def main(argv):
(opts, args) = parser.parse_args()
if check_arguments(opts, args):
print usage
sys.exit(0)
input_folder = opts.input_folder
output_file = opts.output_file
filePATTERN = re.compile(r'.*COG[0-9]*.*\.fa')
cogSeqMatchesPATTERN = re.compile(
r'[a-zA-Z]*_(.*)__[0-9]*__*(COG[0-9]*).*.fa')
list = []
for file in listdir(input_folder):
if filePATTERN.match(file):
hits = cogSeqMatchesPATTERN.search(file)
if hits:
list.append((hits.group(1), hits.group(2)))
try:
outputfile = open(output_file, 'w')
except:
print "Cannot open file to MLTreeMap hits"
sys.exit(0)
fprintf(outputfile, "Sequences\tCOG\n")
for seq, cog in list:
fprintf(outputfile, "%s\t%s\n", seq, cog)
outputfile.close()
def write_annotation_for_orf(outputgff_file, candidatedbname, dbname_weight, results_dictionary, orf_dictionary, contig, candidate_orf_pos, orfid):
fields = [ 'source', 'feature', 'start', 'end', 'score', 'strand', 'frame' ]
output_line= orf_dictionary[contig][candidate_orf_pos]['seqname']
for field in fields:
# printf("\t%s", orf_dictionary[contig][candidate_orf_pos][field])
output_line += "\t"+ str(orf_dictionary[contig][candidate_orf_pos][field])
attributes = "ID="+orf_dictionary[contig][candidate_orf_pos]['id']
attributes += ";" + "locus_tag="+orf_dictionary[contig][candidate_orf_pos]['locus_tag']
attributes += ";" + "contig_length="+orf_dictionary[contig][candidate_orf_pos]['contig_length']
attributes += ";" + "orf_length="+orf_dictionary[contig][candidate_orf_pos]['orf_length']
attributes += ";" + "partial="+orf_dictionary[contig][candidate_orf_pos]['partial']
attributes += ";" + "sourcedb="+candidatedbname
if candidatedbname in results_dictionary:
attributes += ";" + "annotvalue="+str(results_dictionary[candidatedbname][orfid]['value'])
attributes += ";" + "ec="+str(results_dictionary[candidatedbname][orfid]['ec'])
attributes += ";" + "product="+results_dictionary[candidatedbname][orfid]['product']
else:
attributes += ";" + "annotvalue="+str('0')
attributes += ";" + "ec="+str('')
attributes += ";" + "product="+'hypothetical protein'
output_line += '\t' + attributes
fprintf(outputgff_file, "%s\n", output_line);
def main(argv):
(opts, args) = parser.parse_args()
if check_arguments(opts, args):
print usage
sys.exit(0)
input_folder = opts.input_folder
output_file = opts.output_file
filePATTERN = re.compile(r'.*COG[0-9]*.*\.fa');
cogSeqMatchesPATTERN = re.compile(r'[a-zA-Z]*_(.*)__[0-9]*__*(COG[0-9]*).*.fa');
list= []
for file in listdir(input_folder):
if filePATTERN.match(file):
hits = cogSeqMatchesPATTERN.search( file)
if hits:
list.append( (hits.group(1), hits.group(2)) )
try:
outputfile = open(output_file, 'w')
except:
print "Cannot open file to MLTreeMap hits"
sys.exit(0)
fprintf(outputfile, "Sequences\tCOG\n")
for seq, cog in list:
fprintf(outputfile, "%s\t%s\n",seq, cog)
outputfile.close()
def print_orf_table(results, refseq2peg, output_dir):
if not path.exists(output_dir):
makedirs(output_dir)
outputfile = open( output_dir +'/ORF_annotation_table.txt', 'w')
orf_dict = {}
for dbname in ['refseq', 'cog', 'kegg' ]:
for seqname in results[dbname]:
for orf in results[dbname][seqname]:
if not orf['query'] in orf_dict:
orf_dict[orf['query']] = {}
if dbname =='cog':
cog = cog_id(orf['product'])
orf_dict[orf['query']][dbname] = cog
if dbname =='kegg':
kegg = kegg_id(orf['product'])
orf_dict[orf['query']][dbname] = kegg
if dbname=='refseq':
refseq = refseq_id(orf['target'])
if refseq in refseq2peg:
refseq = refseq2peg[refseq]
else:
refseq = ""
orf_dict[orf['query']][dbname] = refseq
orf_dict[orf['query']]['contig'] = seqname
for orfn in orf_dict:
if 'cog' in orf_dict[orfn]:
cogFn = orf_dict[orfn]['cog']
else:
cogFn = ""
if 'kegg' in orf_dict[orfn]:
keggFn = orf_dict[orfn]['kegg']
else:
keggFn = ""
if 'metacyc' in orf_dict[orfn]:
metacycPwy = orf_dict[orfn]['metacyc']
else:
metacycPwy = ""
if 'refseq' in orf_dict[orfn]:
refseqFn = orf_dict[orfn]['refseq']
else:
refseqFn = ""
fprintf(outputfile, "%s\n", orfn + "\t" + orf_dict[orfn]['contig'] + '\t' + cogFn + '\t' + keggFn +'\t' + refseqFn + '\t' + metacycPwy)
outputfile.close()
def copy_faa_gff_orf_prediction(source_files, target_files):
for source, target in zip(source_files, target_files):
#print source + ' ' + target
sourcefile = open(source, 'r')
targetfile = open(target, 'w')
sourcelines = sourcefile.readlines()
for line in sourcelines:
fprintf(targetfile, "%s\n", line.strip())
sourcefile.close()
targetfile.close()
def print_orf_table(results, output_dir):
if not path.exists(output_dir):
makedirs(output_dir)
outputfile = open( output_dir +'/ORF_annotation_table.txt', 'w')
orf_dict = {}
for dbname in results.iterkeys():
for seqname in results[dbname]:
for orf in results[dbname][seqname]:
if not orf['query'] in orf_dict:
orf_dict[orf['query']] = {}
if dbname =='cog':
cog = cog_id(orf['product'])
orf_dict[orf['query']][dbname] = cog
if dbname =='kegg':
kegg = kegg_id(orf['product'])
orf_dict[orf['query']][dbname] = kegg
if dbname=='seed':
seed = orf['product']
orf_dict[orf['query']][dbname] = re.sub(r'\[.*\]','', seed).strip()
orf_dict[orf['query']]['contig'] = seqname
for orfn in orf_dict:
if 'cog' in orf_dict[orfn]:
cogFn = orf_dict[orfn]['cog']
else:
cogFn = ""
