Releases · monarch-initiative/pheval

What's Changed

Update test_cli.py by @matentzn in #13
Adding stricter flake8 checking by @matentzn in #15
fixing issue #19 by @souzadevinicius in #21
Runner setup by @souzadevinicius in #25
Merge main into PhEval-Benchmarking by @julesjacobsen in #27
Add pytest to QC checks by @matentzn in #16
Merge pytest changes from main by @julesjacobsen in #29
Ph eval benchmarking by @julesjacobsen in #30
#45 pheval analysis methods (WIP) by @matentzn in #47
#51 define dataclasses required in the tool-specific output for variant and gene prioritisation results (WIP) by @yaseminbridges in #52
Visualising Semantic Similarity Profiles and their diffs by @souzadevinicius in #48
#53 #55 post-processing methods - creation of pheval output by @yaseminbridges in #54
69 update phenopackets corpus by @yaseminbridges in #72
67 add version option to pheval run by @yaseminbridges in #71
56 merge multi input and single input commands by @yaseminbridges in #65
82 calculate end pos for variant from start and ref allele by @yaseminbridges in #85
81 obtain the sample id from a phenopacket by @yaseminbridges in #84
80 obtain negated phenotypic features from a phenopacket by @yaseminbridges in #83
Docs by @matentzn in #59
79 obtain the gene symbol from a gene identifier by @yaseminbridges in #86
66 extend pheval runner with getters for subdirectory structure by @yaseminbridges in #70
91 retrieving genes from interpretations in a phenopacket by @yaseminbridges in #95
adding 281 samples from phen2gene paper by @yaseminbridges in #88
60 add some basic visualisation for analysis by @yaseminbridges in #62
74 provide provisional output for existing runners by @yaseminbridges in #94
removing files object from phenopackets by @yaseminbridges in #102
100 merge post processing methods by @yaseminbridges in #103
Alter spike vcfs methods to create a valid URI for the phenopacket by @yaseminbridges in #99
adding variation descriptor id field to interpretations by @yaseminbridges in #110
fixing bug in generate_pheval_result() by @yaseminbridges in #112
108 add missing fields to resources in the metadata by @yaseminbridges in #109
106 formatting time at last encounter field by @yaseminbridges in #107
122 add info variable to probandcausativevariant dataclass by @yaseminbridges in #123
decode encoded characters from uri path by @yaseminbridges in #119
changing VCF file format to be expected in file attributes by @yaseminbridges in #115
adding structural variant phenopackets by @yaseminbridges in #93
120 strip non numeric characters from the chromosome length in the vcf header by @yaseminbridges in #121
#125 Makefile creation using Jinja template by @souzadevinicius in #126
Removing whitelines from structural blocks by @souzadevinicius in #144
adding structural variant phenopackets by @yaseminbridges in #137
Fix end SV position on structural variant phenopackets by @yaseminbridges in #133
delete print statement in generate_summary_outputs.py by @yaseminbridges in #130
fix naming of rank comparison file names by @yaseminbridges in #128
fix blank info field in spiked vcf records by @yaseminbridges in #143
makefile bugfix by @souzadevinicius in #149
145 randomised semsim etl by @souzadevinicius in #147
fixes Update Makefile to satisfy new semsim scramble/conversion parameters #152 by @souzadevinicius in #153
150 adding tool version and absolute paths in pheval run parameters by @souzadevinicius in #151
replacing shell pwd by directories.workspace in Makefile j2 template by @souzadevinicius in #157
146 altering the PhEval result types defined in the post-processing methods by @yaseminbridges in #148
160 update pheval dependencies by @yaseminbridges in #161
134 create dataclasses for pheval disease results by @yaseminbridges in #135
138 implement post processing methods to create pheval disease result by @yaseminbridges in #139
162 create pheval disease results directory by @yaseminbridges in #163
168 fixing phenotype and software symlinks in makefile by @souzadevinicius in #169
113 makefile testing by @souzadevinicius in #170
165 implement support within analysis methods for disease matching by @yaseminbridges in #166
176 update and rename hgnc complete set in resources by @yaseminbridges in #177
164 split configyaml phenotype only into gene and variant fields by @yaseminbridges in #175
removing pheval_gene_results duplicated mkdir statement by @yaseminbridges in #179
182 generalise parsing methods for reading in pheval result tsv files by @yaseminbridges in #183
184 generalise methods for generating plots by @yaseminbridges in #185
186 generalise rankcomparisongenerator class by @yaseminbridges in #192
191 calculate percentages in the top top3 top5 from total number in corpus by @yaseminbridges in #194
195 move click commands out of analysispy and move into pheval utils by @yaseminbridges in #196