From b622d1bca3e485af3564fbc0206356c7bd775eab Mon Sep 17 00:00:00 2001
From: naumenko-sa <evolgenomicslab@gmail.com>
Date: Thu, 12 Oct 2017 23:33:54 -0400
Subject: [PATCH] 	new file:   cre.annotate_w_phenome_central_genes.py

---
 cre.annotate_w_phenome_central_genes.py | 44 +++++++++++++++++++++++++
 1 file changed, 44 insertions(+)
 create mode 100755 cre.annotate_w_phenome_central_genes.py

diff --git a/cre.annotate_w_phenome_central_genes.py b/cre.annotate_w_phenome_central_genes.py
new file mode 100755
index 0000000..0aab634
--- /dev/null
+++ b/cre.annotate_w_phenome_central_genes.py
@@ -0,0 +1,44 @@
+#!/usr/bin/python
+
+#annotates cre report with genes list from PhenomeCentral
+
+import csv
+import sys
+
+pc_number_of_occurrences = {}
+pc_features = {}
+pc_hpo_ids = {}
+
+with open(sys.argv[2],'r') as f_genes:
+    reader = csv.DictReader(f_genes, delimiter='\t')
+    for row in reader:
+	gene_id=row['Gene ID']
+	pc_number_of_occurrences[gene_id] = row['Number of occurrences']
+	pc_features[gene_id] = row['Features']
+	pc_hpo_ids[gene_id] = row['HPO IDs']
+
+f_genes.close()
+
+with open(sys.argv[1],'rb') as f_csv:
+    with open(sys.argv[3],'wb') as f_out:
+	writer = csv.writer(f_out,quotechar='"', quoting = csv.QUOTE_ALL, lineterminator='\n')
+        reader = csv.DictReader(f_csv)
+	fieldnames = reader.fieldnames
+	new_fields = ['PC_number_of_occurrences','PC_features','PC_HPO_IDs']
+	for field in new_fields:
+    	    fieldnames.append(field)
+
+	writer.writerow(fieldnames)
+	
+	for row in reader:
+	    ensembl_gene = row['Ensembl_gene_id']
+	    row['PC_number_of_occurrences'] = pc_number_of_occurrences.get(ensembl_gene,'NA')
+	    row['PC_features'] = pc_features.get(ensembl_gene,'NA')
+	    row['PC_HPO_IDs'] = pc_hpo_ids.get(ensembl_gene,'NA')
+	    ll = []
+	    for field in fieldnames:
+		ll.append(row[field])
+	    writer.writerow(ll)
+
+f_csv.close()
+f_out.close()