py2ls 0.2.4.2__py3-none-any.whl → 0.2.4.4__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (11) hide show
  1. py2ls/.DS_Store +0 -0
  2. py2ls/.git/index +0 -0
  3. py2ls/bio.py +1225 -47
  4. py2ls/data/mygenes_fields_241022.txt +355 -0
  5. py2ls/ips.py +523 -110
  6. py2ls/ml2ls.py +1094 -0
  7. py2ls/netfinder.py +12 -1
  8. py2ls/plot.py +290 -75
  9. {py2ls-0.2.4.2.dist-info → py2ls-0.2.4.4.dist-info}/METADATA +1 -1
  10. {py2ls-0.2.4.2.dist-info → py2ls-0.2.4.4.dist-info}/RECORD +11 -9
  11. {py2ls-0.2.4.2.dist-info → py2ls-0.2.4.4.dist-info}/WHEEL +0 -0
py2ls/data/mygenes_fields_241022.txt ADDED
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+ accession object
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+ accession.genomic text
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+ accession.protein text
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+ accession.rna text
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+ accession.translation object
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+ agr object
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+ agr.orthologs object
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+ agr.orthologs.algorithmsmatch integer
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+ agr.orthologs.geneid keyword
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+ agr.orthologs.isbestrevscore boolean
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+ agr.orthologs.isbestscore boolean
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+ agr.orthologs.outofalgorithms integer
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+ agr.orthologs.symbol keyword
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+ agr.orthologs.taxid integer
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+ alias keyword
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+ AllianceGenome keyword
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+ AnimalQTLdb text
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+ biocarta text
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+ chembl object
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+ chembl.chembl_target keyword
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+ chembl.uniprot_accession keyword
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+ clingen object
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+ clingen.clinical_validity object
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+ clingen.clinical_validity.classification keyword
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+ clingen.clinical_validity.classification_date date
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+ clingen.clinical_validity.disease_label text
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+ clingen.clinical_validity.gcep text
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+ clingen.clinical_validity.moi keyword
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+ clingen.clinical_validity.mondo keyword
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+ clingen.clinical_validity.online_report text
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+ clingen.clinical_validity.sop keyword
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+ ec keyword
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+ ensembl object
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+ ensembl.gene keyword
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+ ensembl.protein keyword
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+ ensembl.transcript keyword
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+ ensembl.translation object
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+ ensembl.type_of_gene keyword
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+ entrezgene keyword
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+ exac object
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+ exac.all object
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+ exac.bp integer
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+ exac.cds_end integer
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+ exac.cds_start integer
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+ exac.n_exons integer
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+ exac.nonpsych object
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+ exac.nontcga object
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+ exac.transcript text
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+ exons object
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+ exons_hg19 object
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+ exons_mm10 object
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+ exons_mm9 object
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+ FLYBASE keyword
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+ generif object
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+ generif.pubmed long
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+ generif.text text
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+ genomic_pos object
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+ genomic_pos.chr keyword
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+ genomic_pos.end long
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+ genomic_pos.start long
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+ genomic_pos.strand byte
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+ genomic_pos_hg19 object
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+ genomic_pos_hg19.chr keyword
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+ genomic_pos_hg19.end long
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+ genomic_pos_hg19.start long
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+ genomic_pos_hg19.strand byte
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+ genomic_pos_mm9 object
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+ genomic_pos_mm9.chr keyword
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+ genomic_pos_mm9.end long
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+ genomic_pos_mm9.start long
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+ genomic_pos_mm9.strand byte
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+ go object
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+ go.BP object
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+ go.BP.category keyword
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+ go.BP.evidence keyword
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+ go.BP.id keyword
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+ go.BP.pubmed long
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+ go.BP.term text
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+ go.CC object
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+ go.CC.category keyword
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+ go.CC.evidence keyword
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+ go.CC.id keyword
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+ go.CC.pubmed long
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+ go.CC.term text
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+ go.MF object
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+ go.MF.category keyword
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+ go.MF.evidence keyword
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+ go.MF.id keyword
