modify range in every loop of the range

Question

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)

Answer 1

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.

Answer 2

What about using a while loop to control the range() parameters?

end = 0
start = 0
while end < 1000:
    for species in range(start, end):         
        ...do something

    end += 1

Answer 3

The list of all non-empty subsets of a set of N items (your set of all species) is 2^N – 1

That's because it is just like a binary number of N bits, where each bit can be 1 (take that species in the subset) or 0 (exclude that species from the subset.) The -1 excludes the empty set (all bits 0)

Therefore you can enumerate all the subsets of species with a simple integer loop:

# sample data
listOfAllSpecies = ['A', 'B', 'C']

# enumerate all subsets of listOfAllSpecies, 0 excluded (the empty set)
for bits in range(1, 2**len(listOfAllSpecies)):

    # build the subset
    subset = []
    for n in range(len(listOfAllSpecies)):
        # test if the current subset includes bit n
        if bits & 2**n:
            subset.append(listOfAllSpecies[n])

    # see which groups contain the given subset
    print "species", ",".join(subset), "are in groups TODO"

Result:

species A are in groups TODO
species B are in groups TODO
species A,B are in groups TODO
species C are in groups TODO
species A,C are in groups TODO
species B,C are in groups TODO
species A,B,C are in groups TODO

If you also need the code to test if a group contains a subset, you need to specify how the groups are stored in your program.

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