding sequence and UTR/intronic regions respectively.
        
        * "A\*02:01:01"
        * "A\*02:01:01:01"
        
        ### Annotations
        
        Sometimes, alleles are bundled with modifier suffixes which specify 
        the functionality or abundance of the MHC. Here's an example with an allele
        which is secreted instead of membrane-bound:
        
        * "HLA-A\*02:01:01S"
        
        These are collected in the `annotations` field of an 
        [`Allele`](https://github.com/til-unc/mhcgnomes/blob/main/mhcgnomes/allele.py)
        result.
        
        ### Mutations
        
        MHC proteins are sometimes described in terms of mutations to a known allele. 
        
        * "HLA-B\*08:01 N80I mutant"
        
        These mutations are collected in the `mutations` field of an 
        [`Allele`](https://github.com/til-unc/mhcgnomes/blob/main/mhcgnomes/allele.py) result.
        
        ### Beyond humans
        
        To make things worse, several model organisms (like mice and rats) use archaic
        naming systems, where there is no notion of allele groups or four/six/eight
        digit alleles but every allele is simply given a name, such as:
        
        * "H2-Kk"
        * "RT1-9.5f"
        
        
        In the above example "H2"/"RT1" correspond to species, "K"/"9.5" are
        the gene names and "k"/"f" are the allele names.
        
        To make these even worse, the name of a species is subject to variation (e.g. "H2" vs. "RT-1") as well as drift over time (e.g. ChLA -> MhcPatr -> Patr).  
        
        ### Serotypes, haplotypes, and other named entitites
        
        Besides alleles are also other named MHC related entities you'll encounter in immunological data. Closely related to alleles are serotypes, which effectively denote a grouping of alleles that are all recognized by the same antibody:
        
        * "HLA-A2"
        * "A2"
        
        In many datasets the exact allele is not known but an experiment might note the genetic background of a model animal, resulting in loose haplotype restrictions such as: 
        
        * "H2-k class I"
        
        Yes, good luck disambiguating "H2-k" the haplotype from "H2-K" the gene, especially since capitalization is not stable enough to be relied on for parsing. 
        
        In some cases immunological data comes only with a denoted species (e.g. "mouse"), a gene (e.g. "HLA-A"), or an MHC class ("human class I"). MHCgnomes has a structured representation for all of these cases and more. 
        
        ## Parsing strategy
        
        It is a fool's errand to curate *all* possible MHC allele names since that list grows daily as the MHC loci of more people (and non-human animals) are sequenced. Instead, MHCgnomes contains an ontology of curated species and genes and then attempts to parse any given string into a multiple candidates of the following types:
        
        * [`Species`](https://github.com/til-unc/mhcgnomes/blob/main/mhcgnomes/species.py)
        * [`Gene`](https://github.com/til-unc/mhcgnomes/blob/main/mhcgnomes/gene.py)
        * [`Allele`](https://github.com/til-unc/mhcgnomes/blob/main/mhcgnomes/allele.py)
        * [`AlleleWithoutGene`](https://github.com/til-unc/mhcgnomes/blob/main/mhcgnomes/allele_without_gene.py)
        * [`Class2Pair`](https://github.com/til-unc/mhcgnomes/blob/main/mhcgnomes/class2_pair.py)
        * [`Class2Locus`](https://github.com/til-unc/mhcgnomes/blob/main/mhcgnomes/class2_locus.py)
        * [`MhcClass`](https://github.com/til-unc/mhcgnomes/blob/main/mhcgnomes/mhc_class.py)
        * [`Haplotype`](https://github.com/til-unc/mhcgnomes/blob/main/mhcgnomes/haplotype.py)
        * [`Serotype`](https://github.com/til-unc/mhcgnomes/blob/main/mhcgnomes/serotype.py)
        
        
        The set of candidate interpretations for each string are then 
        ranked according to heuristic rules. For example, a string will be 
        preferentially interpreted as an [`Allele`](https://github.com/til-unc/mhcgnomes/blob/main/mhcgnomes/allele.py) rather 
        than a [`Serotype`](https://github.com/til-unc/mhcgnomes/blob/main/mhcgnomes/serotype.py)
        or [`Haplotype`](https://github.com/til-unc/mhcgnomes/blob/main/mhcgnomes/haplotype.py). 
        
        ## References
        
        * [IPD-MHC: nomenclature requirements for the non-human major histocompatibility complex in the next-generation sequencing era](https://link.springer.com/article/10.1007%2Fs00251-018-1072-4)
        * [Comparative MHC nomenclature: report from the ISAG/IUIS-VIC committee 2018]()
        * [ISAG/IUIS-VIC Comparative MHC Nomenclature
        Committee report, 2005](https://link.springer.com/content/pdf/10.1007%2Fs00251-005-0071-4.pdf)
        * [Marsupial MHC Class II β Genes Are Not Orthologous to the Eutherian β Gene Families]()
        * [Nomenclature for factors of the SLA system, update 2008](https://www.ncbi.nlm.nih.gov/pubmed/19317739)
        
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Operating System :: OS Independent
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Programming Language :: Python
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Description-Content-Type: text/markdown