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+ go.MF.pubmed long
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+ go.MF.term text
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+ HGNC keyword
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+ homologene object
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+ homologene.genes long
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+ homologene.id long
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+ HPRD keyword
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+ humancyc text
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+ interpro object
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+ interpro.desc text
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+ interpro.id keyword
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+ interpro.short_desc text
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+ ipi keyword
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+ kegg text
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+ locus_tag keyword
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+ map_location text
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+ MGI keyword
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+ MIM keyword
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+ miRBase keyword
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+ mousecyc text
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+ name text
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+ netpath text
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+ other_names text
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+ pantherdb object
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+ pantherdb.Araport keyword
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+ pantherdb.dictyBase keyword
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+ pantherdb.EcoGene keyword
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+ pantherdb.Ensembl keyword
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+ pantherdb.EnsemblGenome keyword
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+ pantherdb.FlyBase keyword
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+ pantherdb.Gene keyword
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+ pantherdb.Gene_Name keyword
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+ pantherdb.Gene_OrderedLocusName keyword
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+ pantherdb.Gene_ORFName keyword
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+ pantherdb.GeneID keyword
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+ pantherdb.HGNC keyword
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+ pantherdb.MGI keyword
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+ pantherdb.ortholog object
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+ pantherdb.ortholog.Araport keyword
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+ pantherdb.ortholog.dictyBase keyword
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+ pantherdb.ortholog.EcoGene keyword
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+ pantherdb.ortholog.Ensembl keyword
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+ pantherdb.ortholog.EnsemblGenome keyword
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+ pantherdb.ortholog.FlyBase keyword
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+ pantherdb.ortholog.Gene keyword
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+ pantherdb.ortholog.Gene_Name keyword
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+ pantherdb.ortholog.Gene_OrderedLocusName keyword
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+ pantherdb.ortholog.Gene_ORFName keyword
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+ pantherdb.ortholog.GeneCards keyword
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+ pantherdb.ortholog.GeneID keyword
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+ pantherdb.ortholog.HGNC keyword
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+ pantherdb.ortholog.MGI keyword
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+ pantherdb.ortholog.ortholog_type keyword
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+ pantherdb.ortholog.panther_family keyword
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+ pantherdb.ortholog.PomBase keyword
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+ pantherdb.ortholog.RGD keyword
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+ pantherdb.ortholog.SGD keyword
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+ pantherdb.ortholog.TAIR keyword
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+ pantherdb.ortholog.taxid integer
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+ pantherdb.ortholog.uniprot_kb keyword
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+ pantherdb.ortholog.WormBase keyword
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+ pantherdb.ortholog.ZFIN keyword
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+ pantherdb.PomBase keyword
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+ pantherdb.RGD keyword
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+ pantherdb.SGD keyword
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+ pantherdb.TAIR keyword
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+ pantherdb.uniprot_kb keyword
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+ pantherdb.WormBase keyword
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+ pantherdb.ZFIN keyword
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+ pathway object
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+ pathway.biocarta object
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+ pathway.biocarta.id text
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+ pathway.biocarta.name text
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+ pathway.humancyc object
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+ pathway.humancyc.id text
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+ pathway.humancyc.name text
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+ pathway.kegg object
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+ pathway.kegg.id text
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+ pathway.kegg.name text
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+ pathway.mousecyc object
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+ pathway.mousecyc.id text
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+ pathway.mousecyc.name text
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+ pathway.netpath object
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+ pathway.netpath.id text
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+ pathway.netpath.name text
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+ pathway.pharmgkb object
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+ pathway.pharmgkb.id text
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+ pathway.pharmgkb.name text
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+ pathway.pid object
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+ pathway.pid.id text
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+ pathway.pid.name text
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+ pathway.reactome object
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+ pathway.reactome.id text
