Merge branch 'develop' into 'master'

release 0.5.2

See merge request tron/addannot!178

.github/workflows/release.yml

@@ -0,0 +1,24 @@
+name: Upload Python Package
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  deploy:
+    runs-on: ubuntu-20.04
+
+    steps:
+    - uses: actions/checkout@v2
+    - uses: actions/setup-python@v2
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install setuptools wheel twine
+    - name: Build and publish
+      env:
+        TWINE_USERNAME: __token__
+        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+      run: |
+        python setup.py sdist bdist_wheel
+        twine upload dist/*

README.md

@@ -1,7 +1,8 @@
-# NeoFox - NEOantigen Feature tOolboX
+# <img src="docs/figures/neofox_logo_small.png" width="10%">  NeoFox - NEOantigen Feature tOolboX   
 
 [![DOI](https://zenodo.org/badge/294667387.svg)](https://zenodo.org/badge/latestdoi/294667387)
 [![PyPI version](https://badge.fury.io/py/neofox.svg)](https://badge.fury.io/py/neofox)
+[![Documentation Status](https://readthedocs.org/projects/neofox/badge/?version=latest)](https://neofox.readthedocs.io/en/latest/?badge=latest)
 
 
 NeoFox annotates neoantigen candidate sequences with published neoantigen features. 
@@ -63,7 +64,7 @@ NeoFox depends on the following tools:
 NeoFox can be used from the command line as shown below or programmatically (see [https://neofox.readthedocs.io](https://neofox.readthedocs.io/) for more information).
 
 ````commandline
-neofox --candidate-file/--json-file neoantigens_candidates.tab/neoantigens_candidates.json --patient-data/--patient-data-json patient_data.txt/patient_data.json --output-folder /path/to/out --output-prefix out_prefix [--patient-id] [--with-short-wide-table] [--with-tall-skinny-table] [--with-json] [--num_cpus] [--affinity-threshold]
+neofox --candidate-file/--json-file neoantigens_candidates.tab/neoantigens_candidates.json --patient-data/--patient-data-json patient_data.txt/patient_data.json --output-folder /path/to/out --output-prefix out_prefix [--patient-id] [--with-table] [--with-json] [--num_cpus] [--affinity-threshold]
 ````
 - `--candidate-file`: tab-separated values table with neoantigen candidates represented by long mutated peptide sequences as described [here](#41-neoantigen-candidates-in-tabular-format)
 - `--json-file`: JSON file neoantigens in NeoFox model format as  described [here](#42-neoantigen-candidates-in-json-format)
@@ -123,7 +124,6 @@ Besides tabular format, neoantigen candidates can be provided as a list of neoan
 
 ```json
 [{
-    "identifier": "odJ99FdqvJoK1znK+iCpWQ==",
     "patientIdentifier": "Ptx",
     "gene": "BRCA2",
     "mutation": {
@@ -151,4 +151,4 @@ where:
 
 ## 5 Output data
 
-The output data is returned by default in a short wide tab separated values file (`--with-short-wide-table`). Optionally, it can be provided in a tall skinny tab separated values file (`--with-tall-skinny-table`) or in JSON format (`--with-json`).  
+The output data is returned by default in a short wide tab separated values file (`--with-table`). Optionally, it can be provided in JSON format (`--with-json`).  

docs/requirements.txt

@@ -6,4 +6,5 @@ ipython==7.16.1
 ipykernel==5.3.4
 #sphinx_rtd_theme==0.5.0
 #insipid_sphinx_theme==0.2.1
-pydata-sphinx-theme==0.4.1
+pydata-sphinx-theme==0.4.1
+Jinja2==2.11

docs/source/01_overview.md

@@ -1,4 +1,4 @@
-# Overview
+# <img src="docs/figures/neofox_logo_small.png" width="10%"> Overview
 
 Welcome to the documentation of **NeoFox**!
 

docs/source/02_installation.md

@@ -165,7 +165,7 @@ The user can test if all the installations have been successful by testing NeoFo
 [test_patients](https://github.com/TRON-Bioinformatics/neofox/tree/master/docs/test_patients.txt)  
 
