ortholg pair

Author: sinamajidian

utils/orthoxml2pairs.py

@@ -0,0 +1,48 @@
+
+from FastOMA.zoo.hog import transform
+
+#from zoo.tree_utils import collapse, gene_species, transform, HOG_coverages
+
+import io
+import lxml.etree
+import sys
+orthoxml_file = sys.argv[1]
+#"/work/FAC/FBM/DBC/cdessim2/default/smajidi1/gethog3_qfo/benchmark-webservice3/orthoxml/euk_omamer200.dev8_13oct.orthoxml"
+
+
+orthxml_str = []
+with open(orthoxml_file, "r") as f:
+    for i in f:
+        orthxml_str.append(i)
+print(len(orthxml_str))
+dic_gene_integer={}
+for line in orthxml_str:
+    if "gene id" in line:
+        found=False
+        gene_int= line.split("\"")[1]
+        gene_name = line.split("\"")[3]
+        dic_gene_integer[gene_int] = gene_name
+
+
+
+orthoxml_etree=lxml.etree.parse(orthoxml_file)
+
+pw_orthologs_integer = sorted(list(transform.iter_pairwise_relations(orthoxml_etree)))
+# iter_pairwise_relations(obj, rel_type=None    (def:'ortholog' , but possible to use 'paralog')
+print(len(pw_orthologs_integer))
+print(pw_orthologs_integer[:2])
+pw_orthologs_gene =[]
+for pair in pw_orthologs_integer:
+    pw_orthologs_gene.append((dic_gene_integer[pair[0]],dic_gene_integer[pair[1]]))
+
+
+
+print(len(pw_orthologs_gene))
+print(pw_orthologs_gene[:2])
+
+
+output_file = open(orthoxml_file+"_pairs.tsv","w")
+for  pair in pw_orthologs_gene:
+    output_file.write(pair[0]+"\t"+pair[1]+"\n")
+
+output_file.close()