eukref_dbparser02.py

'''
usage
python annotateclusters.py thecamoebids.clustered.fasttree.txt thecamoebids.clusters.uc expandedclusters.txt

'''

import sys

infile = open(sys.argv[1], "r")  # tab delimited outfile of annotatetree.py
lines = infile.readlines()
infile.close()
clusterfile = open(sys.argv[2], "r")  # *.uc file
clusterlines = clusterfile.readlines()
clusterfile.close()
outfile = open('temp_expandedcluster.txt', "w")  # tab delimited outfile

for line in clusterlines:
    cluster = line.split("\t")[9]
    cluster = cluster.strip()
    fullname = line.split("\t")[8]
    if fullname.count("noginumber") > 0:
        accession = line.split('|')[-1]
        accession = accession.split()[0]

    elif fullname.startswith("gi+"):
        accession = fullname.split('+')[3]

    elif fullname.startswith("gi|"):
        accession = fullname.split("|")[3]

    else:
        pass
    accession.strip()
    if cluster == "*":
        for i in lines:
            if i.startswith(accession):
                outfile.write(i)
            else:
                pass

    else:
        for i in lines:
            if cluster.count(i.split()[0]) > 0:
                annotation = i.split("\t")[1]
                outfile.write(accession + "\t" + annotation)
            else:
                pass

outfile.close()

# remove duplicated lines
infile = open('temp_expandedcluster.txt')
lines = infile.readlines()
infile.close()

list_lines = []

for line in lines:
    list_lines.append(line.strip())

new_lines = set(list_lines)
out = open(sys.argv[3], 'w')

for i in new_lines:
    out.write('%s\n' % (i))

out.close()

sys.exit()