 ````commandline
-neofox --candidate-file /path/to/test_data.txt --patient-data /path/to/test_patients.txt --output-folder  /path/to/outputfolder --with-short-wide-table --with-tall-skinny-table --with-json --output-prefix test
+neofox --candidate-file /path/to/test_data.txt --patient-data /path/to/test_patients.txt --output-folder  /path/to/outputfolder --with-short-wide-table --with-json --output-prefix test
 ````
 
 The resulting output files can be compared to the following test output file:  

docs/source/03_01_input_data.md

@@ -37,7 +37,6 @@ Besides tabular format, neoantigen candidates can be provided as a list of neoan
 
 ```json
 [{
-    "identifier": "odJ99FdqvJoK1znK+iCpWQ==",
     "patientIdentifier": "Ptx",
     "gene": "BRCA2",
     "mutation": {

docs/source/03_03_usage.md

@@ -17,8 +17,7 @@ where:
 - `--patient-data`: a table of tab separated values containing metadata on the patient as  described [here](03_01_input_data.md#file-with-patient-information)
 - `--output-folder`: path to the folder to which the output files should be written 
 - `--output-prefix`: prefix for the output files (*optional*)
-- `--with-short-wide-table`: output file in [short-wide](03_02_output_data.md#short-wide-format) format (*optional*)
-- `--with-tall-skinny-table`: output file in [tall-skinny](03_02_output_data.md#tall-skinny-format) format (*optional*)
+- `--with-table`: output file in [short-wide](03_02_output_data.md#tabular-format) format (*optional*)
 - `--with-json`: output file in [JSON](03_02_output_data.md#json-format) format (*optional*)
 - `--num_cpus`: number of CPUs to use (*optional*)
 - `--config`: a config file with the paths to dependencies as shown below  (*optional*)
@@ -180,11 +179,10 @@ validated_patient = ModelValidator.validate_patient(patient=patient)
 Run NeoFox by passing the validated neoantigen object and the validated patient object to get the neoantigen features. The output is a list of type `NeoantigenAnnotations`:  
 
 ```python
-annotations = NeoFox(neoantigens=[validated_neoantigen], patients=[validated_patient], num_cpus=2).get_annotations()
+annotated_neoantigens = NeoFox(neoantigens=[validated_neoantigen], patients=[validated_patient], num_cpus=2).get_annotations()
 ```  
 
-where:  
-       - `anotations`: list of type `NeoantigenAnnotations`, i.e. a list of neoantigen features and there values for given neoantigen candidates (further explanation is provided [here](05_models.md#neoantigenannotations))  
+where:
        - `neoantigens`: a list of validated neoantigen objects  
        - `patients`: a list of validated patient objects  
        - `num_cpus`: number of CPUs to use (*optional*)
@@ -194,13 +192,10 @@ where:
 Depending on the use case, the user can transform the resulting neoantigen feature annotations into the formats described [here](03_02_output_data.md).
 
 ```python
-# short-wide 
-annotations_sw = ModelConverter.annotations2short_wide_table(neoantigen_annotations=annotations, neoantigens=[validated_neoantigen])
-# tall-skinny
-annotations_ts = ModelConverter.annotations2tall_skinny_table(neoantigen_annotations=annotations)
+# table
+annotations_table = ModelConverter.annotations2table(neoantigens=[validated_neoantigen])
 # JSON 
 neoantigen_json = ModelConverter.objects2json(model_objects=[validated_neoantigen])
-annotations_json = ModelConverter.objects2json(model_objects=annotations)
 ```
 
 
@@ -220,15 +215,15 @@ neoantigens_json = ModelConverter.objects2json(model_objects=[validated_neoantig
 
 ```python
 model_file = "/path/to/neoantigen_candidates.tab"
-neoantigens, external_annotations = ModelConverter.parse_neoantigens_dataframe(neoantigens_file=model_file)
+neoantigens = ModelConverter.parse_neoantigens_dataframe(neoantigens_file=model_file)
 ```
 
 
 or in [JSON format](03_01_input_data.md#json-file-format). 
 
 ```python
 json_file = "/path/to/neoantigen_candidates.json"
-neoantigens, external_annotations = ModelConverter.parse_neoantigens_json_file(json_file=json_file)  
+neoantigens = ModelConverter.parse_neoantigens_json_file(json_file=json_file)  
 ```  
 
 The patient information should be provided in [tabular format](03_01_input_data.md#file-with-patient-information)
@@ -241,7 +236,7 @@ patients = ModelConverter.parse_patients_file(patients_data)
 Then, run NeoFox as explained in step 6 by calling:
 
 ```python
-annotations = NeoFox(neoantigens=neoantigens, patients=patients, num_cpus=2).get_annotations()
+neoantigens_annotated = NeoFox(neoantigens=neoantigens, patients=patients, num_cpus=2).get_annotations()
 ```
 
