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__init__.py

#!/usr/bin/env python
# Created: Wed May 29 08:07:18 2002
# thomas@cbs.dtu.dk, Cecilia.Alsmark@ebc.uu.se
# Copyright 2001 by Thomas Sicheritz-Ponten and Cecilia Alsmark.
# 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.

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


######################################
# DNA
######################
# {{{ 

def reverse(seq):
   """Reverse the sequence. Works on string sequences.
   """
   r = map(None, seq)
   r.reverse()
   return ''.join(r)

def GC(seq):
   """ calculates G+C content """
#      19/8/03: Iddo: added provision for lowercase
#      19/8/03: Iddo: divide by the sequence's length rather than by the
#      A+T+G+C number. In that way, make provision for N.
       
   d = {}
   for nt in ['A','T','G','C','a','t','g','c','S','s']:
      d[nt] = seq.count(nt)
      gc = d.get('G',0) + d.get('C',0) + d.get('g',0) + d.get('c',0) + \
           d.get('S',0) + d.get('s',0)

   if gc == 0: return 0
#   return gc*100.0/(d['A'] +d['T'] + gc)
   return gc*100.0/len(seq)
    
def GC123(seq):
   " calculates total G+C content plus first, second and third position "

   d= {}
   for nt in ['A','T','G','C']:
      d[nt] = [0,0,0]

   for i in range(0,len(seq),3):
      codon = seq[i:i+3]
      if len(codon) <3: codon += '  '
      for pos in range(0,3):
         for nt in ['A','T','G','C']:
            if codon[pos] == nt or codon[pos] == nt.lower():
                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
   return gcall, gc[0], gc[1], gc[2]

def GC_skew(seq, window = 100):
   """ calculates GC skew (G-C)/(G+C) """
      # 8/19/03: Iddo: added lowercase 
   values = []
   for i in range(0, len(seq), window):
      s = seq[i: i + window]
      g = s.count('G') + s.count('g')
      c = s.count('C') + s.count('c')
      skew = (g-c)/float(g+c)
      values.append(skew)
   return values

# 8/19/03 Iddo: moved these imports from within the function as
# ``import * '' is only
# allowed within the module
# Brad -- added an import check so you don't have to have Tkinter
# installed to use other sequtils functions. A little ugly but
# it really should be fixed by not using 'import *' which I'm not
# really excited about doing right now.
try:
    from Tkinter import *
except ImportError:
    pass
from math import pi, sin, cos, log
def xGC_skew(seq, window = 1000, zoom = 100,
                         r = 300, px = 100, py = 100):
   " calculates and plots normal and accumulated GC skew (GRAPHICS !!!) "
   

   yscroll = Scrollbar(orient = VERTICAL)
   xscroll = Scrollbar(orient = HORIZONTAL)
   canvas = Canvas(yscrollcommand = yscroll.set,
                   xscrollcommand = xscroll.set, background = 'white')
   win = canvas.winfo_toplevel()
   win.geometry('700x700')
   
   yscroll.config(command = canvas.yview)
   xscroll.config(command = canvas.xview)
   yscroll.pack(side = RIGHT, fill = Y)
   xscroll.pack(side = BOTTOM, fill = X)
   canvas.pack(fill=BOTH, side = LEFT, expand = 1)
   canvas.update()

   X0, Y0  = r + px, r + py
   x1, x2, y1, y2 = X0 - r, X0 + r, Y0 -r, Y0 + r
   
   ty = Y0
   canvas.create_text(X0, ty, text = '%s...%s (%d nt)' % (seq[:7], seq[-7:], len(seq)))
   ty +=20
   canvas.create_text(X0, ty, text = 'GC %3.2f%%' % (GC(seq)))
   ty +=20
   canvas.create_text(X0, ty, text = 'GC Skew', fill = 'blue')
   ty +=20
   canvas.create_text(X0, ty, text = 'Accumulated GC Skew', fill = 'magenta')
   ty +=20
   canvas.create_oval(x1,y1, x2, y2)

   acc = 0
   start = 0
   for gc in GC_skew(seq, window):
      r1 = r
      acc+=gc
      # GC skew
      alpha = pi - (2*pi*start)/len(seq)
      r2 = r1 - gc*zoom
      x1 = X0 + r1 * sin(alpha)
      y1 = Y0 + r1 * cos(alpha)
      x2 = X0 + r2 * sin(alpha)
      y2 = Y0 + r2 * cos(alpha)
      canvas.create_line(x1,y1,x2,y2, fill = 'blue')
      # accumulated GC skew
      r1 = r - 50
      r2 = r1 - acc
      x1 = X0 + r1 * sin(alpha)
      y1 = Y0 + r1 * cos(alpha)
      x2 = X0 + r2 * sin(alpha)
      y2 = Y0 + r2 * cos(alpha)
      canvas.create_line(x1,y1,x2,y2, fill = 'magenta')