if 'kegg' in orf_dict[orfn]:
keggFn = orf_dict[orfn]['kegg']
else:
keggFn = ""
if 'metacyc' in orf_dict[orfn]:
metacycPwy = orf_dict[orfn]['metacyc']
else:
metacycPwy = ""
if 'seed' in orf_dict[orfn]:
seedFn = orf_dict[orfn]['seed']
else:
seedFn = ""
fprintf(outputfile, "%s\n", orfn + "\t" + orf_dict[orfn]['contig'] + '\t' + cogFn + '\t' + keggFn +'\t' + seedFn + '\t' + metacycPwy)
outputfile.close()
def print_counts_at_level(hierarchical_map, field_to_description, depth, level, outputfile):
if type(hierarchical_map) is type(0):
return hierarchical_map
count = 0
for key in hierarchical_map:
tempcount = print_counts_at_level(hierarchical_map[key],field_to_description, depth+1, level, outputfile)
if depth==level:
if key in field_to_description:
fprintf(outputfile, "%s\n", key + '\t' + field_to_description[key] + '\t' + str(tempcount) )
else:
fprintf(outputfile, "%s\n", key + '\t' + ' ' + '\t' + str(tempcount))
count+=tempcount
return count
def write_16S_tRNA_gene_info(rRNA_dictionary, outputgff_file, tag):
fields = ['source', 'feature', 'start', 'end', 'score', 'strand', 'frame']
for rRNA in rRNA_dictionary:
output_line = rRNA_dictionary[rRNA]['seqname']
for field in fields:
output_line += "\t" + str(rRNA_dictionary[rRNA][field])
attributes = "ID=" + rRNA_dictionary[rRNA]['seqname'] + tag
attributes += ";" + "locus_tag=" + rRNA_dictionary[rRNA][
'seqname'] + tag
attributes += ";" + "ec="
attributes += ";" + "product=" + rRNA_dictionary[rRNA]['product']
output_line += '\t' + attributes
fprintf(outputgff_file, "%s\n", output_line)
def write_16S_tRNA_gene_info(rRNA_dictionary, outputgff_file, tag):
fields = [ 'source', 'feature', 'start', 'end', 'score', 'strand', 'frame' ]
for rRNA in rRNA_dictionary:
output_line= rRNA_dictionary[rRNA]['seqname']
for field in fields:
output_line += "\t"+ str(rRNA_dictionary[rRNA][field])
attributes = "ID="+rRNA_dictionary[rRNA]['seqname'] + tag
attributes += ";" + "locus_tag="+rRNA_dictionary[rRNA]['seqname'] + tag
attributes += ";" + "orf_length=0"
attributes += ";" + "contig_length=0"
attributes += ";" + "ec="
attributes += ";" + "product="+rRNA_dictionary[rRNA]['product']
output_line += '\t' + attributes
fprintf(outputgff_file, "%s\n", output_line);
def add_refscore_to_file(blast_table_out, refscore_file, allNames):
infile = open(blast_table_out, 'r')
refscores = {}
lines = infile.readlines()
for line in lines:
line = line.rstrip()
fields = line.split('\t')
if len(fields) != 12:
print 'Error in the blastout file'
sys.exit(1)
for key, value in refscores.iteritems():
allNames[key] = True
fprintf(refscore_file, "%s\t%s\n", key, value)
infile.close()
def add_refscore_to_file(blast_table_out, refscore_file, allNames):
infile = open( blast_table_out,'r')
refscores = {}
lines = infile.readlines()
for line in lines:
line=line.rstrip()
fields = line.split('\t')
if len(fields) != 12:
print 'Error in the blastout file'
sys.exit(1)
for key, value in refscores.iteritems():
allNames[key] = True
fprintf(refscore_file, "%s\t%s\n",key, value)
infile.close()
def print_counts_at_level(hierarchical_map, field_to_description, depth, level,
outputfile):
if type(hierarchical_map) is type(0):
return hierarchical_map
count = 0
for key in hierarchical_map:
tempcount = print_counts_at_level(hierarchical_map[key],
field_to_description, depth + 1,
level, outputfile)
if depth == level:
if key in field_to_description:
fprintf(
outputfile, "%s\n", key + '\t' +
field_to_description[key] + '\t' + str(tempcount))
else:
fprintf(outputfile, "%s\n",
key + '\t' + ' ' + '\t' + str(tempcount))
count += tempcount
return count
def process_gbk_file(input_gbk, output_gbk, headers, gff_dictionary):
tag = re.sub(r'[.]gbk', '', input_gbk)
tag = re.sub(r'.*/', '', tag)
output_gbk_file = open(output_gbk, 'w')
serializer = genbank.GenBankRecordSerializer()
with open(input_gbk, 'r') as genbank_file:
out_list = []
count = 0
for record in genbank.GenBankRecordParser(genbank_file.read()):
count += 1
record.locus = tag + str(count)
if count % 1000 == 0:
print 'Count = ' + str(count)
if headers and 'REFERENCES' in headers:
record.references_ = headers['REFERENCES']
i = 0
for feature in record.features:
if feature.type == "CDS":
if feature.locus_tag in gff_dictionary:
record.features[i].product = 'aaaaa ' + gff_dictionary[
feature.locus_tag]['product']
i += 1
#record.locus = "hello"
out_list.append(serializer.serialize(record))
if count % 1000 == 0:
output_str = '\n'.join(out_list)
out_list = []
fprintf(output_gbk_file, '%s\n', output_str)
output_str = '\n'.join(out_list)
fprintf(output_gbk_file, '%s\n', output_str)
output_gbk_file.close()
def process_file(genbank_filename, output_fna, output_faa, output_gff):
with open(genbank_filename, 'r') as genbank_file:
outputfnafile = open(output_fna, 'w')
outputfaafile = open(output_faa, 'w')
outputgfffile = open(output_gff, 'w')
for record in genbank.GenBankRecordParser(genbank_file.read()):
fprintf(outputfnafile, ">%s\n%s\n", record.locus, record.sequence)
for feature in record.features:
if feature.type == 'CDS':
fprintf(outputfaafile, ">%s\n%s\n", feature.locus_tag,
feature.translation)
start, end, strand = feature.coordinates
gff_Str = record.locus
gff_Str += '\t' + 'Genbank file'
gff_Str += '\t' + 'CDS'