 ## Performance

docs/source/04_developer_guide.md

@@ -47,4 +47,18 @@ python -m unittest discover neofox.tests.unit_tests
 
 ## Logging
 
-Logs are written to the standard error and to the output folder by default. Optionally they can be written to a file by setting the environment variable `NEOFOX_LOGFILE` pointing to the desired file.
+Logs are written to the standard error and to the output folder by default. Optionally they can be written to a file by setting the environment variable `NEOFOX_LOGFILE` pointing to the desired file.
+
+
+## Build the protocol buffers models
+
+The protocol buffers model rely on the betterproto library. Install it as follows:
+```
+pip install "betterproto[compiler]"
+```
+
+The models and the required scripts are in the folder `neofox/models`
+
+Build the models into Python code with `make models`.
+
+Build the HTML documentation with `make html`.

docs/source/05_models.md

@@ -164,13 +164,15 @@ A neoantigen minimal definition
 
 | Field | Type | Label | Description |
 | ----- | ---- | ----- | ----------- |
-| identifier | [string](#string) |  | A unique identifier of a neoantigen |
 | patientIdentifier | [string](#string) |  | Patient identifier |
 | gene | [string](#string) |  | The HGNC gene symbol or gene identifier |
 | mutation | [Mutation](#neoantigen.Mutation) |  | The mutation |
 | rnaExpression | [float](#float) |  | Expression value of the transcript from RNA data. Range [0, +inf]. |
+| imputedGeneExpression | [float](#float) |  | Expression value of the transcript from TCGA data. Range [0, +inf]. |
 | dnaVariantAlleleFrequency | [float](#float) |  | Variant allele frequency from the DNA. Range [0.0, 1.0] |
 | rnaVariantAlleleFrequency | [float](#float) |  | Variant allele frequency from the RNA. Range [0.0, 1.0] |
+| neofoxAnnotations | [NeoantigenAnnotations](#neoantigen.NeoantigenAnnotations) |  | The NeoFox neoantigen annotations |
+| externalAnnotations | [Annotation](#neoantigen.Annotation) | repeated | List of external annotations |
 
 
 
@@ -185,7 +187,6 @@ A set of annotations for a neoantigen
 
 | Field | Type | Label | Description |
 | ----- | ---- | ----- | ----------- |
-| neoantigenIdentifier | [string](#string) |  | A unique identifier of a neoantigen |
 | annotations | [Annotation](#neoantigen.Annotation) | repeated | List of annotations |
 | annotator | [string](#string) |  | The annotator |
 | annotatorVersion | [string](#string) |  | The version of the annotator |
@@ -206,6 +207,7 @@ The metadata required for analysis for a given patient + its patient identifier
 | Field | Type | Label | Description |
 | ----- | ---- | ----- | ----------- |
 | identifier | [string](#string) |  | Patient identifier |
+| isRnaAvailable | [bool](#bool) |  | Is RNA expression available? |
 | tumorType | [string](#string) |  | Tumor entity in TCGA study abbrevation style as described here: https://gdc.cancer.gov/resources-tcga-users/tcga-code-tables/tcga-study-abbreviations |
 | mhc1 | [Mhc1](#neoantigen.Mhc1) | repeated | MHC I classic molecules |
 | mhc2 | [Mhc2](#neoantigen.Mhc2) | repeated | MHC II classic molecules |
@@ -224,9 +226,9 @@ Valid names for MHC I classic genes
 
 | Name | Number | Description |
 | ---- | ------ | ----------- |
-| A | 0 | HLA-A |
-| B | 1 | HLA-B |
-| C | 2 |  HLA-C|
+| A | 0 |  |
+| B | 1 |  |
+| C | 2 |  |
 
 
 
@@ -239,11 +241,11 @@ considered constant.
 
 | Name | Number | Description |
 | ---- | ------ | ----------- |
-| DRB1 | 0 | HLA-DRB1 |
-| DPA1 | 1 |  HLA-DPA1|
-| DPB1 | 2 |  HLA-DPB1|
-| DQA1 | 3 |  HLA-DQA1|
-| DQB1 | 4 |  HLA-DQB1|
+| DRB1 | 0 |  |
+| DPA1 | 1 |  |
+| DPB1 | 2 |  |
+| DQA1 | 3 |  |
+| DQB1 | 4 |  |
 
