056e469252385766eda11785f44b081af9c69fa9
lrnassar
  Fri Feb 5 11:04:27 2021 -0800
Adjusting clinGen otto script to account for the 6 new fields added to the files, and adding the .as files to the git repo, no RM

diff --git src/hg/utils/otto/clinGen/processClinGenDosage.py src/hg/utils/otto/clinGen/processClinGenDosage.py
index fe22d0f..69b651c 100755
--- src/hg/utils/otto/clinGen/processClinGenDosage.py
+++ src/hg/utils/otto/clinGen/processClinGenDosage.py
@@ -1,32 +1,32 @@
 #!/usr/bin/env python3
 
 """
 Turn ClinGen gene_curation_list and region_curation_list into
 two bed files, one for haploinsufficient and one for triplosensitive
 """
 
 import os,sys
 import argparse
 
 bed8Fields = ["chrom", "chromStart", "chromEnd", "name", "score", "strand", "thickStart",
     "thickEnd"]
 
 # we only use some of these fields depending on whether we are working with haplo or triplo scores
-commonFields = ["cytoBand", "Genomic Location", "Haploinsufficiency Score", "Haploinsufficiency Description", "Haploinsufficiency PMID1", "Haploinsufficiency PMID2", "Haploinsufficiency PMID3", "Triplosensitivity Score", "Triplosensitivity Description", "Triplosensitivity PMID1", "Triplosensitivity PMID2", "Triplosensitivity PMID3", "Date Last Evaluated", "Loss phenotype OMIM ID", "Triplosensitive phenotype OMIM ID"] #, 
-haploFields = ["Haploinsufficiency Score", "Haploinsufficiency Description", "Haploinsufficiency PMID1", "Haploinsufficiency PMID2", "Haploinsufficiency PMID3"]
-triploFields = ["Triplosensitivity Score", "Triplosensitivity Description", "Triplosensitivity PMID1", "Triplosensitivity PMID2", "Triplosensitivity PMID3"]
+commonFields = ["cytoBand", "Genomic Location", "Haploinsufficiency Score", "Haploinsufficiency Description", "Haploinsufficiency PMID1", "Haploinsufficiency PMID2", "Haploinsufficiency PMID3", "Haploinsufficiency PMID4", "Haploinsufficiency PMID5", "Haploinsufficiency PMID6", "Triplosensitivity Score", "Triplosensitivity Description", "Triplosensitivity PMID1", "Triplosensitivity PMID2", "Triplosensitivity PMID3", "Triplosensitivity PMID4", "Triplosensitivity PMID5", "Triplosensitivity PMID6", "Date Last Evaluated", "Loss phenotype OMIM ID", "Triplosensitive phenotype OMIM ID"] #, 
+haploFields = ["Haploinsufficiency Score", "Haploinsufficiency Description", "Haploinsufficiency PMID1", "Haploinsufficiency PMID2", "Haploinsufficiency PMID3", "Haploinsufficiency PMID4", "Haploinsufficiency PMID5", "Haploinsufficiency PMID6"]
+triploFields = ["Triplosensitivity Score", "Triplosensitivity Description", "Triplosensitivity PMID1", "Triplosensitivity PMID2", "Triplosensitivity PMID3", "Triplosensitivity PMID4", "Triplosensitivity PMID5", "Triplosensitivity PMID6"]
 geneListFields = ["Gene Symbol", "Gene ID"]
 regionListFields = ["ISCA ID", "ISCA Region Name"]
 omimOutFields = ["OMIM ID", "OMIM Description"]
 
 # the gene and region files get merged:
 combinedFields = ["Gene Symbol/ISCA ID", "Gene ID/ISCA Region Name"]
 
 clinGenGeneUrl = "https://www.ncbi.nlm.nih.gov/projects/dbvar/clingen/clingen_gene.cgi?sym="
 clinGenIscaUrl = "https://www.ncbi.nlm.nih.gov/projects/dbvar/clingen/clingen_region.cgi?id="
 
 scoreExplanation = {
     -1: "not yet evaluated",
     0: "no evidence for dosage pathogenicity",
     1: "little evidence for dosage pathogenicity",
     2: "some evidence for dosage pathogenicity",