AAIndex.py

'''
This module is used for obtaining the properties of amino acids or their pairs

from the aaindex database. You can freely use and distribute it. If you hava 

any problem, you could contact with us timely!

Authors: Dongsheng Cao and Yizeng Liang.

Date: 2012.09.10

Email: oriental-cds@163.com
 
'''
from Scripts.filterPeptides import getFilteredList
import sys, os, string

AALetter=["A","R","N","D","C","E","Q","G","H","I","L","K","M","F","P","S","T","W","Y","V"]
_aaindex = dict()

#####################################################################################################
class Record:
	'''
	Amino acid index (AAindex) Record
	'''
	aakeys = 'ARNDCQEGHILKMFPSTWYV'
	def __init__(self):
		self.key = None
		self.desc = ''
		self.ref = ''
		self.authors = ''
		self.title = ''
		self.journal = ''
		self.correlated = dict()
		self.index = dict()
		self.comment = ''
	def extend(self, row):
		i = len(self.index)
		for x in row:
			self.index[self.aakeys[i]] = x
			i += 1
	def get(self, aai, aaj=None, d=None):
		assert aaj is None
		return self.index.get(aai, d)
	def __getitem__(self, aai):
		return self.get(aai)
	def median(self):
		x = sorted(filter(None, self.index.values()))
		half = len(x)/2
		if len(x) % 2 == 1:
			return x[half]
		return (x[half-1] + x[half])/2.0
	def __str__(self):
		desc = self.desc.replace('\n', ' ').strip()
		return '%s(%s: %s)' % (self.__class__.__name__, self.key, desc)
		
#####################################################################################################
class MatrixRecord(Record):
	'''
	Matrix record for mutation matrices or pair-wise contact potentials
	'''
	def __init__(self):
		Record.__init__(self)
		self.index = []
		self.rows = dict()
		self.cols = dict()
	def extend(self, row):
		self.index.append(row)
	def _get(self, aai, aaj):
		i = self.rows[aai]
		j = self.cols[aaj]
		return self.index[i][j]
	def get(self, aai, aaj, d=None):
		try:
			return self._get(aai, aaj)
		except:
			pass
		try:
			return self._get(aaj, aai)
		except:
			return d
	def __getitem__(self, aaij):
		return self.get(aaij[0], aaij[1])
	def median(self):
		x = []
		for y in self.index:
			x.extend(filter(None, y))
		x.sort()
		if len(x) % 2 == 1:
			return x[len(x)/2]
		return sum(x[len(x)/2-1:len(x)/2+1])/2.0
#####################################################################################################
def search(pattern, searchtitle=True, casesensitive=False):
	'''
	Search for pattern in description and title (optional) of all records and
	return matched records as list. By default search case insensitive.
	'''
	whatcase = lambda i: i
	if not casesensitive:
		pattern = pattern.lower()
		whatcase = lambda i: i.lower()
	matches = []
	for record in _aaindex.itervalues():
		if pattern in whatcase(record.desc) or searchtitle and pattern in whatcase(record.title):
			matches.append(record)
	return matches

#####################################################################################################
def grep(pattern):
	'''
	Search for pattern in title and description of all records (case
	insensitive) and print results on standard output.

	'''
	for record in search(pattern):
		print(record)
#####################################################################################################
def get(key):
	'''
	Get record for key
	'''
	if len(_aaindex) == 0:
		init()
	return _aaindex[key]

def getAllIndexes():
	return _aaindex.keys()

#####################################################################################################
def _float_or_None(x):
	if x == 'NA' or x == '-':
		return None
	return float(x)

#####################################################################################################
def init(path=None, index='123'):
	'''
	Read in the aaindex files. You need to run this (once) before you can
	access any records. If the files are not within the current directory,
	you need to specify the correct directory path. By default all three
	aaindex files are read in.
	'''
	index = "1"
	if path is None:
		for path in [os.path.split(__file__)[0], '.']:
			if os.path.exists(os.path.join(path, 'aaindex' + index[0])):
				break
		print(sys.stderr, 'path =', path)
	if '1' in index:
		_parse(path + '/aaindex1', Record)
	if '2' in index:
		_parse(path + '/aaindex2', MatrixRecord)
	if '3' in index:
		_parse(path + '/aaindex3', MatrixRecord)
#####################################################################################################
def init_from_file(filename, type=Record):
	_parse(filename, type)
#####################################################################################################
def _parse(filename, rec, quiet=True):
	print(filename)
	'''
	Parse aaindex input file. `rec` must be `Record` for aaindex1 and
	`MarixRecord` for aaindex2 and aaindex3.
	'''
	if not os.path.exists(filename):
		#import urllib
		#url = 'ftp://ftp.genome.jp/pub/db/community/aaindex/' + os.path.split(filename)[1]
#		#print 'Downloading "%s"' % (url)
		filename = "./aaindex/" + filename
#		#print 'Saved to "%s"' % (filename)
	f = open(filename)