gff_Str += '\t' + start
gff_Str += '\t' + end
gff_Str += '\t' + '0'
gff_Str += '\t' + strand
gff_Str += '\t' + '0'
gff_Str += '\tID=' + feature.locus_tag
gff_Str += ';locus_tag=' + feature.locus_tag
if feature.product:
gff_Str += ';product=' + feature.product
fprintf(outputgfffile, "%s\n", gff_Str)
outputfnafile.close()
outputgfffile.close()
outputfaafile.close()
def process_file(genbank_filename, output_fna, output_faa, output_gff):
with open(genbank_filename, 'r') as genbank_file:
outputfnafile = open(output_fna,'w')
outputfaafile = open(output_faa,'w')
outputgfffile = open(output_gff,'w')
for record in genbank.GenBankRecordParser(genbank_file.read()):
fprintf(outputfnafile, ">%s\n%s\n", record.locus, record.sequence)
for feature in record.features:
if feature.type=='CDS':
fprintf(outputfaafile, ">%s\n%s\n", feature.locus_tag, feature.translation)
start, end, strand = feature.coordinates
gff_Str = record.locus
gff_Str += '\t' + 'Genbank file'
gff_Str += '\t' + 'CDS'
gff_Str += '\t' + start
gff_Str += '\t' + end
gff_Str += '\t' + '0'
gff_Str += '\t' + strand
gff_Str += '\t' + '0'
gff_Str += '\tID=' + feature.locus_tag
gff_Str += ';locus_tag=' + feature.locus_tag
if feature.product:
gff_Str += ';product=' + feature.product
fprintf(outputgfffile, "%s\n", gff_Str)
outputfnafile.close()
outputgfffile.close()
outputfaafile.close()
def process_gbk_file(input_gbk, output_gbk, headers, gff_dictionary):
tag = re.sub(r"[.]gbk", "", input_gbk)
tag = re.sub(r".*/", "", tag)
output_gbk_file = open(output_gbk, "w")
serializer = genbank.GenBankRecordSerializer()
with open(input_gbk, "r") as genbank_file:
out_list = []
count = 0
for record in genbank.GenBankRecordParser(genbank_file.read()):
count += 1
record.locus = tag + str(count)
if count % 1000 == 0:
print "Count = " + str(count)
if headers and "REFERENCES" in headers:
record.references_ = headers["REFERENCES"]
i = 0
for feature in record.features:
if feature.type == "CDS":
if feature.locus_tag in gff_dictionary:
record.features[i].product = "aaaaa " + gff_dictionary[feature.locus_tag]["product"]
i += 1
# record.locus = "hello"
out_list.append(serializer.serialize(record))
if count % 1000 == 0:
output_str = "\n".join(out_list)
out_list = []
fprintf(output_gbk_file, "%s\n", output_str)
output_str = "\n".join(out_list)
fprintf(output_gbk_file, "%s\n", output_str)
output_gbk_file.close()
def write_annotation_for_orf(outputgff_file, candidatedbname, dbname_weight,
results_dictionary, orf_dictionary, contig,
candidate_orf_pos, orfid):
fields = ['source', 'feature', 'start', 'end', 'score', 'strand', 'frame']
# print contig
# print orf_dictionary[contig]
# print results_dictionary
output_line = orf_dictionary[contig][candidate_orf_pos]['seqname']
for field in fields:
# printf("\t%s", orf_dictionary[contig][candidate_orf_pos][field])
output_line += "\t" + str(
orf_dictionary[contig][candidate_orf_pos][field])
attributes = "ID=" + orf_dictionary[contig][candidate_orf_pos]['id']
attributes += ";" + "locus_tag=" + orf_dictionary[contig][
candidate_orf_pos]['locus_tag']
attributes += ";" + "partial=" + orf_dictionary[contig][candidate_orf_pos][
'partial']
attributes += ";" + "sourcedb=" + candidatedbname
if candidatedbname in results_dictionary:
attributes += ";" + "annotvalue=" + str(
results_dictionary[candidatedbname][orfid]['value'])
attributes += ";" + "ec=" + str(
results_dictionary[candidatedbname][orfid]['ec'])
attributes += ";" + "product=" + results_dictionary[candidatedbname][
orfid]['product']
else:
attributes += ";" + "annotvalue=" + str('0')
attributes += ";" + "ec=" + str('')
attributes += ";" + "product=" + 'hypothetical protein'
output_line += '\t' + attributes
fprintf(outputgff_file, "%s\n", output_line)
def add_last_refscore_to_file(blast_table_out, refscore_file, allNames):
commentPATTERN = re.compile(r'^#')
infile = open(blast_table_out, 'r')
refscores = {}
lines = infile.readlines()
for line in lines:
if commentPATTERN.match(line):
continue
line = line.rstrip()
fields = line.split('\t')
if len(fields) != 12:
print 'Error in the blastout file'
sys.exit(1)
if fields[6].rstrip() == fields[1].rstrip():
# fprintf(refscore_file, "%s\t%s\n",fields[0], fields[11])
refscores[fields[1]] = fields[0]
for key, value in refscores.iteritems():
allNames[key] = True
fprintf(refscore_file, "%s\t%s\n", key, value)
infile.close()
def add_last_refscore_to_file(blast_table_out, refscore_file, allNames):
commentPATTERN = re.compile(r'^#')
infile = open( blast_table_out,'r')
refscores = {}
lines = infile.readlines()
for line in lines:
if commentPATTERN.match(line):
continue
line=line.rstrip()
fields = line.split('\t')
if len(fields) != 12:
print 'Error in the blastout file'
sys.exit(1)
if fields[6].rstrip()==fields[1].rstrip():
# fprintf(refscore_file, "%s\t%s\n",fields[0], fields[11])
refscores[fields[1]]=fields[0]
for key, value in refscores.iteritems():
allNames[key] = True
fprintf(refscore_file, "%s\t%s\n",key, value)
infile.close()
def print_counts_at_level(hierarchical_map, field_to_description, depth, level, outputfile, printKey=True, header=None):
if type(hierarchical_map) is type(0):
return hierarchical_map
if header:
fprintf(outputfile, "%s\n",header )
count = 0
