Scripts update

Author: mrbarbitoff

analysis_scripts/expression_viz.R

@@ -0,0 +1,53 @@
+setwd("/mnt/2EA01BDBA01BA7FB/Working issues/BI_Science/Systems Genetics/Pleiotropy/Paper/Revision/Figures/expression")
+
+library(ggplot2)
+library(reshape2)
+
+
+# Incrementing degree
+#############gtex########################################
+#########################################################
+#########################################################
+
+all_exp = read.table('../../new_eqtl_tpm/gtex.tsv', sep='\t', header = T)
+
+strat1 = read.table('../../final_loci/1_noHLA_index_genes.GTEx.medians.tsv', sep='\t', header=F)
+strat2 = read.table('../../final_loci/2_noHLA_index_genes.GTEx.medians.tsv', sep='\t', header=F)
+strat3 = read.table('../../final_loci/3_noHLA_index_genes.GTEx.medians.tsv', sep='\t', header=F)
+strat4 = read.table('../../final_loci/4_noHLA_index_genes.GTEx.medians.tsv', sep='\t', header=F)
+strat5 = read.table('../../final_loci/5_noHLA_index_genes.GTEx.medians.tsv', sep='\t', header=F)
+strat6 = read.table('../../final_loci/6_noHLA_index_genes.GTEx.medians.tsv', sep='\t', header=F)
+strat7 = read.table('../../final_loci/7_noHLA_index_genes.GTEx.medians.tsv', sep='\t', header=F)
+strat8 = read.table('../../final_loci/8_noHLA_index_genes.GTEx.medians.tsv', sep='\t', header=F)
+strat9 = read.table('../../final_loci/9_noHLA_index_genes.GTEx.medians.tsv', sep='\t', header=F)
+strat10 = read.table('../../final_loci/10_noHLA_index_genes.GTEx.medians.tsv', sep='\t', header=F)
+
+
+summaries_med = data.frame(tpm = c(apply(all_exp[, 3:56], 1, median),
+                                   apply(strat1, 1, median),
+                                   apply(strat2, 1, median),
+                                   apply(strat3, 1, median),
+                                   apply(strat4, 1, median),
+                                   apply(strat5, 1, median),
+                                   apply(strat6, 1, median),
+                                   apply(strat7, 1, median),
+                                   apply(strat8, 1, median),
+                                   apply(strat9, 1, median),
+                                   apply(strat10, 1, median)),
+                           pleio = c(rep(0, nrow(all_exp)),
+                                     rep(1, nrow(strat1)),
+                                     rep(2, nrow(strat2)),
+                                     rep(3, nrow(strat3)),
+                                     rep(4, nrow(strat4)),
+                                     rep(5, nrow(strat5)),
+                                     rep(6, nrow(strat6)),
+                                     rep(7, nrow(strat7)),
+                                     rep(8, nrow(strat8)),
+                                     rep(9, nrow(strat9)),
+                                     rep(10, nrow(strat10))))
+
+ggplot(summaries_med, aes(x=as.factor(pleio), y=log2(tpm+1), 
+                          fill=as.factor(pleio))) + 
+  geom_violin(scale='width') +
+  geom_boxplot(width=0.4, fill='white', outlier.shape=NA) +
+  scale_y_continuous(limits=c(0, 10)) + theme_bw() + guides(fill=F)

analysis_scripts/select_index_vars_genes.py

@@ -0,0 +1,26 @@
+#!/usr/bin/env python3
+
+import sys
+import re
+
+clfile, vcf = sys.argv[1:]
+
+index_list = []
+with open(clfile, 'r') as cf:
+    next(cf)
+    for line in cf:
+        try:
+            index_list.append(line.split()[2])
+        except:
+            pass
+
+index_coords = []
+with open(vcf, 'r') as vf:
+    for line in vf:
+        if line.startswith('#'):
+            continue
+        content = line.strip().split('\t')
+        if content[0] == '6' and int(content[1]) > 25000528 and int(content[1]) < 33775446:
+            continue
+        if content[2] in index_list:
+            print(content[0] + '\t' + str(int(content[1]) - 5000) + '\t' + str(int(content[1]) + 5000))