	current = rec()
	lastkey = None
	for line in f:
		key = line[0:2]
		if key[0] == ' ':
			key = lastkey
		if key == '//':
			_aaindex[current.key] = current
			current = rec()
		elif key == 'H ':
			current.key = line[2:].strip()
		elif key == 'R ':
			current.ref += line[2:]
		elif key == 'D ':
			current.desc += line[2:]
		elif key == 'A ':
			current.authors += line[2:]
		elif key == 'T ':
			current.title += line[2:]
		elif key == 'J ':
			current.journal += line[2:]
		elif key == '* ':
			current.comment += line[2:]
		elif key == 'C ':
			a = line[2:].split()
			for i in range(0, len(a), 2):
				current.correlated[a[i]] = float(a[i+1])
		elif key == 'I ':
			a = line[1:].split()
			if a[0] != 'A/L':
				current.extend(map(_float_or_None, a))
			elif list(Record.aakeys) != [i[0] for i in a] + [i[-1] for i in a]:
				print('Warning: wrong amino acid sequence for', current.key)
			else:
				try:
					assert list(Record.aakeys[:10]) == [i[0] for i in a]
					assert list(Record.aakeys[10:]) == [i[2] for i in a]
				except:
					print('Warning: wrong amino acid sequence for', current.key)
		elif key =='M ':
			a = line[2:].split()
			if a[0] == 'rows':
				if a[4] == 'rows':
					a.pop(4)
				assert a[3] == 'cols' and len(a) == 6
				i = 0
				for aa in a[2]:
					current.rows[aa] = i
					i += 1
				i = 0
				for aa in a[5]:
					current.cols[aa] = i
					i += 1
			else:
				current.extend(map(_float_or_None, a))
		elif not quiet:
			print('Warning: line starts with "%s"' % (key))
		lastkey = key
	f.close()
#####################################################################################################
def getWDoutfile(filename):
	wd = r"D:\PycharmProjects\Secretome\Data"
	return wd + "\\" + filename

def GetAAIndex1(name,path='.'):
	"""
	Get the amino acid property values from aaindex1
	
	Usage:
	
	result=GetAAIndex1(name)
	
	Input: name is the name of amino acid property (e.g., KRIW790103)
	
	Output: result is a dict form containing the properties of 20 amino acids
	"""

	init(path=path)
	name=str(name)
	print(name)
	temp=get(name)
	res={}
	for i in AALetter:
		res[i]=temp.get(i)
	return res

#####################################################################################################
def GetAAIndex23(name,path='.'):
	"""
	Get the amino acid property values from aaindex2 and aaindex3
	
	Usage:
	
	result=GetAAIndex23(name)
	
	Input: name is the name of amino acid property (e.g.,TANS760101,GRAR740104)
	
	Output: result is a dict form containing the properties of 400 amino acid pairs
	"""
	init(path=path)
	name=str(name)
	temp=get(name)
	res={}
	for i in AALetter:
		for j in AALetter:
			res[i+j]=temp.get(i,j)
	return res
#####################################################################################################
from Bio import SeqIO
temp1=GetAAIndex1('KRIW790103')
def mean(numbers):
	numbers2 = numbers
	if None in numbers:
		numbers2 = [i for i in numbers2 if i != None]
	return float(sum(numbers2)) / max(len(numbers2), 1)
def parseFasta(fastaFile):
	whiteList = getFilteredList()
	with open(fastaFile.split(".fa")[0] +  ".aaindexestab", "w") as outTab:
		outTab.write("Sequence id" + "\t" + "\t".join(getAllIndexes()) + "\t" + "Sequence" +"\n")
		for seq in SeqIO.parse(fastaFile, "fasta"):
			if seq.seq in whiteList:
				outTab.write(seq.id)
				#print(seq.id)
				for indexes in _aaindex:
					#print(indexes)
					values = []
					for aa in str(seq.seq):
						values.append(_aaindex[indexes][aa])
					mv = mean(values)

					outTab.write("\t" + str(mv))
				outTab.write("\t" + str(seq.seq) + "\n")



parseFasta(getWDoutfile("fastaSets/Secretome_pep.txtMeJa.fasta"))
# parseFasta(getWDoutfile("Secretome_pep.txtMeJa.fasta"))
#	init(path='.')

#	grep('volume')
#	x = get('KRIW790103')
#	print x
#	print x.get('W')
"""
for i in _aaindex:
	print(i, _aaindex.get(i))
	for i2 in _aaindex.get(i).index:
		print(list(i2))
print(len(_aaindex))

"""