TomConlin
/ cluster_trait.tab
Created
April 2, 2016 21:10
clinvar submitter trait-free-text clustered by triglyph scoring
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| 1 infantile-onset spinocerebellar ataxia | |
| 1 spinocerebellar ataxia 1 | |
| 1 spinocerebellar ataxia 10 | |
| 1 spinocerebellar ataxia 11 | |
| 1 spinocerebellar ataxia 12 | |
| 1 spinocerebellar ataxia 13 | |
| 1 spinocerebellar ataxia 14 | |
| 1 spinocerebellar ataxia 15 | |
| 1 spinocerebellar ataxia 17 | |
| 1 spinocerebellar ataxia 19 |
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| <http://www.informatics.jax.org/accession/MGI:101759> <http://purl.obolibrary.org/obo/GO_0001786> | |
| <http://www.informatics.jax.org/accession/MGI:101764> <http://purl.obolibrary.org/obo/GO_0004693> | |
| <http://www.informatics.jax.org/accession/MGI:101835> <http://purl.obolibrary.org/obo/GO_0008766> | |
| <http://www.informatics.jax.org/accession/MGI:101835> <http://purl.obolibrary.org/obo/GO_0018169> | |
| <http://www.informatics.jax.org/accession/MGI:101835> <http://purl.obolibrary.org/obo/GO_0043773> | |
| <http://www.informatics.jax.org/accession/MGI:101835> <http://purl.obolibrary.org/obo/GO_0043774> | |
| <http://www.informatics.jax.org/accession/MGI:101835> <http://purl.obolibrary.org/obo/GO_0070735> | |
| <http://www.informatics.jax.org/accession/MGI:101835> <http://purl.obolibrary.org/obo/GO_0070736> | |
| <http://www.informatics.jax.org/accession/MGI:101835> <http://purl.obolibrary.org/obo/GO_0070737> | |
| <http://www.informatics.jax.org/accession/MGI:101835> <http://purl.obolibrary.org/obo/GO_0070738> |
TomConlin
/ collatz_tree64_final.jl
Last active
October 2, 2017 18:41
ncats puzzle 2 backend: Collatz sibblings
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| import JSON | |
| function init(mytype) | |
| # vector of vectors of whatever type is passed in | |
| vv = Vector{Vector{mytype}}(64) | |
| vv[1]=[mytype(1)] # | |
| vv[2]=[mytype(2)] # even double -1,/3 == .333 not int | |
| vv[3]=[mytype(4)] # even double -1,/3 == 1 is previously done | |
| vv[4]=[mytype(8)] # even double -1,/3 == 7/3 not int | |
| vv[5]=[mytype(16)] # even double -1,/3 == 5 (start a new chain @ 5) |
TomConlin
/ balanced_triangular_allocation.jl
Last active
November 3, 2017 23:48
Fair allocation of a triangular matrix for parallel processing
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| ignore = """ | |
| given N side of (lower) triangle matrix | |
| k is number of processors | |
| N^2 / 2 is the apx area of work to be done | |
| N^2 / 2k is each processors fairish share | |
| a:x is an interval in 1:N |
TomConlin
/ v2file_survey
Created
February 24, 2018 04:38
survey of proposed hpo v2 small file format
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| 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 |
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| 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 |
TomConlin
/ v2 big file survey
Created
March 18, 2018 18:30
HPO rare disease annotation bigfile survey
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| 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 |
TomConlin
/ v2small_check_20180318.txt
Created
March 19, 2018 03:26
Third pass on the hpo rare disease annotation v2 small files
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| 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 |
TomConlin
/ cellosaurus.readme
Last active
March 29, 2018 23:48
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| CELL | |
| pub | |
| species | |
| disease | |
| sex | |
| age | |
| category/type | |
| anatomy | |
| marker/allele |
TomConlin
/ upheno_pattern
Created
August 6, 2018 21:50
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| 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 |
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