 
 
@@ -254,9 +256,9 @@ Valid names for MHC II classic molecules
 
 | Name | Number | Description |
 | ---- | ------ | ----------- |
-| DR | 0 |  HLA-DR|
-| DP | 1 |  HLA-DP|
-| DQ | 2 |  HLA-DQ|
+| DR | 0 |  |
+| DP | 1 |  |
+| DQ | 2 |  |
 
 
 

docs/source/test_neoantigen_candidates_annotated.tsv

@@ -1,3 +1,3 @@
-identifier	dnaVariantAlleleFrequency	gene	imputedGeneExpression	mutation.mutatedXmer	mutation.position	mutation.wildTypeXmer	patientIdentifier	rnaExpression	rnaVariantAlleleFrequency	ADN_MHCI	ADN_MHCII	Amplitude_MHCII_rank	Amplitude_MHCI_affinity	Amplitude_MHCI_affinity_9mer	Best_affinity_MHCII_allele	Best_affinity_MHCII_allele_WT	Best_affinity_MHCII_epitope	Best_affinity_MHCII_epitope_WT	Best_affinity_MHCII_score	Best_affinity_MHCII_score_WT	Best_affinity_MHCI_9mer_allele	Best_affinity_MHCI_9mer_allele_WT	Best_affinity_MHCI_9mer_anchor_mutated	Best_affinity_MHCI_9mer_epitope	Best_affinity_MHCI_9mer_epitope_WT	Best_affinity_MHCI_9mer_position_mutation	Best_affinity_MHCI_9mer_score	Best_affinity_MHCI_9mer_score_WT	Best_affinity_MHCI_allele	Best_affinity_MHCI_allele_WT	Best_affinity_MHCI_epitope	Best_affinity_MHCI_epitope_WT	Best_affinity_MHCI_score	Best_affinity_MHCI_score_WT	Best_rank_MHCII_score	Best_rank_MHCII_score_WT	Best_rank_MHCII_score_allele	Best_rank_MHCII_score_allele_WT	Best_rank_MHCII_score_epitope	Best_rank_MHCII_score_epitope_WT	Best_rank_MHCI_9mer_allele	Best_rank_MHCI_9mer_allele_WT	Best_rank_MHCI_9mer_epitope	Best_rank_MHCI_9mer_epitope_WT	Best_rank_MHCI_9mer_score	Best_rank_MHCI_9mer_score_WT	Best_rank_MHCI_score	Best_rank_MHCI_score_WT	Best_rank_MHCI_score_allele	Best_rank_MHCI_score_allele_WT	Best_rank_MHCI_score_epitope	Best_rank_MHCI_score_epitope_WT	CDN_MHCI	CDN_MHCII	DAI_MHCI_affinity_cutoff500nM	Dissimilarity_MHCI_cutoff500nM	Expression_mutated_transcript	Generator_rate	IEDB_Immunogenicity_MHCI_cutoff500nM	Improved_Binder_MHCI	MixMHC2pred_best_allele	MixMHC2pred_best_peptide	MixMHC2pred_best_rank	MixMHCpred_best_allele	MixMHCpred_best_peptide	MixMHCpred_best_rank	MixMHCpred_best_score	Neoag_immunogenicity	Number_of_mismatches_MCHI	PHBR-I	PHBR-II	Pathogensimiliarity_MHCI_affinity_9mer	Priority_score	Recognition_Potential_MHCI_affinity_9mer	Selfsimilarity_MHCI_conserved_binder	Tcell_predictor_score_cutoff500nM	mutation_not_found_in_proteome	transcript_expression	vaxrank_binding_score	vaxrank_total_score