      canvas.update()
      start = start + window
      

   canvas.configure(scrollregion = canvas.bbox(ALL))

def molecular_weight(seq):
   if type(seq) == type(''): seq = Seq(seq, IUPAC.unambiguous_dna)
   weight_table = IUPACData.unambiguous_dna_weights
   sum = 0
   for x in seq:
      sum += weight_table[x]
   return sum

def nt_search(seq, subseq):
   """ search for a DNA subseq in sequence
       use ambiguous values (like N = A or T or C or G, R = A or G etc.)
       searches only on forward strand
   """
   pattern = ''
   for nt in subseq:
      value = IUPACData.ambiguous_dna_values[nt]
      if len(value) == 1:
         pattern += value
      else:
         pattern += '[%s]' % value

   pos = -1
   result = [pattern]
   l = len(seq)
   while 1:
      pos+=1
      s = seq[pos:]
      m = re.search(pattern, s)
      if not m: break
      pos += int(m.start(0))
      result.append(pos)

   return result

# }}}
   
######################################
# Protein
######################
# {{{ 

# temporary hack for exception free translation of "dirty" DNA
# should be moved to ???

00208 class ProteinX(Alphabet.ProteinAlphabet):
   letters = IUPACData.extended_protein_letters + "X"

proteinX = ProteinX()

00213 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'

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)


# end of hacks

def seq3(seq):
   """
   Method that returns the amino acid sequence as a
   list of three letter codes. Output follows the IUPAC standard plus 'Ter' for
   terminator. Any unknown character, including the default
   unknown character 'X', is changed into 'Xaa'. A noncoded
   aminoacid selenocystein is recognized (Sel, U).
   """
   threecode = {'A':'Ala', 'B':'Asx', 'C':'Cys', 'D':'Asp',
                'E':'Glu', 'F':'Phe', 'G':'Gly', 'H':'His',
                'I':'Ile', 'K':'Lys', 'L':'Leu', 'M':'Met',
                'N':'Asn', 'P':'Pro', 'Q':'Gln', 'R':'Arg',
                'S':'Ser', 'T':'Thr', 'V':'Val', 'W':'Trp',
                'Y':'Tyr', 'Z':'Glx', 'X':'Xaa', '*':'Ter',
                'U':'Sel'
                }

   return ''.join([threecode.get(aa,'Xer') for aa in seq])


# }}}

######################################
# Mixed ??? 
######################
# {{{ 

def translate(seq, frame = 1, genetic_code = 1, translator = None):
   " translation of DNA in one of the six different reading frames "
   if frame not in [1,2,3,-1,-2,-3]:
      raise ValueError, 'invalid frame'

   if not translator:
      table = makeTableX(CodonTable.ambiguous_dna_by_id[genetic_code])
      translator = Translate.Translator(table)

   return translator.translate(Seq(seq[frame-1:], IUPAC.ambiguous_dna)).data

def GC_Frame(seq, genetic_code = 1):
   " just an alias for six_frame_translations "
   return six_frame_translations(seq, genetic_code)

def six_frame_translations(seq, genetic_code = 1):
   """
   nice looking 6 frame translation with GC content - code from xbbtools
   similar to DNA Striders six-frame translation
   """
   from Bio.Seq import reverse_complement
   anti = reverse_complement(seq)
   comp = anti[::-1]
   length = len(seq)
   frames = {}
   for i in range(0,3):
      frames[i+1]  = translate(seq[i:], genetic_code)
      frames[-(i+1)] = reverse(translate(anti[i:], genetic_code))

   # create header
   if length > 20:
      short = '%s ... %s' % (seq[:10], seq[-10:])
   else:
      short = seq
   date = time.strftime('%y %b %d, %X', time.localtime(time.time()))
   header = 'GC_Frame: %s, ' % date
   for nt in ['a','t','g','c']:
      header += '%s:%d ' % (nt, seq.count(nt.upper()))
      
   header += '\nSequence: %s, %d nt, %0.2f %%GC\n\n\n' % (short.lower(),length, GC(seq))       
   res = header
   
