PhEval 0.1 Release

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

New Contributors

• @matentzn made their first contribution in #13
• @julesjacobsen made their first contribution in #27
• @yaseminbridges made their first contribution in #52

Full Changelog: https://github.com/monarch-initiative/pheval/commits/0.1