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nextorf.py

#!/usr/bin/env python
# Created: Thu Feb 15 14:22:12 2001
# Last changed: Time-stamp: <01/02/18 11:16:42 thomas>
# Copyright 2000 by Thomas Sicheritz-Ponten.  All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license.  Please see the LICENSE file that should have been included
# as part of this package.
# Authors: Thomas Sicheritz-Ponten and Jan O. Andersson
# thomas@cbs.dtu.dk, http://www.cbs.dtu.dk/thomas
# Jan.O.Andersson@home.se
# File: nextorf.py

import re
import os, sys, commands
import getopt

from Bio import SeqIO
from Bio.Seq import Seq
from Bio import Alphabet
from Bio.Alphabet import IUPAC
from Bio.Data import IUPACData, CodonTable

class ProteinX(Alphabet.ProteinAlphabet):
   letters = IUPACData.extended_protein_letters + "X"

proteinX = ProteinX()

class MissingTable:
  def __init__(self, table):
    self._table = table
  def get(self, codon, stop_symbol):
    try:
      return self._table.get(codon, stop_symbol)
    except CodonTable.TranslationError:
      return 'X'

# Make the codon table given an existing table
def makeTableX(table):
  assert table.protein_alphabet == IUPAC.extended_protein
  return CodonTable.CodonTable(table.nucleotide_alphabet, proteinX,
                               MissingTable(table.forward_table),
                               table.back_table, table.start_codons,
                               table.stop_codons)



class NextOrf:
    def __init__(self, file, options):
        self.options = options
        self.file = file
        self.genetic_code = int(self.options['table'])
        self.table = makeTableX(CodonTable.ambiguous_dna_by_id[self.genetic_code])
        self.counter = 0
        self.ReadFile()
        
    def ReadFile(self):
        handle = open(self.file)
        for record in SeqIO.parse(handle, "fasta"):
            self.header = record.id
            frame_coordinates = ''
            dir = self.options['strand']
            plus = dir in ['both', 'plus']
            minus = dir in ['both', 'minus']
            start, stop = int(self.options['start']), int(self.options['stop'])
            s = str(record.seq).upper()
            if stop > 0:
               s = s[start:stop]
            else:
               s = s[start:]
            self.seq = Seq(s,IUPAC.ambiguous_dna)
            self.length = len(self.seq)
            self.rseq = None
            CDS = []
            if plus:
                CDS.extend(self.GetCDS(self.seq))
            if minus:
                self.rseq = self.seq.reverse_complement()
                CDS.extend(self.GetCDS(self.rseq, strand = -1))
            self.Output(CDS)

    def ToFasta(self, header, seq):
       seq = re.sub('(............................................................)','\\1\n',seq)
       return '>%s\n%s' % (header, seq)

    def Gc(self, seq):
       d = {}
       for nt in 'ATGC':
          d[nt] = seq.count(nt)
       gc = d['G'] + d['C']
       if gc == 0: return 0
       return round(gc*100.0/(d['A'] +d['T'] + gc),1)

    def Gc2(self,seq):
       l = len(seq)
       d= {}
       for nt in ['A','T','G','C']:
          d[nt] = [0,0,0]
          
       for i in range(0,l,3):
          codon = seq[i:i+3]
          if len(codon) <3: codon = codon + '  '
          for pos in range(0,3):
             for nt in ['A','T','G','C']:
                if codon[pos] == nt: d[nt][pos] = d[nt][pos] +1

       gc = {}
       gcall = 0
       nall = 0
       for i in range(0,3):
          try:
             n = d['G'][i] + d['C'][i] +d['T'][i] + d['A'][i]
             gc[i] = (d['G'][i] + d['C'][i])*100.0/n
          except:
             gc[i] = 0

          gcall = gcall + d['G'][i] + d['C'][i]
          nall = nall + n

       gcall = 100.0*gcall/nall
       res = '%.1f%%, %.1f%%, %.1f%%, %.1f%%' % (gcall, gc[0], gc[1], gc[2])
       return res

    def GetOrfCoordinates(self, seq):
        s = seq.data
        letters = []
        table = self.table
        get = self.table.forward_table.get
        n = len(seq)
        start_codons = self.table.start_codons
        stop_codons = self.table.stop_codons
#        print 'Start codons', start_codons
#        print 'Stop codons', stop_codons
        frame_coordinates = []
        for frame in range(0,3):
            coordinates = []
            for i in range(0+frame, n-n%3, 3):
                codon = s[i:i+3]
                if codon in start_codons: coordinates.append((i+1,1,codon))
                elif codon in stop_codons: coordinates.append((i+1,0,codon))
            frame_coordinates.append(coordinates)
        return frame_coordinates