for key in hierarchical_map:
tempcount = print_counts_at_level(hierarchical_map[key],field_to_description, depth+1, level, outputfile, printKey=printKey)
if depth==level:
if key in field_to_description:
if printKey:
fprintf(outputfile, "%s\n", key + '\t' + field_to_description[key] + '\t' + str(tempcount) )
else:
fprintf(outputfile, "%s\n", field_to_description[key] + '\t' + str(tempcount) )
else:
if printKey:
print "True 2"
fprintf(outputfile, "%s\n", key + '\t' + ' ' + '\t' + str(tempcount))
else:
fprintf(outputfile, "%s\n", key + '\t' + str(tempcount))
count+=tempcount
return count
def process_blastoutput(dbname, blastoutput, mapfile, refscore_file, opts):
blastparser = BlastOutputParser(dbname, blastoutput, mapfile, refscore_file, opts)
fields = ['q_length', 'bitscore', 'bsr', 'expect', 'aln_length', 'identity', 'ec' ]
if opts.taxonomy:
fields.append('taxonomy')
fields.append('product')
output_blastoutput_parsed = blastoutput + '.parsed.txt'
outputfile = open(output_blastoutput_parsed, 'w')
fprintf(outputfile, "#%s",'query')
for field in fields:
fprintf(outputfile,"\t%s",field)
fprintf(outputfile, "\n")
for data in blastparser:
if not data:
continue
try:
fprintf(outputfile, "%s",data['query'])
except:
print data
sys.exit()
for field in fields:
fprintf(outputfile, "\t%s",data[field])
fprintf(outputfile, "\n")
outputfile.close()
# add_refscore_to_file(blastoutput,refscore_file, allNames)
return None
def create_annotation(results_dictionary, annotated_gff, output_dir, ncbi_taxonomy_tree_file, min_score, top_percent, min_support):
meganTree = None
lca = None
if 'refseq' in results_dictionary:
lca = LCAComputation(ncbi_taxonomy_tree_file)
lca.setParameters(min_score, top_percent, min_support)
meganTree = MeganTree(lca)
if not path.exists(output_dir):
makedirs(output_dir)
orf_dictionary={}
#process_gff_file(annotated_gff, orf_dictionary)
gffreader = GffFileParser(annotated_gff)
output_table_file = open(output_dir + '/functional_and_taxonomic_table.txt', 'w')
fprintf(output_table_file, "ORF_ID\tORF_length\tstart\tend\tContig_Name\tContig_length\tstrand\tec\ttaxonomy\tproduct\n")
count = 0
for contig in gffreader:
for orf in gffreader.orf_dictionary[contig]:
taxonomy = None
if count%10000==0 :
pass
species = []
if 'refseq' in results_dictionary:
if orf['id'] in results_dictionary['refseq']:
for hit in results_dictionary['refseq'][orf['id']]:
if hit['bitscore'] >= min_score:
names = get_species(hit)
if names:
species.append(names)
#print '---------------------------'
# else:
# print "hit " + hit['query'] + ' ' + hit['dbname'] + ' ' + str(hit['bitscore'] )
if lca:
taxonomy=lca.getTaxonomy(species)
fprintf(output_table_file, "%s", orf['id'])
fprintf(output_table_file, "\t%s", orf['orf_length'])
fprintf(output_table_file, "\t%s", orf['start'])
fprintf(output_table_file, "\t%s", orf['end'])
fprintf(output_table_file, "\t%s", orf['seqname'])
fprintf(output_table_file, "\t%s", orf['contig_length'])
fprintf(output_table_file, "\t%s", orf['strand'])
fprintf(output_table_file, "\t%s", orf['ec'])
# fprintf(output_table_file, "\t%s", str(species))
fprintf(output_table_file, "\t%s", taxonomy)
fprintf(output_table_file, "\t%s\n", orf['product'])
if meganTree and taxonomy != '':
meganTree.insertTaxon(taxonomy)
# print 'inserted taxon of taxonomy : ', taxonomy
#print meganTree.getChildToParentMap()
output_table_file.close()
# print meganTree.getParentToChildrenMap()
if meganTree:
print output_dir + '/megan_tree.tre'
megan_tree_file = open(output_dir + '/megan_tree.tre', 'w')
#print meganTree.printTree('1')
# exit()
fprintf(megan_tree_file, "%s;", meganTree.printTree('1'))
# print 'wrote out megan_tree_file'
megan_tree_file.close()
def main(argv):
(opts, args) = parser.parse_args()
if not valid_arguments(opts, args):
print usage
sys.exit(0)
min_length = opts.min_length
inputfile = open(opts.input_fasta,'r')
outfile = open(opts.output_fasta, 'w')
logfile = open(opts.log_file, 'w')
if opts.map_file:
mapfile = open(opts.map_file, 'w')
else:
mapfile = None
sample_name = opts.input_fasta;
sample_name = re.sub(r'^.*/','',sample_name, re.I)
sample_name = re.sub(r'^.*\\','',sample_name, re.I)
sample_name = re.sub(r'\.fasta$','',sample_name, re.I)
sample_name = re.sub(r'\.fna$','',sample_name, re.I)
sample_name = re.sub(r'\.faa$','',sample_name, re.I)
sample_name = re.sub(r'\.fas$','',sample_name, re.I)
BEFORE = 'BEFORE'
AFTER = 'AFTER'
NUMSEQ = "Number of sequences :"
NUMSEQ_SHORTER = "Number of sequences shorter than "
AV_LENGTH= "Average length of sequences:"
MIN_LENGTH= "Minimum length of sequences:"
MAX_LENGTH= "Maximum length of sequences:"
stats = {
MIN_LENGTH: { 'BEFORE':10000000, 'AFTER':1000000 },
MAX_LENGTH: { 'BEFORE': 0, 'AFTER':0 },
NUMSEQ : { 'BEFORE' :0, 'AFTER':0},
NUMSEQ_SHORTER : { 'BEFORE':0, 'AFTER':0 },
AV_LENGTH : { 'BEFORE':0, 'AFTER':0 },
}
length_distribution = {}
length_cumulative_distribution = {}
for i in range(0,31):
length_distribution[i]= 0
length_cumulative_distribution[i]= 0
seq_count = 0
allNames= dict()
outputStr = ""
outputLines = []
for record in read_fasta_records(inputfile):
seqname = record.name
seq = record.sequence
length = len(seq)
index = int(len(seq) / 50);
if index >= 30:
index = 30
