Create HOGcomposition.py

Author: sinamajidian

utils/HOGcomposition.py

@@ -0,0 +1,83 @@
+
+import os
+import sys
+
+in_folder=sys.argv[1] 
+fastoma_out_folder=sys.argv[2] 
+
+```
+To run
+python HOGcomposition.py in_folder output
+in_folder : where proteome folder is
+output: where RootHOGs.tsv is
+
+output: 
+species composition table (HOGs in rows, species in columns and each cell to be the protein names of that HOG for each species)
+
+```
+
+project_files = os.listdir(in_folder+"/proteome/")
+
+
+fasta_format_keep = ""
+species_names = []  # query/input species name based on the file name
+for file in project_files:
+    species_name, ext = file.rsplit('.', 1)
+    if ext in ("fa", "fasta"):
+        species_names.append(species_name)
+        fasta_format_keep = ext  # last one is stored either fa or fasta
+print("number of species:", len(species_names))
+
+
+
+prot2species = {} 
+for species_name in species_names:
+    prot_address = os.path.join(in_folder+"/proteome/", species_name + "." + fasta_format_keep)
+
+    file_prot = open(prot_address,'r')
+    for line in file_prot:
+        if line.startswith(">"):
+            prot_name=line.strip().split(" ")[0][1:]
+            prot2species[prot_name] = species_name
+print("total number of proteins in the fasta files",len(prot2species))
+
+roothog_dic={}
+roothog_file= open(fastoma_out_folder+"/RootHOGs.tsv",'r')
+for line in roothog_file:
+    if line.startswith("RootHOG"):
+        continue
+    roothog,protein, omamerroothog= line.strip().split("\t")
+    if roothog in roothog_dic:
+        roothog_dic[roothog].append(protein)
+    else:
+        roothog_dic[roothog]=[protein]
+print("number of HOGs", len(roothog_dic))
+
+
+file_out=open("HOGcomposition.tsv",'w')
+file_out.write('RootHOG'+'\t'+'\t'.join(species_names)+'\n')
+for roothog, prots in roothog_dic.items():
+
+    prot_species_dic={}
+    for species_name in species_names:
+        prot_species_dic[species_name]=[]
+    
+    for prot in prots:
+        species_name=prot2species[prot]
+        prot_species_dic[species_name].append(prot)
+
+    prot_species=[]
+    for species_name in species_names:
+        prots_raw= prot_species_dic[species_name]
+        if prots:
+            prot_species.append(str(prots_raw)[1:-1])
+        else:
+            prot_species.append('')
+        
+            
+    #prot_species_str=','.join(prot_species)
+    file_out.write(roothog+'\t'+'\t'.join(prot_species)+'\n')
+    
+file_out.close()
+
+print("output is written as file ", "HOGcomposition.tsv")