-rT5Q2N5SYsLmyEfvVchbQg==	0.857	BRCA2	0.5365996317	AAAAAAAAAAAAALAAAAAAAAAAAAA	14	AAAAAAAAAAAAAFAAAAAAAAAAAAA	Ptx	0.5365996317	0.294	0	0	1	2.5475	2.5475	HLA-DQA10102-DQB10602	HLA-DQA10102-DQB10602	AAAAAAAAALAAAAA	AAAAAAAAAFAAAAA	29.39	27.2	HLA-C*03:04	HLA-C*03:04	1	AAAAAAAAL	AAAAAAAAF	9	5.2	13.3	HLA-C*03:04	HLA-C*03:04	AAAAAAAAL	AAAAAAAAF	5.2	13.3	0.01	0.01	HLA-DQA10301-DQB10602	HLA-DQA10301-DQB10602	AAAAAAAAAAALAAA	AAAAAAAAAAAFAAA	HLA-C*03:04	HLA-C*03:04	AAAAAAAAL	AAAAAAAAF	0.019	0.0495	0.019	0.0495	HLA-C*03:04	HLA-C*03:04	AAAAAAAAL	AAAAAAAAF	1	1	8.1	0.99994	0.45987	1	0.18288	1	DPA1_01_03__DPB1_06_01	AAAALAAAAAAAAAAA	0.296	B0702	AAAAAAAAL	0.03	0.622	13.16998	1	0.10424	0.05128	0	0.21014	0	NA	0.40831263969265064	1	0.5195068939999999	6.9366	3.1899
-VZ6DH92YXawIebl1Q9qE/g==	0.556	BRCA2	0.5365996317	AAAAAAAAAAAAARAAAAAAAAAAAAA	14	AAAAAAAAAAAAAMAAAAAAAAAAAAA	Ptx	0.5365996317	0.17300000000000001	0	0	2	4.3574	4.3574	HLA-DQA10102-DQB10602	HLA-DQA10102-DQB10602	AAAAAAAARAAAAAA	AAAAAAAAMAAAAAA	29.75	24.29	HLA-B*07:02	HLA-B*07:02	0	AARAAAAAA	AAMAAAAAA	3	96.8	482.9	HLA-B*07:02	HLA-B*07:02	AARAAAAAA	AAMAAAAAA	96.8	482.9	0.01	0.02	HLA-DQA10301-DQB10602	HLA-DQA10301-DQB10602	AAAAAAAAAAAARAA	AAAAAAAAAAAAMAA	HLA-B*07:02	HLA-B*07:02	AARAAAAAA	AAMAAAAAA	0.2895	0.8137	0.2895	0.8137	HLA-B*07:02	HLA-B*07:02	AARAAAAAA	AAMAAAAAA	0	1	386.1	1	0.29835	0	0.18698	1	DPA1_01_03__DPB1_06_01	AAAARAAAAAAAAAA	0.0176	B0702	AARAAAAAA	0.06	0.54766	13.16998	1	1.0223	0.05913	0	0.13667	0	NA	0.4769777371767941	1	0.715756594	3.7801	1.1278
+dnaVariantAlleleFrequency	gene	imputedGeneExpression	mutation.mutatedXmer	mutation.position	mutation.wildTypeXmer	patientIdentifier	rnaExpression	rnaVariantAlleleFrequency	ADN_MHCI	ADN_MHCII	Amplitude_MHCII_rank	Amplitude_MHCI_affinity	Amplitude_MHCI_affinity_9mer	Best_affinity_MHCII_allele	Best_affinity_MHCII_allele_WT	Best_affinity_MHCII_epitope	Best_affinity_MHCII_epitope_WT	Best_affinity_MHCII_score	Best_affinity_MHCII_score_WT	Best_affinity_MHCI_9mer_allele	Best_affinity_MHCI_9mer_allele_WT	Best_affinity_MHCI_9mer_anchor_mutated	Best_affinity_MHCI_9mer_epitope	Best_affinity_MHCI_9mer_epitope_WT	Best_affinity_MHCI_9mer_position_mutation	Best_affinity_MHCI_9mer_score	Best_affinity_MHCI_9mer_score_WT	Best_affinity_MHCI_allele	Best_affinity_MHCI_allele_WT	Best_affinity_MHCI_epitope	Best_affinity_MHCI_epitope_WT	Best_affinity_MHCI_score	Best_affinity_MHCI_score_WT	Best_rank_MHCII_score	Best_rank_MHCII_score_WT	Best_rank_MHCII_score_allele	Best_rank_MHCII_score_allele_WT	Best_rank_MHCII_score_epitope	Best_rank_MHCII_score_epitope_WT	Best_rank_MHCI_9mer_allele	Best_rank_MHCI_9mer_allele_WT	Best_rank_MHCI_9mer_epitope	Best_rank_MHCI_9mer_epitope_WT	Best_rank_MHCI_9mer_score	Best_rank_MHCI_9mer_score_WT	Best_rank_MHCI_score	