Bump version to v0.4.0 for release

CHANGELOG.md

@@ -7,6 +7,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## Unreleased
 
+## [v0.4.0](https://github.com/ivanwilliammd/iderare-pheno/releases/tag/v0.4.0) - 2024-04-07
+- Added export iderare.yml function
+
 ## [v0.3.5](https://github.com/ivanwilliammd/iderare-pheno/releases/tag/v0.3.5) - 2024-04-07
 - Updated pyproject.toml to recursively get the data inside the package
 

iderare_pheno/utils.py

@@ -3,8 +3,22 @@
 
 import pandas as pd
 import scipy.cluster
+import yaml
 from matplotlib import pyplot as plt
 
+iderare_template = os.path.join(os.path.dirname(__file__), "templates", "template_iderare.yml")
+
+
+# Fill template_iderare.yml with the given phenotype
+def generate_yml(hpo_sets, filename="iderare.yml"):
+    with open(iderare_template, "r") as f:
+        y = yaml.safe_load(f)
+        y["analysis"]["hpo_ids"] = hpo_sets
+
+    with open(filename, "w+") as o:
+        yaml.dump(y, o, default_flow_style=False, sort_keys=False)
+        print("File {} has been created.".format(filename))
+
 
 # Convert data(s) to dataframe
 def list2tsv(

iderare_pheno/version.py

@@ -1,8 +1,8 @@
 _MAJOR = "0"
-_MINOR = "3"
+_MINOR = "4"
 # On main and in a nightly release the patch should be one ahead of the last
 # released build.
-_PATCH = "5"
+_PATCH = "0"
 # This is mainly for nightly builds which have the suffix ".dev$DATE". See
 # https://semver.org/#is-v123-a-semantic-version for the semantics.
 _SUFFIX = ""

output/differential_diagnosis_similarity.tsv

@@ -0,0 +1,38 @@
+rank	id	name	score
+1	227810	Fanconi-Bickel syndrome	0.3851177990436554
+2	611881	Glycogen storage disease XII	0.3723735809326172
+3	603902	Thalassemia-beta, dominant inclusion-body	0.3528570234775543
+4	232500	Glycogen storage disease IV	0.3311641216278076
+5	613027	Glycogen storage disease IXc	0.3222183883190155
+6	232700	Glycogen storage disease VI	0.32113826274871826
+7	615895	Polyglucosan body myopathy 1 with or without immunodeficiency	0.3190052807331085
+8	610539	Gaucher disease, atypical	0.3134368658065796
+9	230800	Gaucher disease, type I	0.2948063015937805
+10	257220	Niemann-pick disease, type C1	0.2887139916419983
+11	231000	Gaucher disease, type III	0.28795626759529114
+12	232200	Glycogen storage disease Ia	0.2799232304096222
+13	230900	Gaucher disease, type II	0.2669340968132019
+14	608013	Gaucher disease, perinatal lethal	0.2648431360721588
+15	261750	Glycogen storage disease type IXb	0.25858327746391296
+16	232220	Glycogen storage disease Ib	0.25592923164367676
+17	607625	Niemann-pick disease, type C2	0.2328203171491623
+18	232800	Glycogen storage disease VII	0.21963520348072052
+19	232240	Glycogen storage disease Ic	0.21480496227741241
+20	306000	Glycogen storage disease, type IXa1	0.2114570587873459
+21	231005	Gaucher disease, type IIIC	0.19200804829597473
+22	240600	Glycogen storage disease 0, liver	0.18373343348503113
+23	232300	Glycogen storage disease II	0.17807894945144653
+24	232400	Glycogen storage disease III	0.17743338644504547
+25	612933	Glycogen storage disease XI	0.16075573861598969
+26	612932	Glycogen storage disease XIII	0.12607280910015106
+27	232600	Glycogen storage disease V	0.11939386278390884
+28	263570	Polyglucosan body neuropathy, adult form	0.11525966227054596
+29	261670	Phosphoglycerate mutase, muscle, deficiency of	0.10096176713705063
+30	611556	Glycogen storage disease 0, muscle	0.10010755807161331
+31	613507	Glycogen storage disease XV	0.08989541977643967
+32	300653	Phosphoglycerate kinase 1 deficiency	0.08972006291151047
+33	616199	Polyglucosan body myopathy 2	0.08133861422538757
+34	614128	Lactate dehydrogenase B deficiency	0.07455503195524216
+35	613985	BETA-THALASSEMIA	0.07443328201770782
+36	300257	Danon disease	0.06328766793012619
+37	300559	Muscle glycogenosis, X-linked	0.06328236311674118

output/iderare.yml

@@ -0,0 +1,51 @@
+analysis:
+  data_dir: null
+  proband: null
+  mother: null
+  father: null
+  proband_gender: null
+  proband_phen: null
+  mother_phen: null
+  father_phen: null
+  hpo_ids:
+  - HP:0000007
+  - HP:0001433
+  - HP:0001903
+  - HP:0001541
+  - HP:0010972
+  - HP:0005561
+  - HP:0001396
+  - HP:0001410
+  - HP:0002910
+  - HP:0001399
+  - HP:0000938
+  - HP:0001642
+  - HP:0200114
+  - HP:0003073
+  - HP:0003233
+  - HP:0001873
+  - HP:0002151
+  - HP:0031964
+  - HP:0031956
+  - HP:0002366
+  - HP:0006568
+  - HP:0004333
+  - HP:0001531
+  library: null
+  method: null
+setup:
+  dv_version: null
+  glnexus_version: null
+  tiddit_version: null
+  dv_model: null
+  max_mem: null
+  ref_dir: null
+  ref_fasta: null
+  snpEff_dir: null
+  snpEff_ver: null
+  exomiser_dir: null
+  exomiser_data_ver: null
+  dbNSFP_file: null
+  dbSNP_file: null
+  ClinVar_file: null
+  chr_rename: null