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+ pathway.reactome.name text
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+ pathway.smpdb object
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+ pathway.smpdb.id text
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+ pathway.smpdb.name text
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+ pathway.wikipathways object
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+ pathway.wikipathways.id text
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+ pathway.wikipathways.name text
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+ pathway.yeastcyc object
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+ pathway.yeastcyc.id text
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+ pathway.yeastcyc.name text
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+ pdb keyword
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+ pfam keyword
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+ pharmgkb keyword
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+ pharos object
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+ pharos.target_id integer
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+ pharos.tdl keyword
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+ pid text
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+ pir keyword
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+ prosite keyword
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+ RATMAP keyword
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+ reactome text
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+ reagent object
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+ reagent.CM-LibrX-no-seq object
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+ reagent.CM-LibrX-no-seq.id keyword
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+ reagent.CM-LibrX-no-seq.relationship text
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+ reagent.CondMedia_CM_LibrAB object
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+ reagent.CondMedia_CM_LibrAB.id keyword
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+ reagent.CondMedia_CM_LibrAB.relationship text
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+ reagent.GNF_hs-druggable_lenti-shRNA object
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+ reagent.GNF_hs-druggable_lenti-shRNA.id keyword
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+ reagent.GNF_hs-druggable_lenti-shRNA.relationship text
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+ reagent.GNF_hs-druggable_plasmid-shRNA object
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+ reagent.GNF_hs-druggable_plasmid-shRNA.id keyword
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+ reagent.GNF_hs-druggable_plasmid-shRNA.relationship text
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+ reagent.GNF_hs-druggable_siRNA object
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+ reagent.GNF_hs-druggable_siRNA.id keyword
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+ reagent.GNF_hs-druggable_siRNA.relationship text
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+ reagent.GNF_hs-GPCR_IDT-siRNA object
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+ reagent.GNF_hs-GPCR_IDT-siRNA.id keyword
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+ reagent.GNF_hs-GPCR_IDT-siRNA.relationship text
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+ reagent.GNF_hs-oncomine_IDT-siRNA object
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+ reagent.GNF_hs-oncomine_IDT-siRNA.id keyword
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+ reagent.GNF_hs-oncomine_IDT-siRNA.relationship text
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+ reagent.GNF_hs-ORFeome1_1_reads object
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+ reagent.GNF_hs-ORFeome1_1_reads.id keyword
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+ reagent.GNF_hs-ORFeome1_1_reads.relationship text
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+ reagent.GNF_hs-Origene object
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+ reagent.GNF_hs-Origene.id keyword
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+ reagent.GNF_hs-Origene.relationship text
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+ reagent.GNF_hs-pkinase_IDT-siRNA object
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+ reagent.GNF_hs-pkinase_IDT-siRNA.id keyword
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+ reagent.GNF_hs-pkinase_IDT-siRNA.relationship text
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+ reagent.GNF_hs_LentiORF-HA-MYC object
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+ reagent.GNF_hs_LentiORF-HA-MYC.id keyword
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+ reagent.GNF_hs_LentiORF-HA-MYC.relationship text
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+ reagent.GNF_hs_LentiORF-Jred object
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+ reagent.GNF_hs_LentiORF-Jred.id keyword
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+ reagent.GNF_hs_LentiORF-Jred.relationship text
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+ reagent.GNF_mm+hs-MGC object
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+ reagent.GNF_mm+hs-MGC.id keyword
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+ reagent.GNF_mm+hs-MGC.relationship text
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+ reagent.GNF_mm+hs_RetroCDNA object
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+ reagent.GNF_mm+hs_RetroCDNA.id keyword
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+ reagent.GNF_mm+hs_RetroCDNA.relationship text
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+ reagent.GNF_mm-GIPZ_shRNA object
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+ reagent.GNF_mm-GIPZ_shRNA.id keyword
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+ reagent.GNF_mm-GIPZ_shRNA.relationship text
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+ reagent.GNF_mm-kinase_lenti-shRNA object
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+ reagent.GNF_mm-kinase_lenti-shRNA.id keyword
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+ reagent.GNF_mm-kinase_lenti-shRNA.relationship text
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+ reagent.GNF_mm-kinase_plasmid-shRNA object
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+ reagent.GNF_mm-kinase_plasmid-shRNA.id keyword
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+ reagent.GNF_mm-kinase_plasmid-shRNA.relationship text
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+ reagent.GNF_mm-TLR_lenti_shRNA object
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+ reagent.GNF_mm-TLR_lenti_shRNA.id keyword
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+ reagent.GNF_mm-TLR_lenti_shRNA.relationship text
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+ reagent.GNF_Qia_hs-genome_v1_siRNA object
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+ reagent.GNF_Qia_hs-genome_v1_siRNA.id keyword
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+ reagent.GNF_Qia_hs-genome_v1_siRNA.relationship text
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+ reagent.IDT_27mer_hs_ATPase_siRNAs object
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+ reagent.IDT_27mer_hs_ATPase_siRNAs.id keyword
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+ reagent.IDT_27mer_hs_ATPase_siRNAs.relationship text
