Human mitochondrial variants annotation using HmtVar.
Project description
HmtNote
Human mitochondrial variants annotation using HmtVar.
Free software: MIT license
Documentation: https://hmtnote.readthedocs.io.
Features
HmtNote is a bioinformatics tool that can be used to annotate human mitochondrial variants from a VCF, using data available on HmtVar.
Annotations are grouped into basic, cross-reference, variability and predictions, depending on the type of information they provide.
Basic
Basic information about the variant; they include:
Locus: Locus to which the variant belongs
AaChange: Aminoacidic change determined
Pathogenicity: Pathogenicity predicted by HmtVar
Disease Score: Disease score calculated by HmtVar
Cross-reference
Cross-reference information about the variant; they include:
Clinvar: Clinvar ID of the variant
dbSNP: dbSNP ID of the variant
OMIM: OMIM ID of the variant
MitomapAssociatedDiseases: Diseases associated to the variant according to Mitomap
MitomapSomaticMutations: Diseases associated to the variant according to Mitomap Somatic Mutations
Variability
Variability and allele frequency data about the variant; they include:
NtVarH: Nucleotide variability of the position in healthy individuals
NtVarP: Nucleotide variability of the position in patient individuals
AaVarH: Aminoacid variability of the position in healthy individuals
AaVarP: Aminoacid variability of the position in patient individuals
AlleleFreqH: Allele frequency of the variant in healthy individuals overall
AlleleFreqP: Allele frequency of the variant in patient individuals overall
AlleleFreqH_AF: Allele frequency of the variant in healthy individuals from Africa
AlleleFreqP_AF: Allele frequency of the variant in patient individuals from Africa
AlleleFreqH_AM: Allele frequency of the variant in healthy individuals from America
AlleleFreqP_AM: Allele frequency of the variant in patient individuals from America
AlleleFreqH_AS: Allele frequency of the variant in healthy individuals from Asia
AlleleFreqP_AS: Allele frequency of the variant in patient individuals from Asia
AlleleFreqH_EU: Allele frequency of the variant in healthy individuals from Europe
AlleleFreqP_EU: Allele frequency of the variant in patient individuals from Europe
AlleleFreqH_OC: Allele frequency of the variant in healthy individuals from Oceania
AlleleFreqP_OC: Allele frequency of the variant in patient individuals from Oceania
Predictions
Pathogenicity prediction information of the variant from external resources; they include:
MutPred_Prediction: Pathogenicity prediction offered by MutPred
MutPred_Probability: Confidence of the pathogenicity prediction offered by MutPred
Panther_Prediction: Pathogenicity prediction offered by Panther
Panther_Probability: Confidence of the pathogenicity prediction offered by Panther
PhDSNP_Prediction: Pathogenicity prediction offered by PhD SNP
PhDSNP_Probability: Confidence of the pathogenicity prediction offered by PhD SNP
SNPsGO_Prediction: Pathogenicity prediction offered by SNPs & GO
SNPsGO_Probability: Confidence of the pathogenicity prediction offered by SNPs & GO
Polyphen2HumDiv_Prediction: Pathogenicity prediction offered by Polyphen2 HumDiv
Polyphen2HumDiv_Probability: Confidence of the pathogenicity prediction offered by Polyphen2 HumDiv
Polyphen2HumVar_Prediction: Pathogenicity prediction offered by Polyphen2 HumVar
Polyphen2HumVar_Probability: Confidence of the pathogenicity prediction offered by Polyphen2 HumVar
Usage
Command Line Interface
HmtNote can be used as a command line tool, by simply providing the original VCF and the filename where the annotated VCF will be saved:
hmtnote input_vcf.vcf annotated_vcf.vcf
By default, HmtNote will annotate the VCF using all four groups of annotations (basic, cross-reference, variability and predictions). If desired, you can specify which kind of annotation you want, using respectively --basic, --crossref, --variab and --predict (or -b, -c, -v, -p):
hmtnote input_vcf.vcf annotated_basic_vcf.vcf --basic hmtnote input_vcf.vcf annotated_crossreferences_vcf.vcf --crossref hmtnote input_vcf.vcf annotated_variability_vcf.vcf --variability hmtnote input_vcf.vcf annotated_predictions_vcf.vcf --predict
Python Module
HmtNote can also be imported in a Python script and its function annotate_vcf() can be used to annotated a given VCF:
from hmtnote import annotate_vcf annotate_vcf("input_vcf.vcf", "annotated_vcf.vcf")
By default, annotate_vcf() will annotate the VCF using all four groups of annotations (basic, cross-reference, variability and predictions). If desired, you can specify which kind of annotation you want, using respectively the basic=True, crossref=True, variab=True, predict=True arguments:
annotate_vcf("input_vcf.vcf", "annotated_basic_vcf.vcf", basic=True) annotate_vcf("input_vcf.vcf", "annotated_crossreferences_vcf.vcf", crossref=True) annotate_vcf("input_vcf.vcf", "annotated_variability_vcf.vcf", variab=True) annotate_vcf("input_vcf.vcf", "annotated_predictions_vcf.vcf", predict=True)
Installation
PLEASE NOTE: HmtNote only supports Python 3!
The preferred installation method for HmtNote is using pip in a conda environment:
$ conda install requests
$ conda install -c bioconda cyvcf2
$ pip install hmtnote
If you have issues, please refer to the Installation section of the Documentation.
Credits
This package was created with Cookiecutter and the cc-pypackage project template.
History
0.1.0 (2019-03-03)
First release on PyPI.
0.1.1 (2019-03-04)
Clean installation requirements for conda;
Update documentation.
0.1.2 (2019-03-15)
Classes and methods are protected where needed;
Code style is clean.
0.1.3 (2019-03-17)
Fix issue with –predict annotation, which didn’t retrieve the correct field from HmtVar.
0.1.4 (2019-03-19)
Fix issue that prevented importing annotate_vcf() into Python scripts.
X.X.X (WIP)
Add options to download the required databases locally;
Use local databases to annotate variants (instead of calling HmtVar’s API);
Fallback to using local databases when web connection is not available?
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