Mercurial > repos > davidvanzessen > phenotype_gene_relations

changeset 5:84c6f3bcfd4a draft

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author davidvanzessen
date Wed, 05 Aug 2015 10:22:10 -0400
parents 035600ab7d3c
children 752528a5934d
files OMT_coding.txt phenotype_gene_relations.r phenotype_gene_relations.sh
diffstat 3 files changed, 533 insertions(+), 4 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/OMT_coding.txt	Wed Aug 05 10:22:10 2015 -0400
@@ -0,0 +1,523 @@
+ID	OMT.name
+1	1. Malformation
+2	2. Deformation
+3	3. Dysplasia
+11	1A. Entire limb malformations
+12	1B. Handplate malformations
+21	Constriction ring sequence
+22	Trigger digits
+31	3A. Hypertrophy
+32	3B. Tumorous conditions
+110	1A. NOS entire limb malformation
+111	1A1. Proximal-distal axis (entire limb)
+112	1A2. Radio-ulnar axis (entire limb)
+113	1A4. Unspecified axis (entire limb)
+114	1A3. Dorso-ventral axis (entire limb)
+120	1B. NOS handplate malformation
+121	1B1. Proximal-distal axis (hand)
+122	1B2. Radio-ulnar axis (hand)
+123	1B3. Dorso-ventral axis (hand)
+124	1B4. Unspecified axis (hand)
+210	Constriction ring sequence
+220	Trigger digits
+311	3A1. Whole limb hypertrophy
+312	3A2. Partial Limb hypertrophy
+321	3B1. Vascular tumors
+324	3B4. Skeletal tumors
+1100	1A. NOS malformation (entire limb)
+1110	1A1. NOS prox-distal axis (entire limb)
+1111	1A1i. Brachymelia
+1112	1A1ii. Symbrachydactyly
+1113	1A1iii. Transverse deficiency
+1114	1A1iv. Intersegmental deficiency
+1115	1A1v. Limb duplication
+1120	1A2. NOS rad-uln axis (entire limb)
+1121	1A2i. Radial longitudinal deficiency
+1122	1A2ii. Ulnar longitudinal deficiency
+1124	1A2iv. Radioulnar synostosis
+1125	1A2v. Congenital radial head dislocation
+1126	1A2vi. Humeroradial synostosis
+1127	1A2vii. Madelung deformity
+1131	1A3i. Dorsal dimelia (palmar nail)
+1132	1A3ii. Ventral dimelia 
+1141	1A4i. Abberant shoulder (incl Sprengel deformity)
+1142	1A4ii. Arthrogryposis
+1200	1B. NOS malformation (hand)
+1211	1B1i. Brachydactyly
+1213	1B1iii. Transverse deficiency (no arm involvement)
+1220	1B2. NOS rad-uln axis malformation (hand)
+1221	1B2i. Radial deficiency of the hand
+1222	1B2ii. Ulnar deficiency of the hand
+1223	1B2iii. Radial polydactyly
+1224	1B2iv. Triphalangeal thumb
+1225	1B2v. Ulnar dimelia
+1226	1B2vi. Ulnar polydactyly
+1232	1B3ii. Ventral dimelia (incl hypoplastic/aplastic nail)
+1241	1B4i. Softi tissue malformations
+1242	1B4ii. Sekeltal deficiencies
+1243	1B4iii. Complex anomalies of unspecified axis (hand)
+2100	Constriction ring sequence
+2200	Trigger digits
+3111	3A1i. Hemihypertrophy
+3121	3A2i. Macrodactyly
+3211	3B1i. Hemangioma
+3212	3B1ii. Vascular malformation
+3241	3B4i. Osteochondromatosis
+3242	3B4ii. Echondromatosis
+3244	3B4iv. Epiphyseal abnormalities
+11000	1A. NOS entire limb malformation
+11100	1A1. NOS proximal-distal axis malformation
+11110	1A1i. Brachymelia
+11121	1A1iia. Poland Syndrome
+11130	1A1iii. Transverse deficiency
+11140	1A1iv. Intersegmental deficiency
+11150	1A1v. Limb duplication
+11200	1A2. NOS rad-uln axis (entire limb)
+11210	1A2i. Radial longitudinal deficiency
+11220	1A2ii. Ulnar longitudinal deficiency
+11240	1A2iv. Radioulnar synostosis
+11250	1A2v. Congenital radial head dislocation
+11260	1A2vi. Humeroradial synostosis
+11270	1A2vii. Madelung deformity
+11310	1A3i. Dorsal dimelia (palmar nail)
+11320	1A3ii. Ventral dimelia 
+11411	1A4ia. Sprengel deformity
+11412	1A4ib. Abnormal shoulder muscles
+11413	1A4ic. NOS shoulder malformation
+11420	1A4ii. Arthrogryposis
+12000	1B. NOS handplate malformation
+12110	1B1i. Brachydactyly
+12130	1B1iii. Transverse deficiency (no arm involvement)
+12200	1B2. NOS rad-uln axis malformation (hand)
+12210	1B2i. Radial deficiency of the hand
+12220	1B2ii. Ulnar deficiency of the hand
+12230	1B2iii. Radial polydactyly
+12240	1B2iv. Triphalangeal thumb
+12250	1B2v. Ulnar dimelia
+12260	1B2vi. Ulnar polydactyly
+12320	1B3ii. Ventral dimelia (incl hypoplastic/aplastic nail)
+12411	1B4ia. Syndactyly
+12412	1B4ib. Camptodactyly
+12413	1B4ic. Thumb in palm deformity
+12414	1B4id. Distal arthrogryposis
+12421	1B4iia. Clinodactyly
+12423	1B4iib. Synostosis/symphalangism
+12431	1B4iiia. Complex syndactyly
+12432	1B4iiib. Synpolydactyly
+12433	1B4iiic. Cleft Hand
+12434	1B4iiid. Apert Hand
+21000	Constriction ring sequence
+22000	Trigger digits
+31110	3A1i. Hemihypertrophy
+31210	3A2i. Macrodactyly
+32110	3B1i. Hemangioma
+32120	3B1ii. Vascular malformation
+32410	3B4i. Osteochondromatosis
+32420	3B4ii. Echondromatosis
+32440	3B4iv. Epiphyseal abnormalities
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--- a/phenotype_gene_relations.r	Fri Jul 24 07:04:56 2015 -0400
+++ b/phenotype_gene_relations.r	Wed Aug 05 10:22:10 2015 -0400
@@ -15,7 +15,8 @@
 phenotypic.groups.file = args[2]
 hpo.to.omt.file = args[3]
 inheritance.from.group.0.file = args[4]
-final.file = args[5]
+omt.coding.file = args[5]
+final.file = args[6]
 