   for i in range(0,length,60):
      subseq = seq[i:i+60]
      csubseq = comp[i:i+60]
      p = i/3
      res = res + '%d/%d\n' % (i+1, i/3+1)
      res = res + '  ' + '  '.join(map(None,frames[3][p:p+20])) + '\n'
      res = res + ' ' + '  '.join(map(None,frames[2][p:p+20])) + '\n'
      res = res + '  '.join(map(None,frames[1][p:p+20])) + '\n'
      # seq
      res = res + subseq.lower() + '%5d %%\n' % int(GC(subseq))
      res = res + csubseq.lower() + '\n'
      # - frames
      res = res + '  '.join(map(None,frames[-2][p:p+20]))  +' \n'
      res = res + ' ' + '  '.join(map(None,frames[-1][p:p+20])) + '\n'
      res = res + '  ' + '  '.join(map(None,frames[-3][p:p+20])) + '\n\n'
   return res

# }}}

######################################
# FASTA file utilities
######################
# {{{ 

def fasta_uniqids(file):
   " checks and changes the name/ID's to be unique identifiers by adding numbers "
   dict = {}
   txt = open(file).read()
   entries = []
   for entry in txt.split('>')[1:]:
      name, seq= entry.split('\n',1)
      name = name.split()[0].split(',')[0]
      
      if dict.has_key(name):
         n = 1
         while 1:
            n = n + 1
            _name = name + str(n)
            if not dict.has_key(_name):
               name = _name
               break
            
      dict[name] = seq

   for name, seq in dict.items():
      print '>%s\n%s' % (name, seq)

def quick_FASTA_reader(file):
   " simple and FASTA reader, preferable to be used on large files "
   txt = open(file).read()
   entries = []
   for entry in txt.split('>')[1:]:
      name,seq= entry.split('\n',1)
      seq = seq.replace('\n','').replace(' ','').upper()
      entries.append((name, seq))
      
   return entries
    
def apply_on_multi_fasta(file, function, *args):
   " apply function on each sequence in a multiple FASTA file "
   try:
      f = globals()[function]
   except:
      raise NotImplementedError, "%s not implemented" % function
   
   handle = open(file, 'r')
   records = SeqIO.parse(handle, "fasta")
   results = []
   for record in records:
      arguments = [record.sequence]
      for arg in args: arguments.append(arg)
      result = f(*arguments)
      if result:
         results.append('>%s\n%s' % (record.title, result))
   return results
         
def quicker_apply_on_multi_fasta(file, function, *args):
   " apply function on each sequence in a multiple FASTA file "
   try:
      f = globals()[function]
   except:
      raise NotImplementedError, "%s not implemented" % function
   
   entries = quick_FASTA_reader(file)
   results = []
   for name, seq in entries:
      arguments = [seq]
      for arg in args: arguments.append(arg)
      result = f(*arguments)
      if result:
         results.append('>%s\n%s' % (name, result))
   return results

# }}}

######################################
# Main
#####################
# {{{ 

if __name__ == '__main__':
   import sys, getopt
   # crude command line options to use most functions directly on a FASTA file
   options = {'apply_on_multi_fasta':0,
              'quick':0,
              'uniq_ids':0,
              }

   optlist, args = getopt.getopt(sys.argv[1:], '', ['describe', 'apply_on_multi_fasta=',
                                                    'help', 'quick', 'uniq_ids', 'search='])
   for arg in optlist:
      if arg[0] in ['-h', '--help']:
         pass
      elif arg[0] in ['--describe']:
         # get all new functions from this file
         mol_funcs = [x[0] for x in locals().items() if type(x[1]) == type(GC)]
         mol_funcs.sort()
         print 'available functions:'
         for f in mol_funcs: print '\t--%s' % f
         print '\n\ne.g.\n./sequtils.py  --apply_on_multi_fasta GC test.fas'

         sys.exit(0)
      elif arg[0] in ['--apply_on_multi_fasta']:
         options['apply_on_multi_fasta'] = arg[1]
      elif arg[0] in ['--search']:
         options['search'] = arg[1]
      else:
         key = re.search('-*(.+)', arg[0]).group(1)
         options[key] = 1

         
   if options.get('apply_on_multi_fasta'):
      file = args[0]
      function = options['apply_on_multi_fasta']
      arguments = []
      if options.get('search'):
         arguments = options['search']
      if function == 'xGC_skew':
         arguments = 1000
      if options.get('quick'):
         results = quicker_apply_on_multi_fasta(file, function, arguments)
      else:
         results = apply_on_multi_fasta(file, function, arguments)
      for result in results: print result
      
   elif options.get('uniq_ids'):
      file = args[0]
      fasta_uniqids(file)

# }}}


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