5-CreateCAFEtable.py

import os
import numpy as np

# List to be used to create the table
main_list = [] 

# Species-ID dictionary
species_id_dic = {"7159": "Aedes", "7165": "Anopheles", "315563": "Belgica", "7176": "Culex", "7200": "Lutzomyia", "39758": "Mayetiola", "29031": "Phlebotomus", "7227": "Drosophila", "7394": "Glossina", "7213": "Ceratitis", "7375": "Lucilia", "36166": "Megaselia", "7370": "Musca", "7460": "Apis", "34740": "Heliconius", "7070": "Tribolium", "1218281": "Limnephilus", "1155016": "Mengenilla", "7029": "Acyrthosiphon", "79782": "Cimex", "121845": "Diaphorina", "56086": "Gerris", "286706": "Halyomorpha", "197043": "Homalodisca", "7536": "Oncopeltus", "38123": "Pachypsylla", "13249": "Rhodnius", "52612": "Calopteryx", "1049336": "Ephemera", "6973": "Blattella", "133901": "Frankliniella", "121225": "Pediculus", "136037": "Zootermopsis"}

# To create a table head and the first two headers. Then loop to fill with other headers with the species name
header = ["FAMILYDESC", "FAMILY"]
for key, value in species_id_dic.iteritems():
    header.append(str(value))

# To change header to numpy array
header = np.array(header) 
main_list.append(header)

# Loop to create a list with the number of gene copies per species
for item in os.listdir("/path/to/orthologous/groups/fastas/"):
    lista_num_genes = ["NONE", str(item[:-6])]
    dic_table_zero = {"7159": 0,"7165": 0,"315563": 0,"7176": 0,"7200": 0,"39758": 0,"29031": 0,"7227": 0,"7394": 0,"7213": 0,"7375": 0,"36166": 0,"7370": 0,"7460": 0,"34740": 0,"7070": 0,"1218281": 0,"1155016": 0,"7029": 0,"79782": 0,"121845": 0,"56086": 0,"286706": 0,"197043": 0,"7536": 0,"38123": 0,"13249": 0,"52612": 0,"1049336": 0,"6973": 0,"133901": 0,"121225": 0,"136037": 0}
    arquivo = open("/path/to/orthologous/groups/fastas/" + item, "r")
    for line in arquivo:
        line = line.rstrip()
        if line.startswith(">"):
            fasta_header = line[1:]
            count_sp_id = fasta_header.split(":")
            count_sp_id = count_sp_id[0]
            dic_table_zero[count_sp_id] += 1
        else:
            pass
    arquivo.close()
    for key, value in dic_table_zero.items():
        lista_num_genes.append(str(value))
    lista_num_genes = np.array(lista_num_genes)
    main_list.append(lista_num_genes)

table = np.stack(main_list)
np.savetxt('CAFEinput.txt', table, fmt = '%s', delimiter = '\t')