filtering.py

import re # for Regular expressions
import sys
from Bio import AlignIO

#infile=sys.argv[1]

infile = 'all.prunned.list'

with open(infile) as f:
    reflist = f.read().splitlines() 



f.close()
missing = '[(+*)]'
ambiguous = '[N]'


badsimiosNs = []
badsimiosAsk = []
goodsimios = []

for i in reflist:
	myfile= open(i, 'r')
	mydata = myfile.read()
	fasta = AlignIO.read(i, "fasta")
	myfile.close()
	if fasta.get_alignment_length() > 350 : 
		maxNs = len(re.findall(ambiguous, str(mydata), re.I))
		maxAsk = len(re.findall(missing, str(mydata), re.I))
		if maxNs > 2:
			print ')-B'
			badsimiosNs.append(i)
		elif maxAsk > 1:
			print ')-;'
			badsimiosAsk.append(i)
		else:
			print 'lol'
			goodsimios.append(i)
		




thefile3 = open('goodalignments.txt', 'w')
for item in goodsimios:
  thefile3.write("%s\n" % item)





thefile3.close()





thefile1 = open('ambiguous.txt', 'w')
for item in badsimiosNs:
  thefile1.write("%s\n" % item)




thefile1.close()

thefile2 = open('asterisks.txt', 'w')
for item in badsimiosAsk:
  thefile2.write("%s\n" % item)





thefile2.close()


######### Run this python script