This graph is generated with git logs and python's builtin static analysis tool 'pylint'.
Pylint is called with only the default configuration.
For each series-of-commits by an author, the first & last are checked out and static analysis of the code base is preformed. capturing the first & final score (<= 10) of the interval.
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| gvcf is not just "gzipped" vcf it is some "genomic" extension to the format | |
| # test | |
| vcftools --gzvcf ./data/gvcf/IDTX_PCRfree_PI562985_ATTACTCG-ATAGAGGC_Sorghum_I549_L1.bwa_pcr_free.raw.snps.indels.g.vcf.gz \ | |
| --non-ref-ac-any 1 \ | |
| --recode \ | |
| --recode-INFO-all \ | |
| --stdout > test_vcftools_filtered |
| 2019 - almost a decade ago now I helped mentor | |
| a CS student writing a bioinformatics exercise in C++. | |
| To help avoid doing his work I did not use C++. | |
| Instead I experimented in Julia; probably v0.2 or v0.3. | |
| The task was to compare ginormas metagenomics studies quickly. | |
| abnormalBehavior.yaml: text: "'has_part' some ('quality' and ('inheres_in' some %s) and ('qualifier' some 'abnormal'))" | |
| abnormalCellProliferation.yaml: text: "'has_part' some ('process quality' and ('inheres_in_part_of' some (cell_proliferation and ('occurs in' some %s))) and ('qualifier' some 'abnormal'))" | |
| abnormalFunctionality.yaml: text: "'has_part' some ('functionality' and ('inheres_in_part_of' some %s) and ('qualifier' some 'abnormal'))" | |
| abnormalLevelOfChemicalInEntity.yaml: text: "'has_part' some (amount and ('inheres_in' some (%s and ('part_of' some %s))) and ('qualifier' some abnormal))" | |
| abnormalLevelOfChemical.yaml: text: "'has_part' some ('amount' and ('inheres_in' some %s) and ('qualifier' some 'abnormal'))" | |
| abnormalLevelOfMolecularEntityInLocation.yaml: text: "'has_part' some ('amount' and ('inheres_in' some (%s and ('part_of' some %s))) and ('qualifier' some 'abnormal'))" | |
| abnormalLevelOfMolecularEntity.yaml: text: "'has_part' some ('amount' and ('inheres_in' some %s) and ('qualifier' some |
| CELL | |
| pub | |
| species | |
| disease | |
| sex | |
| age | |
| category/type | |
| anatomy | |
| marker/allele |
| head -1 rare-diseases/annotated/v2smallFiles/DECIPHER-18.tab | tr '\t' '\n' | grep -n . | |
| 1:#diseaseID <- inconsistant capatilization | |
| 2:diseaseName | |
| 3:phenotypeId | |
| 4:phenotypeName | |
| 5:onsetId | |
| 6:onsetName | |
| 7:frequency | |
| 8:sex | |
| 9:negation |
| big files are already a single file | |
| give a short pathname for ease | |
| and bring it to the root directory | |
| so I don't make a mess in the data directories | |
| ln -s rare-diseases/annotated/v2bigfiles/phenotype.hpoa v2big.tab | |
| Giving the file a non standard suffix which does not denote the format | |
| is not doing anyone a favor, phenotype is redundant in hpo |
| head -1 rare-diseases/annotated/v2smallFiles/DECIPHER-18.tab | tr '\t' '\n' | grep -n . | |
| 1:#diseaseID | |
| 2:diseaseName | |
| 3:phenotypeId | |
| 4:phenotypeName | |
| 5:onsetId | |
| 6:onsetName | |
| 7:frequency | |
| 8:sex | |
| 9:negation |
| head -1 DECIPHER-18.tab | tr '\t' '\n' | grep -n . | |
| 1:#DiseaseID | |
| 2:DiseaseName | |
| 3:HpoId | |
| 4:HpoName | |
| 5:ageOfOnsetId | |
| 6:ageOfOnsetName | |
| 7:evidenceCode | |
| 8:frequencyModifier | |
| 9:sex |
