hits

gistfile1.py

import MetagenomeDB as mdb

names = ['check1', 'check2', 'check3']
def run():
	
	c = mdb.Collection.find_one({"name": "NL10_1002_vRNA:contigs-strict"})
	output=[]
	for sequence in c.list_sequences():
		if (not "alignments" in sequence):
			continue
		for hit in sequence["alignments"]:
			checks= [
				("rdrp" in hit["hit"]["description"].lower()) and ("blastx" in hit["run"]["algorithm"]["name"].lower()),
				("virus" in hit["hit"]["description"].lower()) and ("blastx" in hit["run"]["algorithm"]["name"].lower()) and 0.02 > (hit["score"]["e_value"]),
				("rdrp" in hit["hit"]["description"].lower()) and ("rpstblastn" in hit["run"]["algorithm"]["name"].lower())
			]
			names = ['check1', 'check2', 'check3']
			l=[names[v] for v in range(0,3) if checks[v]]
			m=[names[x] for x in range(0,3) if checks[x] else '']
			score=len(l)
			if score>0:
				output.append({
					'name': sequence.get_property("name"),
					'score': score,
					'checks_passed': ' '.join(l),
					'e_value': hit["score"]["e_value"],
					'checks_as_list': m
				})
	return output

items = run()

print len(item)

output=[]
for item in items:
	output.append(item['name'])
	output.append(':')
	output.append(str(item['score']))
	output.append(':')
	output.append(str(item['e_value']))
	output.append(':')
	output.append(':'.join(item['checks_as_list']))
	output.append("\n")

print ''.join(output)

import MetagenomeDB as mdb
c = mdb.Collection.find_one({"name": "NL10_1006_vRNA:contigs-strict"})
for sequence in c.list_sequences():
if (not "alignments" in sequence):
continue
for hit in sequence["alignments"]:
if ("rdrp" in hit["hit"]["description"].lower()) and ("blastx" in hit["run"]["algorithm"]["name"].lower()):
print "RdRp hit in BlastX " + sequence.get_property("name") + " " + str(hit["score"]["e_value"])
if ("virus" in hit["hit"]["description"].lower()) and ("blastx" in hit["run"]["algorithm"]["name"].lower()) and 0.02 > (hit["score"]["e_value"]):
print "Significant BlastX Virus Hit " + sequence.get_property("name") + " " + str(hit["score"]["e_value"])
if ("rdrp" in hit["hit"]["description"].lower()) and ("rpstblastn" in hit["run"]["algorithm"]["name"].lower()):
print "Conserved Domain RdRp Hit " + sequence.get_property("name") + " " + str(hit["score"]["e_value"])

from cStringIO import StringIO

def Score(l):
return len([item for item in l if item])

import MetagenomeDB as mdb
c = mdb.Collection.find_one({"name": "NL10_1006_vRNA:contigs-strict"})
output=[]
for sequence in c.list_sequences():
if (not "alignments" in sequence):
continue
for hit in sequence["alignments"]:
checks=[("rdrp" in hit["hit"]["description"].lower()) and ("blastx" in hit["run"]["algorithm"]["name"].lower()),
("virus" in hit["hit"]["description"].lower()) and ("blastx" in hit["run"]["algorithm"]["name"].lower()) and 0.02 > (hit["score"]["e_value"]),
("rdrp" in hit["hit"]["description"].lower()) and ("rpstblastn" in hit["run"]["algorithm"]["name"].lower())]
if Score(checks)>1:
output.append('')
print ''.join(output)

http://bitbucket.org/Bill_Barry/hgattic/src/c4f70f7f6ea7/attic.py