Best_rank_MHCI_score_WT	Best_rank_MHCI_score_allele	Best_rank_MHCI_score_allele_WT	Best_rank_MHCI_score_epitope	Best_rank_MHCI_score_epitope_WT	CDN_MHCI	CDN_MHCII	DAI_MHCI_affinity_cutoff500nM	Dissimilarity_MHCI_cutoff500nM	Expression_mutated_transcript	Generator_rate	IEDB_Immunogenicity_MHCI_cutoff500nM	Improved_Binder_MHCI	MixMHC2pred_best_allele	MixMHC2pred_best_peptide	MixMHC2pred_best_rank	MixMHCpred_best_allele	MixMHCpred_best_peptide	MixMHCpred_best_rank	MixMHCpred_best_score	Neoag_immunogenicity	Number_of_mismatches_MCHI	PHBR-I	PHBR-II	Pathogensimiliarity_MHCI_affinity_9mer	Priority_score	Recognition_Potential_MHCI_affinity_9mer	Selfsimilarity_MHCI_conserved_binder	Tcell_predictor_score_cutoff500nM	mutation_not_found_in_proteome	transcript_expression	vaxrank_binding_score	vaxrank_total_score
+0.857	BRCA2	0.5365996317	AAAAAAAAAAAAALAAAAAAAAAAAAA	14	AAAAAAAAAAAAAFAAAAAAAAAAAAA	Ptx	0.5365996317	0.294	0	0	1	2.5475	2.5475	HLA-DQA10102-DQB10602	HLA-DQA10102-DQB10602	AAAAAAAAALAAAAA	AAAAAAAAAFAAAAA	29.39	27.2	HLA-C*03:04	HLA-C*03:04	1	AAAAAAAAL	AAAAAAAAF	9	5.2	13.3	HLA-C*03:04	HLA-C*03:04	AAAAAAAAL	AAAAAAAAF	5.2	13.3	0.01	0.01	HLA-DQA10301-DQB10602	HLA-DQA10301-DQB10602	AAAAAAAAAAALAAA	AAAAAAAAAAAFAAA	HLA-C*03:04	HLA-C*03:04	AAAAAAAAL	AAAAAAAAF	0.019	0.0495	0.019	0.0495	HLA-C*03:04	HLA-C*03:04	AAAAAAAAL	AAAAAAAAF	1	1	8.1	0.99994	0.45987	1	0.18288	1	DPA1_01_03__DPB1_06_01	AAAALAAAAAAAAAAA	0.296	B0702	AAAAAAAAL	0.03	0.622	13.16998	1	0.10424	0.05128	0	0.21014	0	NA	0.40831263969265064	1	0.5195068939999999	6.9366	3.1899
+0.556	BRCA2	0.5365996317	AAAAAAAAAAAAARAAAAAAAAAAAAA	14	AAAAAAAAAAAAAMAAAAAAAAAAAAA	Ptx	0.5365996317	0.17300000000000001	0	0	2	4.3574	4.3574	HLA-DQA10102-DQB10602	HLA-DQA10102-DQB10602	AAAAAAAARAAAAAA	AAAAAAAAMAAAAAA	29.75	24.29	HLA-B*07:02	HLA-B*07:02	0	AARAAAAAA	AAMAAAAAA	3	96.8	482.9	HLA-B*07:02	HLA-B*07:02	AARAAAAAA	AAMAAAAAA	96.8	482.9	0.01	0.02	HLA-DQA10301-DQB10602	HLA-DQA10301-DQB10602	AAAAAAAAAAAARAA	AAAAAAAAAAAAMAA	HLA-B*07:02	HLA-B*07:02	AARAAAAAA	AAMAAAAAA	0.2895	0.8137	0.2895	0.8137	HLA-B*07:02	HLA-B*07:02	AARAAAAAA	AAMAAAAAA	0	1	386.1	1	0.29835	0	0.18698	1	DPA1_01_03__DPB1_06_01	AAAARAAAAAAAAAA	0.0176	B0702	AARAAAAAA	0.06	0.54766	13.16998	1	1.0223	0.05913	0	0.13667	0	NA	0.4769777371767941	1	0.715756594	3.7801	1.1278

neofox/__init__.py

@@ -16,7 +16,7 @@
 #
 # You should have received a copy of the GNU General Public License
 # along with this program. If not, see <http://www.gnu.org/licenses/>.#
-VERSION = "0.5.1"
+VERSION = "0.5.2"
 
 
 REFERENCE_FOLDER_ENV = "NEOFOX_REFERENCE_FOLDER"