annotate smart_toolShed/commons/core/parsing/FastaParser.py @ 0:e0f8dcca02ed

Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

#
# Copyright INRA-URGI 2009-2010
# 
# This software is governed by the CeCILL license under French law and
# abiding by the rules of distribution of free software. You can use,
# modify and/ or redistribute the software under the terms of the CeCILL
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# "http://www.cecill.info".
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import sys
from commons.core.parsing.SequenceListParser import SequenceListParser
from SMART.Java.Python.structure.Sequence import Sequence
from SMART.Java.Python.misc.UnlimitedProgress import UnlimitedProgress

class FastaParser(SequenceListParser):
	"""A class that reads a list of sequences in FASTA"""

	def __init__(self, fileName, verbosity = 0):
		super(FastaParser, self).__init__(fileName, verbosity)
		self.tags = {}
		
		
	def getTags(self):
		return self.tags


	def getFileFormats():
		return ["fasta", "mfa", "fas"]
	getFileFormats = staticmethod(getFileFormats)


	def getInfos(self):
		"""
		Get some generic information about the sequences
		"""
		self.nbSequences = 0
		self.size		= 0
		self.reset()
		progress = UnlimitedProgress(100000, "Reading input file", self.verbosity - 9)
		for line in self.handle:
			line = line.strip()
			if line == "":
				continue
			if line[0] == ">":
				self.nbSequences += 1
			else:
				self.size += len(line)
			progress.inc()
		progress.done()
		self.reset()


	def parseOne(self):
		"""
		Parse only one element in the file
		"""
		name	 = None
		string = ""

		if self.currentLine != None:
			if self.currentLine[0] != ">":
				raise Exception("First line is weird: %s" % (self.currentLine))
			name = self.currentLine[1:].split()[0]
			self.currentLine = None

		for line in self.handle:
			line = line.strip()
			if line == "":
				pass
			elif line[0] == ">":
				if name == None:
					name = line[1:].split()[0]
				else:
					self.currentLine = line
					return Sequence(name, string)
			else:
				string += line

		if name == None:
			return None
		return Sequence(name, string)
	
	
	def setTags(self):
		mark	= self.handle.tell()
		thisTag = mark
		
		line = self.handle.readline()
		while line != "":
			if line[0] == ">":
				line = line.strip()
				self.tags[line[1:].split()[0]] = thisTag
			thisTag = self.handle.tell()
			line = self.handle.readline()
			
		self.handle.seek(mark)
		

	def getSubSequence(self, chromosome, start, end, direction, name = None):
		if not self.tags:
			self.setTags()

		if chromosome not in self.tags:
			raise Exception("Cannot find " + chromosome)
			
		if name == None:
			name = "%s:%d-%d (%d)" % (chromosome, start, end, direction)
		sequence = Sequence(name)

		# switch from 0-based to 1-based coordinates
		start -= 1
		end   -= 1
		
		self.handle.seek(self.tags[chromosome])
		line = self.handle.readline().strip()
		if line != ">" + chromosome:
			raise Exception("Arrived in a wrong place (got %s)" % (line))
			
		position1 = self.handle.tell()
		line	  = self.handle.readline().strip()
		position2 = self.handle.tell()
		size	  = len(line)
		address   = position1 + ((start - (start % size)) / size) * (position2 - position1);

		count	 = max(0, start - (start % size));
		self.handle.seek(address)

		newSequence = ""
		for line in self.handle:
			line = line.strip()

			if line[0] == ">":
				break
			
			subStart = start - count
			if subStart < 0:
				subStart = 0
			subEnd  = end - count
			subSize = subEnd - subStart + 1
			if subSize + subStart > len(line):
				subSize = len(line) - subStart
			if subEnd < 0:
				break
			if subStart <= len(line):
				newSequence += line[subStart:subStart+subSize]
			count += len(line)

		if newSequence == "":
			raise Exception("Error, sequence %s is empty" % (name))
		sequence.sequence = newSequence
		if direction == -1:
			sequence.reverseComplement()
		return sequence