Sorts output of NCBI Conserved Domain search ( to group all of the domains in a PR gene with it's Gene ID.

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#condenses list of domains outputted by CD-Search and combines with other Eval from BLAST search

PRgenelist = open("PRfile") #PR file should be a tab separated file containing gene IDs and E values from BLAST search
PRgenes = [] #list for gene IDs
PRgenesdomains = [] #list to become domains in PR genes
Evals = [] #list of Evalues

for line in PRgenelist:
    word = line.split("\t") #reads according to tab separation
    PRgenes.append(word[1]) #ensure that geneID is second column
    PRgenesdomains.append(word[1]) #ensure that geneID is again second column
    Evals.append(word[2].rstrip('\n')) #ensure that Evalue is third column

PRgenedomainslist = []                  
for i in range(len(PRgenes)):
    PRgenesdomains[i] = [] #makes each entry in PRgenesdomains an empty list to be filled later
    PRgenedomainslist.append(PRgenesdomains[i]) #adds each empty list to new list

Domainlist = open("domainfile") #'domainfile' is data outputted from CD-Search, with headspace removed. Should be tab separated.

#every time a geneID in CD-Search output matches a geneID in the PR file, the domain detected will be added to the domainslist
for lines in Domainlist:
    words = lines.split("\t")
    for m in range(len(PRgenes)):
        if PRgenes[m] == words[0]: #ensure gene ID is first column of domainfile
            PRgenedomainslist[m].append(words[8]) #ensure that domains are in column 9

#create new file containing gene ID, E value from BLAST search, and a list of all domains detected for each PR gene
sortedcondensed = open("newfile", "w") #change 'newfile' to desired filename
for n in range(len(PRgenes)):
    sortedcondensed.write(PRgenes[n] + "\t" + Evals[n] + "\t" + str(PRgenelistlist[n]) + "\n")