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+ reagent.Invitrogen_IVTHSSIPKv2 object
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+ reagent.Invitrogen_IVTHSSIPKv2.id keyword
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+ reagent.Invitrogen_IVTHSSIPKv2.relationship text
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+ reagent.MasterSecretomicsList object
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+ reagent.MasterSecretomicsList.id keyword
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+ reagent.MasterSecretomicsList.relationship text
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+ reagent.NIBRI_hs-Secretome_pDEST object
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+ reagent.NIBRI_hs-Secretome_pDEST.id keyword
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+ reagent.NIBRI_hs-Secretome_pDEST.relationship text
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+ reagent.NOVART_hs-genome_siRNA object
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+ reagent.NOVART_hs-genome_siRNA.id keyword
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+ reagent.NOVART_hs-genome_siRNA.relationship text
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+ reagent.Qiagen_mouse_QMIHSINHIBv1 object
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+ reagent.Qiagen_mouse_QMIHSINHIBv1.id keyword
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+ reagent.Qiagen_mouse_QMIHSINHIBv1.relationship text
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+ reagent.Qiagen_mouse_QMIHSMIMv1 object
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+ reagent.Qiagen_mouse_QMIHSMIMv1.id keyword
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+ reagent.Qiagen_mouse_QMIHSMIMv1.relationship text
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+ refseq object
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+ refseq.genomic text
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+ refseq.protein text
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+ refseq.rna text
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+ refseq.translation object
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+ reporter object
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+ reporter.AraGene-1_0 keyword
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+ reporter.BovGene-1_0 keyword
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+ reporter.CanGene-1_0 keyword
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+ reporter.ChiGene-1_0 keyword
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+ reporter.CynGene-1_0 keyword
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+ reporter.CyRGene-1_0 keyword
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+ reporter.DroGene-1_0 keyword
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+ reporter.EleGene-1_0 keyword
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+ reporter.EquGene-1_0 keyword
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+ reporter.FelGene-1_0 keyword
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+ reporter.GNF1H keyword
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+ reporter.GNF1M keyword
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+ reporter.GuiGene-1_0 keyword
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+ reporter.HG-U133_Plus_2 keyword
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+ reporter.HG-U95Av2 keyword
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+ reporter.HG-U95B keyword
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+ reporter.HTA-2_0 keyword
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+ reporter.HuEx-1_0 keyword
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+ reporter.HuGene-1_1 keyword
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+ reporter.HuGene-2_1 keyword
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+ reporter.MarGene-1_0 keyword
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+ reporter.MG-U74Av2 keyword
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+ reporter.MG-U74Bv2 keyword
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+ reporter.MoEx-1_0 keyword
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+ reporter.MoGene-1_1 keyword
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+ reporter.MoGene-2_1 keyword
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+ reporter.Mouse430_2 keyword
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+ reporter.MTA-1_0 keyword
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+ reporter.PorGene-1_0 keyword
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+ reporter.RabGene-1_0 keyword
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+ reporter.RaEx-1_0 keyword
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+ reporter.RaGene-1_1 keyword
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+ reporter.RaGene-2_1 keyword
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+ reporter.Rat230_2 keyword
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+ reporter.RCnGene-1_0 keyword
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+ reporter.RG-U34A keyword
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+ reporter.RG-U34B keyword
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+ reporter.RheGene-1_0 keyword
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+ reporter.RJpGene-1_0 keyword
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+ reporter.RUSGene-1_0 keyword
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+ reporter.snowball keyword
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+ reporter.SoyGene-1_0 keyword
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+ reporter.ZebGene-1_0 keyword
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+ retired long
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+ RGD keyword
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+ SGD keyword
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+ smpdb text
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+ summary text
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+ symbol keyword
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+ TAIR keyword
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+ taxid integer
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+ type_of_gene keyword
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+ umls object
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+ umls.cui keyword
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+ umls.protein_cui keyword
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+ unigene keyword
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+ unii keyword
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+ uniprot object
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+ uniprot.Swiss-Prot keyword
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+ uniprot.TrEMBL keyword
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+ Vega text
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+ wikipathways text
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+ wikipedia object
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+ wikipedia.url_stub text
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+ WormBase keyword
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+ Xenbase keyword
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+ yeastcyc text
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+ ZFIN