    def GetCDS(self, seq, strand = 1):
        frame_coordinates = self.GetOrfCoordinates(seq)
        START, STOP = 1,0
        so = self.options
        nostart = so['nostart']
        minlength, maxlength = int(so['minlength']), int(so['maxlength'])
        CDS = []
        f = 0
        for frame in frame_coordinates:
            f+=1
            start_site = 0
            if nostart == '1': start_site = 1
            frame.append((self.length, 0, 'XXX'))
            for pos, codon_type, codon in frame:
                if codon_type == START:
                    if start_site == 0: start_site = pos
                elif codon_type == STOP:
                    if start_site == 0: continue
#                    if codon == 'XXX': print 'do something'
                    stop = pos + 2
#                    print stop
                    length = stop - start_site +1
                    if length >= minlength and length <= maxlength:
                        if nostart == '1' and start_site == 1:
                           start_site = start_site + f - 1
                        if codon == 'XXX': stop = start_site + 3*((int((stop-1)-start_site)/3))
                        s = seq[start_site -1 : stop]
                        CDS.append((start_site, stop, length, s, strand*f))
                        start_site = 0
                        if nostart == '1': start_site = stop + 1
                    elif length < minlength or length > maxlength:
                       start_site = 0
                       if nostart == '1': start_site = stop + 1
                    del stop   
        return CDS

    def Output(self, CDS):
        out = self.options['output']
        seqs = (self.seq, self.rseq)
        n = len(self.seq)
        for start, stop, length, subs, strand in CDS:
            self.counter += 1
            if strand > 0: head = 'orf_%s:%s:%d:%d:%d' % (self.counter, self.header, strand, start,stop)
            if strand < 0: head = 'orf_%s:%s:%d:%d:%d' % (self.counter, self.header, strand, n-stop+1,n-start+1)
            if self.options['gc']:
                head = '%s:%s' % (head, self.Gc2(subs.data))
                
            if out == 'aa':
                orf = subs.translate(table=self.genetic_code)
                print self.ToFasta(head, orf.data)
            elif out == 'nt':
                print self.ToFasta(head, subs.data)
            elif out == 'pos':
                print head
                
        
    
def help():
    global options
    print 'Usage:', sys.argv[0], '(<options>) <FASTA file>'
    
    print 'Options:                                                       default'
    print '--start       Start position in sequence                             0'
    print '--stop        Stop position in sequence            (end of seqence)'
    print '--minlength   Minimum length of orf in bp                          100'
    print '--maxlength   Maximum length of orf in bp, default           100000000'
    print '--strand      Strand to analyse [both, plus, minus]               both'
    print '--frame       Frame to analyse [1 2 3]                             all'
    print '--noframe     Ignore start codons [0 1]                              0'  
    print '--output      Output to generate [aa nt pos]                        aa'
    print '--gc          Creates GC statistics of ORF [0 1]                     0'
    print '--table       Genetic code to use (see below)                        1'
    
#    for a,b in options.items(): print '\t', a,b
#    print ''
    print "\nNCBI's Codon Tables:"
    for key, table in CodonTable.ambiguous_dna_by_id.items():
        print '\t',key, table._codon_table.names[0]
    print '\ne.g.\n./nextorf.py --minlength 5 --strand plus --output nt --gc 1 testjan.fas'
    sys.exit(0)
    

options = {
    'start': 0,
    'stop': 0,
    'minlength': 100,
    'maxlength': 100000000,
    'strand': 'both',
    'output': 'aa',
    'frames': [1,2,3],
    'gc': 0,
    'nostart': 0,
    'table': 1,
    }

if __name__ == '__main__':
    args = sys.argv[1:]
    show_help = len(sys.argv)<=1

    shorts = 'hv'
    longs = map(lambda x: x +'=', options.keys()) + ['help']

    optlist, args = getopt.getopt(args,shorts, longs)
    if show_help: help()

    for arg in optlist:
        if arg[0] == '-h' or arg[0] == '--help':
            help()
            sys.exit(0)
        for key in options.keys():
            if arg[1].lower() == 'no': arg[1] = 0
            elif arg[1].lower() == 'yes': arg[1] = 1
            if arg[0][2:] == key: options[key] = arg[1]
            
        if arg[0] == '-v':print 'OPTIONS', options

    file = args[0]
    nextorf = NextOrf(file, options)

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