#print length($seq) ."\t".$index."\n";
length_distribution[index] += 1
if length < stats[MIN_LENGTH][BEFORE] :
stats[MIN_LENGTH][BEFORE] = length
if length > stats[MAX_LENGTH][BEFORE] :
stats[MAX_LENGTH][BEFORE] = length
if length < MIN_LENGTH:
stats[NUMSEQ_SHORTER][BEFORE] += 1
stats[AV_LENGTH][BEFORE] = stats[AV_LENGTH][BEFORE] + length
seqvalue = filter_sequence(seq)
stats[NUMSEQ][BEFORE] += 1
seqlen = len(seqvalue)
if seqlen>= min_length :
stats[NUMSEQ][AFTER] += 1
stats[AV_LENGTH][AFTER] = stats[AV_LENGTH][AFTER] + seqlen
if mapfile==None:
fprintf(outfile, "%s\n", seqname)
else:
fprintf(outfile, ">%s\n", sample_name + '_' + str(seq_count) )
key = re.sub(r'^>','',seqname)
fprintf(mapfile, "%s\n", sample_name+ '_' + str(seq_count) + '\t' + key)
seq_count += 1
fprintf(outfile, "%s\n",seqvalue)
if seqlen < stats[MIN_LENGTH][AFTER] :
stats[MIN_LENGTH][AFTER] = seqlen
if seqlen > stats[MAX_LENGTH][AFTER] :
stats[MAX_LENGTH][AFTER] = seqlen
if stats[NUMSEQ][BEFORE] > 0 :
stats[AV_LENGTH][BEFORE] = stats[AV_LENGTH][BEFORE]/stats[NUMSEQ][BEFORE]
else:
stats[AV_LENGTH][BEFORE] = 0
if stats[NUMSEQ][AFTER] > 0 :
stats[AV_LENGTH][AFTER] = stats[AV_LENGTH][AFTER]/stats[NUMSEQ][AFTER]
else :
stats[AV_LENGTH][AFTER] = 0
outfile.close()
inputfile.close()
if mapfile != None:
mapfile.close()
fprintf(logfile, " %s\n", " \tBEFORE\tAFTER");
fprintf(logfile, " %s\n", NUMSEQ +'\t' + str(stats[NUMSEQ][BEFORE]) + '\t' + str(stats[NUMSEQ][AFTER]));
fprintf(logfile, " %s\n", NUMSEQ_SHORTER + str(MIN_LENGTH) + ':\t'+ str(stats[NUMSEQ_SHORTER][BEFORE]) + '\t' + str(stats[NUMSEQ_SHORTER][AFTER]))
fprintf(logfile, " %s\n", AV_LENGTH +'\t' + str(stats[AV_LENGTH][BEFORE]) + '\t'+ str(stats[AV_LENGTH][AFTER] ))
fprintf(logfile, " %s\n", MIN_LENGTH + '\t' + str(stats[MIN_LENGTH][BEFORE]) +'\t'+ str(stats[MIN_LENGTH][AFTER]))
fprintf(logfile, " %s\n", MAX_LENGTH +'\t'+ str(stats[MAX_LENGTH][BEFORE]) + '\t' + str(stats[MAX_LENGTH][AFTER]))
fprintf(logfile, "\n\n");
fprintf(logfile, " READ_LENGTH_RANGE\tFREQUENCY\t\tMIN_LENGTH\tCUMULATIVE_FREQUENCY\n");
fprintf(logfile, " -----------------\t---------\t\t----------\t--------------------\n");
i = 30
length_cumulative_distribution[i] = length_cumulative_distribution[i];
i -= 1
while i >= 0:
length_cumulative_distribution[i] = length_cumulative_distribution[i+1] + length_distribution[i];
i -= 1
for i in range(0,31):
fprintf(logfile, " %s\n", str(i*50) + '-' + str((i+1)*50) + '\t' +\
str(length_distribution[i]) +'\t\t\t' + str( (i+1)*50) + '\t' + str(length_cumulative_distribution[i]) )
logfile.close()
def create_annotation(results_dictionary, annotated_gff, output_dir):
file = 'blastDB/ncbi_taxonomy_tree.txt'
lca = LCAComputation(file)
if not path.exists(output_dir):
makedirs(output_dir)
orf_dictionary={}
#process_gff_file(annotated_gff, orf_dictionary)
gffreader = GffFileParser(annotated_gff)
output_table_file = open(output_dir + '/functional_and_taxonomic_table.txt', 'w')
fprintf(output_table_file, "id\tseqname\tstart\tend\tstrand\tec\ttaxonomy\tproduct\n")
count = 0
for contig in gffreader:
for orf in gffreader.orf_dictionary[contig]:
#print orf
if count%10000==0 :
# print "fandt " + str(count)
pass
species = []
if 'refseq' in results_dictionary:
if orf['id'] in results_dictionary['refseq']:
for hit in results_dictionary['refseq'][orf['id']]:
names = get_species(hit)
if names:
species.append(names)
#print species
#print '---------------------------'
taxonomy=lca.getTaxonomy(species)
fprintf(output_table_file, "%s", orf['id'])
fprintf(output_table_file, "\t%s", orf['seqname'])
fprintf(output_table_file, "\t%s", orf['start'])
fprintf(output_table_file, "\t%s", orf['end'])
fprintf(output_table_file, "\t%s", orf['strand'])
fprintf(output_table_file, "\t%s", orf['ec'])
#fprintf(output_table_file, "\t%s", str(species))
fprintf(output_table_file, "\t%s", taxonomy)
fprintf(output_table_file, "\t%s\n", orf['product'])
output_table_file.close()
def create_annotation(dbname_weight, results_dictionary, input_gff, rRNA_16S_stats_files, tRNA_stats_files, output_gff, output_comparative_annotation):
orf_dictionary={}
# process_gff_file(input_gff, orf_dictionary)
gffreader = GffFileParser(input_gff)
output_gff_tmp = output_gff + ".tmp"
outputgff_file = open( output_gff_tmp, 'w')
output_comp_annot_file1 = open( output_comparative_annotation + '.1.txt', 'w')
output_comp_annot_file2 = open( output_comparative_annotation + '.2.txt', 'w')
output_comp_annot_file1_Str = 'orf_id\tref dbname\tEC\tproduct\tvalue'
fprintf(output_comp_annot_file1,'%s\n', output_comp_annot_file1_Str)
output_comp_annot_file2_Str = 'orf_id'
dbnames = dbname_weight.keys()
for dbname in dbnames:
weight = dbname_weight[dbname]
output_comp_annot_file2_Str += '\t{0}(EC) \t{0}(product)\t{0}(value)'.format(dbname)
fprintf(output_comp_annot_file2,'%s\n', output_comp_annot_file2_Str)
# gffreader = GffReader(input_gff)
for contig in gffreader:
count = 0
for orf in gffreader.orf_dictionary[contig]:
#print orf
value = 0.0001
success =False
output_comp_annot_file1_Str = ''
output_comp_annot_file2_Str = ''
for dbname in dbnames:
weight = dbname_weight[dbname]
value = 0
if orf['id'] in results_dictionary[dbname]:
if value < results_dictionary[dbname][orf['id']]['value']:
value = results_dictionary[dbname][orf['id']]['value']
candidatedbname=dbname
success =True
candidate_orf_pos = count
if output_comp_annot_file1_Str:
output_comp_annot_file1_Str += '{0}\t{1}\t{2}\t{3}\t{4}\n'.format('', dbname,\
results_dictionary[dbname][orf['id']]['ec'],\
results_dictionary[dbname][orf['id']]['product'],\
str(results_dictionary[dbname][orf['id']]['value']*float(weight)))
else:
output_comp_annot_file1_Str += '{0}\t{1}\t{2}\t{3}\t{4}\n'.format(orf['id'], dbname,\
results_dictionary[dbname][orf['id']]['ec'],\
results_dictionary[dbname][orf['id']]['product'],\
str(results_dictionary[dbname][orf['id']]['value']*float(weight)))
if output_comp_annot_file2_Str:
output_comp_annot_file2_Str += '\t{0}\t{1}\t{2}'.format(\
results_dictionary[dbname][orf['id']]['ec'],\
results_dictionary[dbname][orf['id']]['product'],\
str(results_dictionary[dbname][orf['id']]['value']*float(weight)))
else:
output_comp_annot_file2_Str += '{0}\t{1}\t{2}\t{3}'.format(orf['id'],
results_dictionary[dbname][orf['id']]['ec'],\
results_dictionary[dbname][orf['id']]['product'],\
str(results_dictionary[dbname][orf['id']]['value']*float(weight)))
else:
if not output_comp_annot_file1_Str:
output_comp_annot_file1_Str += '{0}\t{1}\t{2}\t{3}\t{4}\n'.format(orf['id'], '','','','')
if output_comp_annot_file2_Str:
output_comp_annot_file2_Str += '\t{0}\t{1}\t{2}'.format('', '','')
else:
output_comp_annot_file2_Str += '{0}\t{1}\t{2}\t{3}'.format(orf['id'], '','','','')
if success: # there was a database hit
fprintf(output_comp_annot_file1,'%s\n', output_comp_annot_file1_Str)
fprintf(output_comp_annot_file2,'%s\n', output_comp_annot_file2_Str)
write_annotation_for_orf(outputgff_file, candidatedbname, dbname_weight, results_dictionary, gffreader.orf_dictionary, contig, candidate_orf_pos, orf['id'])
else: # if it was not a hit then it is a hypothetical protein
#print gffreader.orf_dictionary
write_annotation_for_orf(outputgff_file, 'None', '0', results_dictionary, gffreader.orf_dictionary, contig, count, orf['id'])
count +=1 #move to the next orf
#del orf_dictionary[contig]
output_comp_annot_file1.close()
output_comp_annot_file2.close()
# now deal with the rRNA sequences if there is rRNA stats file
if len(rRNA_16S_stats_files) > 0 :
rRNA_16S_dictionary={}
for rRNA_16S_stats_file in rRNA_16S_stats_files:
process_rRNA_16S_stats(rRNA_16S_stats_file, rRNA_16S_dictionary)
rRNA_dictionary = {}
add_16S_genes(rRNA_16S_dictionary, rRNA_dictionary)
#print rRNA_dictionary
write_16S_tRNA_gene_info(rRNA_dictionary, outputgff_file, '_rRNA')
# now deal with the tRNA sequences if there is tRNA stats file
if len(tRNA_stats_files) > 0 :
tRNA_dictionary={}
for tRNA_stats_file in tRNA_stats_files:
process_tRNA_stats(tRNA_stats_file, tRNA_dictionary)
tRNA_gff_dictionary = {}
add_tRNA_genes(tRNA_dictionary, tRNA_gff_dictionary)
write_16S_tRNA_gene_info(tRNA_gff_dictionary, outputgff_file, '_tRNA')
#print tRNA_dictionary
outputgff_file.close()
rename(output_gff_tmp, output_gff)
def create_annotation(results_dictionary, annotated_gff, output_dir):
file = 'blastDB/ncbi_taxonomy_tree.txt'
lca = LCAComputation(file)
if not path.exists(output_dir):
makedirs(output_dir)
orf_dictionary = {}
#process_gff_file(annotated_gff, orf_dictionary)
gffreader = GffFileParser(annotated_gff)
output_table_file = open(
output_dir + '/functional_and_taxonomic_table.txt', 'w')
fprintf(output_table_file,
"id\tseqname\tstart\tend\tstrand\tec\ttaxonomy\tproduct\n")
count = 0
for contig in gffreader:
for orf in gffreader.orf_dictionary[contig]:
#print orf
if count % 10000 == 0:
# print "fandt " + str(count)
pass
species = []
if 'refseq' in results_dictionary:
if orf['id'] in results_dictionary['refseq']:
for hit in results_dictionary['refseq'][orf['id']]:
names = get_species(hit)
if names:
species.append(names)
#print species
#print '---------------------------'
taxonomy = lca.getTaxonomy(species)
fprintf(output_table_file, "%s", orf['id'])
fprintf(output_table_file, "\t%s", orf['seqname'])
fprintf(output_table_file, "\t%s", orf['start'])
fprintf(output_table_file, "\t%s", orf['end'])
fprintf(output_table_file, "\t%s", orf['strand'])
fprintf(output_table_file, "\t%s", orf['ec'])
#fprintf(output_table_file, "\t%s", str(species))
fprintf(output_table_file, "\t%s", taxonomy)
fprintf(output_table_file, "\t%s\n", orf['product'])
output_table_file.close()
def process_blastoutput(dbname, blastoutput, mapfile, refscore_file, opts):
blastparser = BlastOutputParser(dbname, blastoutput, mapfile,
refscore_file, opts)
fields = [
'q_length', 'bitscore', 'bsr', 'expect', 'aln_length', 'identity', 'ec'
]
if opts.taxonomy:
fields.append('taxonomy')
fields.append('product')
output_blastoutput_parsed = blastoutput + '.parsed.txt'
outputfile = open(output_blastoutput_parsed, 'w')
fprintf(outputfile, "#%s", 'query')
for field in fields:
fprintf(outputfile, "\t%s", field)
fprintf(outputfile, "\n")
for data in blastparser:
if not data:
continue
try:
fprintf(outputfile, "%s", data['query'])
except:
print data
sys.exit()
for field in fields:
fprintf(outputfile, "\t%s", data[field])
fprintf(outputfile, "\n")
outputfile.close()
# add_refscore_to_file(blastoutput,refscore_file, allNames)
return None
def main(argv):
