I have a groups.txt file which contains ortholog groups with species and geneID in every groups. it looks like :
OG_117996: R_baltica_p|32476565 V_spinosum_v|497645257
OG_117997: R_baltica_p|32476942 S_pleomorpha_s|374317197
OG_117998: R_baltica_p|32477405 V_bacterium_v|198258541
I made a function that created a list of every species in the whole file (66 total) called listOfAllSpecies. I need to create a function that gives me all the groups which contain 1 species from these 66, then all the groups which contain 2 species from these 66, etc.
To simplify it :
OG_1: A|1 A|3 B|1 C|2
OG_2: A|4 B|6
OG_3: C|8 B|9 A|10
and I need to get in this example:
(species) A,B (are in groups) OG_1, OG_2, OG_3
(species) A,C (are in groups) OG_1, OG_3
(species) B,C (are in groups) OG_1, OG_2, OG_3
(species) A,B,C (are in groups) OG_1, OG_3
(species) B (is in groups) OG_1, OG_2, OG_3
I thought to try
for species in range(start, end=None):
if end == None:
start = 0
end = start + 1
to get the first species in my listOfAllSpecies and then tell me in which groups OG_XXXX it is contained. Then get the first and the second species, etc. until it takes all the 66 species. How do I modify the range within the for loop, or is there a different way to do this?
here is my actual code with function that i need without the part I need that i asked :
import sys
if len(sys.argv) != 2:
print("Error, file name to open is missing")
sys.exit([1])
def readGroupFile(groupFileName):
dict_gene_taxonomy = {}
fh = open(groupFileName,"r")
for line in fh:
liste = line.split(": ")
groupName = liste[0]
genesAsString = liste[1]
dict_taxon = {}
liste_gene = genesAsString.split()
for item in liste_gene:
taxonomy_gene = item.split("|")
taxonomy = taxonomy_gene[0]
geneId = taxonomy_gene[1]
if not taxonomy in dict_taxon:
dict_taxon[taxonomy] = []
dict_taxon[taxonomy].append(geneId)
dict_gene_taxonomy[groupName] = dict_taxon
fh.close()
return dict_gene_taxonomy
def showListOfAllSpecies(dictio):
listAllSpecies = []
for groupName in dictio:
dictio_in_dictio = dictio[groupName]
for speciesName in dictio_in_dictio:
if not speciesName in listAllSpecies:
listAllSpecies.append(speciesName)
return listAllSpecies
dico = readGroupFile(sys.argv[1])
listAllSpecies = showListOfAllSpecies(dico)
Not sure if this is exactly what you want, but it's a start :)
from itertools import combinations
# Assume input is a list of strings called input_list
input_list = ['OG_1: A|1 A|3 B|1 C|2','OG_2: A|4 B|6','OG_3: C|8 B|9 A|10']
# Create a dict to store relationships and a list to store OGs
rels = {}
species = set()
# Populate the dict
for item in input_list:
params = item.split(': ')
og = params[0]
raw_species = params[1].split()
s = [rs.split('|')[0] for rs in raw_species]
rels[og] = s
for item in s:
species.add(item)
# Get the possible combinations of species:
combos = [c for limit in range(1, len(l)-1) for c in combinations(species,limit)]
def combo_in_og(combo, og):
for item in combo:
if item not in rels[og]:
return False
return True
# Loop over the combinations and print
for combo in combos:
valid_ogs = []
for og in ogs:
if combo_in_og(combo, og):
valid_ogs.append(og)
print('(species) ' + ','.join(combo) + ' (are in groups) ' + ', '.join(valid_ogs))
Produces:
(species) C (are in groups) OG_1, OG_3
(species) A (are in groups) OG_1, OG_2, OG_3
(species) B (are in groups) OG_1, OG_2, OG_3
(species) C,A (are in groups) OG_1, OG_3
(species) C,B (are in groups) OG_1, OG_3
(species) A,B (are in groups) OG_1, OG_2, OG_3
(species) C,A,B (are in groups) OG_1, OG_3
Just a warning: what you're trying to do will start to take forever with large enough numbers of inputs, as its complexity is 2^N. You can't get around it (that's what the problem demands), but it's there.
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