 #get ALL_SOURCES_ALL_FREQUENCIES.TXT
 all.sources = read.table(all.sources.file, header=T, sep="\t", comment.char="#", quote = "")
@@ -67,8 +68,13 @@
 final = merge(final, subset.hand.filter.0[,c("gene.symbol", "diseaseId", "HPO.term.name")], by=c("gene.symbol", "diseaseId"), all.x=T, all.y=F)
 final$HPO.term.name.y = as.character(final$HPO.term.name.y)
 final$HPO.term.name.y[is.na(final$HPO.term.name.y)] = "No inheritance pattern available"
-final = final[,c("diseaseId", "gene.symbol", "gene.id.entrez.", "HPO.term.name.x", "variable", "GROUP.CODE", "value", "OMT.1", "OMT.2", "OMT.3", "OMT.4", "OMT.5", "HPO.term.name.y")]
-names(final) = c("diseaseId", "gene.symbol", "gene.id.entrez.", "HPO.term.name", "GROUP.CODE", "number", "ratio", "OMT.1", "OMT.2", "OMT.3", "OMT.4", "OMT.5", "inheritance")
+
+omt.coding = read.table(omt.coding.file, header=T, sep="\t", comment.char="#", quote = "", stringsAsFactors=F)
+omt.coding = rbind(omt.coding, c("0", "N/C"))
+final = merge(final, omt.coding, by.x="OMT.5", by.y="ID", all.x=T)
+
+final = final[,c("diseaseId", "gene.symbol", "gene.id.entrez.", "HPO.term.name.x", "variable", "value", "OMT.1", "OMT.2", "OMT.3", "OMT.4", "OMT.5", "HPO.term.name.y", "OMT.name")]
+names(final) = c("diseaseId", "gene.symbol", "gene.id.entrez.", "HPO.term.name", "GROUP.CODE", "ratio", "OMT.1", "OMT.2", "OMT.3", "OMT.4", "OMT.5", "inheritance", "OMT.name")
 write.table(final, file=final.file, quote=F, sep="\t", row.names=F, col.names=T)
 
 
--- a/phenotype_gene_relations.sh	Fri Jul 24 07:04:56 2015 -0400
+++ b/phenotype_gene_relations.sh	Wed Aug 05 10:22:10 2015 -0400
@@ -8,4 +8,4 @@
 inheritence_from_group_0=$4
 output=$5
 
-Rscript --verbose $dir/phenotype_gene_relations.r "$all_sources" "$phenotypic_groups" "$hpo_to_omt" "$inheritence_from_group_0" "$output" 2>&1
+Rscript --verbose $dir/phenotype_gene_relations.r "$all_sources" "$phenotypic_groups" "$hpo_to_omt" "$inheritence_from_group_0" "$dir/OMT_coding.txt" "$output" 2>&1