(opts, args) = parser.parse_args()
if check_arguments(opts, args):
print usage
sys.exit(0)
input_fasta = opts.input_fasta
output_file = opts.output_file
blast_executable = opts.blast_executable
formatdb_executable = opts.formatdb_executable
algorithm = opts.algorithm
# input file to blast with itself to commpute refscore
infile = open(input_fasta, 'r')
#this file has the refscores of the entire file
outfile = open(output_file, 'w')
count = 0
allNames = dict()
for record in read_fasta_records(infile):
if count % SIZE == 0:
if count > 0:
seq_subset_file.close()
compute_refscores(formatdb_executable, blast_executable,
seq_subset_file, outfile, allNames,
algorithm)
# now remove the old file
if algorithm == 'BLAST':
remove_blast_index_files(seq_subset_file.name)
if algorithm == 'LAST':
remove_last_index_files(seq_subset_file.name)
remove(seq_subset_file.name)
seq_subset_file = open(
output_file + '.tmp.' + str(count) + '.fasta', 'w')
allNames[record.name.replace(">", "")] = False
fprintf(seq_subset_file, "%s\n", record.name)
fprintf(seq_subset_file, "%s\n", record.sequence)
count = count + 1
#print str(count) + " " + "going to blast last sequence "
if (count) % SIZE != 0:
#print str(count) + " " + "last sequence "
seq_subset_file.close()
compute_refscores(formatdb_executable, blast_executable,
seq_subset_file, outfile, allNames, algorithm)
remove(seq_subset_file.name)
if algorithm == 'BLAST':
remove_blast_index_files(seq_subset_file.name)
if algorithm == 'LAST':
remove_last_index_files(seq_subset_file.name)
#print count
for key in allNames:
if allNames[key] == False:
fprintf(outfile, "%s\t%s\n", key, 1000000)
outfile.close()
def process_blastoutput(dbname, blastoutput, mapfile, refscore_file, opts):
blastparser = BlastOutputParser(dbname, blastoutput, mapfile, refscore_file, opts)
fields = ['target','q_length', 'bitscore', 'bsr', 'expect', 'aln_length', 'identity', 'ec' ]
if opts.taxonomy:
fields.append('taxonomy')
fields.append('product')
output_blastoutput_parsed = blastoutput + '.parsed.txt'
# temporary file is used to deal with incomplete processing of the file
output_blastoutput_parsed_tmp = output_blastoutput_parsed + ".tmp"
outputfile = open(output_blastoutput_parsed_tmp, 'w')
# write the headers out
fprintf(outputfile, "#%s",'query')
for field in fields:
fprintf(outputfile,"\t%s",field)
fprintf(outputfile, "\n")
for data in blastparser:
if not data:
continue
try:
fprintf(outputfile, "%s",data['query'])
except:
print 'data is : ', data, '\n'
sys.exit()
for field in fields:
fprintf(outputfile, "\t%s",data[field])
fprintf(outputfile, "\n")
outputfile.close()
rename(output_blastoutput_parsed_tmp, output_blastoutput_parsed)
return None
def create_annotation(dbname_weight, results_dictionary, input_gff,
rRNA_16S_stats_files, tRNA_stats_files, output_gff,
output_comparative_annotation):
orf_dictionary = {}
# process_gff_file(input_gff, orf_dictionary)
gffreader = GffFileParser(input_gff)
outputgff_file = open(output_gff, 'w')
output_comp_annot_file1 = open(output_comparative_annotation + '.1.txt',
'w')
output_comp_annot_file2 = open(output_comparative_annotation + '.2.txt',
'w')
output_comp_annot_file1_Str = 'orf_id\tref dbname\tEC\tproduct\tvalue'
fprintf(output_comp_annot_file1, '%s\n', output_comp_annot_file1_Str)
output_comp_annot_file2_Str = 'orf_id'
dbnames = dbname_weight.keys()
for dbname in dbnames:
weight = dbname_weight[dbname]
output_comp_annot_file2_Str += '\t{0}(EC) \t{0}(product)\t{0}(value)'.format(
dbname)
fprintf(output_comp_annot_file2, '%s\n', output_comp_annot_file2_Str)
# gffreader = GffReader(input_gff)
for contig in gffreader:
count = 0
for orf in gffreader.orf_dictionary[contig]:
#print orf
value = 0.0001
success = False
output_comp_annot_file1_Str = ''
output_comp_annot_file2_Str = ''
for dbname in dbnames:
weight = dbname_weight[dbname]
value = 0
if orf['id'] in results_dictionary[dbname]:
if value < results_dictionary[dbname][orf['id']]['value']:
value = results_dictionary[dbname][orf['id']]['value']
candidatedbname = dbname
success = True
candidate_orf_pos = count
if output_comp_annot_file1_Str:
output_comp_annot_file1_Str += '{0}\t{1}\t{2}\t{3}\t{4}\n'.format('', dbname,\
results_dictionary[dbname][orf['id']]['ec'],\
results_dictionary[dbname][orf['id']]['product'],\
str(results_dictionary[dbname][orf['id']]['value']*float(weight)))
else:
output_comp_annot_file1_Str += '{0}\t{1}\t{2}\t{3}\t{4}\n'.format(orf['id'], dbname,\
results_dictionary[dbname][orf['id']]['ec'],\
results_dictionary[dbname][orf['id']]['product'],\
str(results_dictionary[dbname][orf['id']]['value']*float(weight)))
if output_comp_annot_file2_Str:
output_comp_annot_file2_Str += '\t{0}\t{1}\t{2}'.format(\
results_dictionary[dbname][orf['id']]['ec'],\
results_dictionary[dbname][orf['id']]['product'],\
str(results_dictionary[dbname][orf['id']]['value']*float(weight)))
else:
output_comp_annot_file2_Str += '{0}\t{1}\t{2}\t{3}'.format(orf['id'],
results_dictionary[dbname][orf['id']]['ec'],\
results_dictionary[dbname][orf['id']]['product'],\
str(results_dictionary[dbname][orf['id']]['value']*float(weight)))
else:
if not output_comp_annot_file1_Str:
output_comp_annot_file1_Str += '{0}\t{1}\t{2}\t{3}\t{4}\n'.format(
orf['id'], '', '', '', '')
if output_comp_annot_file2_Str:
output_comp_annot_file2_Str += '\t{0}\t{1}\t{2}'.format(
'', '', '')
else:
output_comp_annot_file2_Str += '{0}\t{1}\t{2}\t{3}'.format(
orf['id'], '', '', '', '')
if success: # there was a database hit
fprintf(output_comp_annot_file1, '%s\n',
output_comp_annot_file1_Str)
fprintf(output_comp_annot_file2, '%s\n',
output_comp_annot_file2_Str)
write_annotation_for_orf(outputgff_file, candidatedbname,
dbname_weight, results_dictionary,
gffreader.orf_dictionary, contig,
candidate_orf_pos, orf['id'])
else: # if it was not a hit then it is a hypothetical protein
#print gffreader.orf_dictionary
write_annotation_for_orf(outputgff_file, 'None', '0',
results_dictionary,
gffreader.orf_dictionary, contig,
count, orf['id'])
count += 1 #move to the next orf
#del orf_dictionary[contig]
output_comp_annot_file1.close()
output_comp_annot_file2.close()
# now deal with the rRNA sequences if there is rRNA stats file
if len(rRNA_16S_stats_files) > 0:
rRNA_16S_dictionary = {}
for rRNA_16S_stats_file in rRNA_16S_stats_files:
process_rRNA_16S_stats(rRNA_16S_stats_file, rRNA_16S_dictionary)
rRNA_dictionary = {}
add_16S_genes(rRNA_16S_dictionary, rRNA_dictionary)
#print rRNA_dictionary
write_16S_tRNA_gene_info(rRNA_dictionary, outputgff_file, '_rRNA')
# now deal with the tRNA sequences if there is tRNA stats file
if len(tRNA_stats_files) > 0:
tRNA_dictionary = {}
for tRNA_stats_file in tRNA_stats_files:
process_tRNA_stats(tRNA_stats_file, tRNA_dictionary)
tRNA_gff_dictionary = {}
add_tRNA_genes(tRNA_dictionary, tRNA_gff_dictionary)
write_16S_tRNA_gene_info(tRNA_gff_dictionary, outputgff_file, '_tRNA')
#print tRNA_dictionary
outputgff_file.close()
def main(argv):
global parser
(opts, args) = parser.parse_args(argv)
if check_arguments(opts, args):
print usage
sys.exit(0)
input_fasta = opts.input_fasta
output_file = opts.output_file
blast_executable = opts.blast_executable
formatdb_executable = opts.formatdb_executable
algorithm = opts.algorithm
# input file to blast with itself to commpute refscore
infile = open(input_fasta,'r')
#this file has the refscores of the entire file
outfile = open(output_file, 'w')
count = 0
allNames= dict()
for record in read_fasta_records(infile):
if count % SIZE == 0:
if count > 0:
seq_subset_file.close()
compute_refscores(formatdb_executable, blast_executable,seq_subset_file, outfile, allNames, algorithm);
# now remove the old file
if algorithm == 'BLAST' :
remove_blast_index_files(seq_subset_file.name)
if algorithm == 'LAST' :
remove_last_index_files(seq_subset_file.name)
remove(seq_subset_file.name)
seq_subset_file = open(output_file +'.tmp.'+ str(count) +'.fasta','w')
allNames[record.name.replace(">","")] = False;
fprintf(seq_subset_file, "%s\n", record.name)
fprintf(seq_subset_file, "%s\n", record.sequence)
count = count + 1
#print str(count) + " " + "going to blast last sequence "
if (count) % SIZE != 0:
#print str(count) + " " + "last sequence "
seq_subset_file.close()
compute_refscores(formatdb_executable, blast_executable,seq_subset_file, outfile, allNames, algorithm);
remove(seq_subset_file.name)
if algorithm == 'BLAST' :
remove_blast_index_files(seq_subset_file.name)
if algorithm == 'LAST' :
remove_last_index_files(seq_subset_file.name)
#print count
for key in allNames:
if allNames[key] ==False:
fprintf(outfile, "%s\t%s\n",key, 1000000)
outfile.close()
def create_annotation(results_dictionary, annotated_gff, output_dir, ncbi_taxonomy_tree_file):
lca = LCAComputation(ncbi_taxonomy_tree_file)
if not path.exists(output_dir):
makedirs(output_dir)
orf_dictionary={}
#process_gff_file(annotated_gff, orf_dictionary)
gffreader = GffFileParser(annotated_gff)
output_table_file = open(output_dir + '/functional_and_taxonomic_table.txt', 'w')
fprintf(output_table_file, "ORF_ID\tORF_length\tstart\tend\tContig_Name\tContig_length\tstrand\tec\ttaxonomy\tproduct\n")
meganTree = MeganTree(lca)
count = 0
for contig in gffreader:
for orf in gffreader.orf_dictionary[contig]:
if count%10000==0 :
# print "fandt " + str(count)
pass
species = []
if 'refseq' in results_dictionary:
if orf['id'] in results_dictionary['refseq']:
for hit in results_dictionary['refseq'][orf['id']]:
names = get_species(hit)
if names:
species.append(names)
#print species
#print '---------------------------'
taxonomy=lca.getTaxonomy(species)
fprintf(output_table_file, "%s", orf['id'])
fprintf(output_table_file, "\t%s", orf['orf_length'])
fprintf(output_table_file, "\t%s", orf['start'])
fprintf(output_table_file, "\t%s", orf['end'])
fprintf(output_table_file, "\t%s", orf['seqname'])
fprintf(output_table_file, "\t%s", orf['contig_length'])
fprintf(output_table_file, "\t%s", orf['strand'])
fprintf(output_table_file, "\t%s", orf['ec'])
#fprintf(output_table_file, "\t%s", str(species))
fprintf(output_table_file, "\t%s", taxonomy)
fprintf(output_table_file, "\t%s\n", orf['product'])
meganTree.insertTaxon(taxonomy)
#print meganTree.getChildToParentMap()
output_table_file.close()
#print meganTree.getChildToParentMap()
# print meganTree.getParentToChildrenMap()
megan_tree_file = open(output_dir + '/megan_tree.tre', 'w')
fprintf(megan_tree_file, "%s;", meganTree.printTree('1'))
megan_tree_file.close()