content: # The above copyright notice and this permission notice shall be included in all copies or substantial portions of the
  # Software.
  
  # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE
  # WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
  # COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
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  # Using BLAST, create a CSV file that lists the % identity of the specified sequence to all sequences from the specified germline 
  
  __author__ = 'William Lees'
  __docformat__ = "restructuredtext en"
  
  import os.path
  import sys
  import argparse
  import csv
  import re
  import subprocess
  import numpy as np
  import pandas as pd
  import matplotlib.pyplot as plt
  import matplotlib as mpl
  from Bio.Seq import Seq
  from Bio.SeqRecord import SeqRecord
  from Bio import pairwise2
  from Bio.Alphabet import generic_nucleotide
  from Bio import SeqIO
  from Bio import Phylo
  from itertools import izip
  
  def main(argv):
      parser = argparse.ArgumentParser(description='Create an Identity/Divergence plot.')
      parser.add_argument('repertoire', help='file containing repertoire sequence identities (CSV)')
      parser.add_argument('-a', '--adjust', help='Adjust labels to prevent overlap (requires package adjustText)', action='store_true')
      parser.add_argument('-b', '--bar', help='Plot a colour bar', action='store_true')
      parser.add_argument('-c', '--colourmap', help='colourmap')
      parser.add_argument('-g', '--background', help='Set the contour colourwhere the density is zero')
      parser.add_argument('-mx', '--maxx', help='max divergence value to show')
      parser.add_argument('-my', '--miny', help='min identity value to show')
      parser.add_argument('-p', '--points', help='comma-seperated list of identity files and formats')
      parser.add_argument('-s', '--save', help='Save output to file (as opposed to interactive display)')
      args = parser.parse_args()
  
      if args.adjust:
          from adjustText import adjust_text
          
      colourmap = args.colourmap if args.colourmap else 'hot_r'
  
      plist = args.points.split(',')
      points = []
      
      repertoire = read_file(args.repertoire)
      
      def pairwise(iterable):
          a = iter(iterable)
          return izip(a, a)
      
      if len(plist) > 0:
          try:
              for file, format in pairwise(plist):
                  points.append((read_file(file), format))
          except IOError:
              print 'file "%s" cannot be opened.' % file  
          except:
              print '"points" must consist of pairs of files and formats.'
              quit()
  
      max_divergence = int(args.maxx) if args.maxx else None
      min_identity = int(args.miny) if args.miny else None
      savefile = args.save if args.save else None
  
      if not max_divergence:
          max_divergence = max(repertoire['GermlineDist'])
          for point in points:
              max_divergence = max(max_divergence, max(point[0]['GermlineDist']))
          max_divergence = int(max_divergence) + 1
          
      if not min_identity:
          min_identity = min(repertoire['TargetDist'])
          for point in points:
              min_identity = min(min_identity, min(point[0]['TargetDist']))
          min_identity = int(min_identity)
  
      H, yedges, xedges = np.histogram2d(repertoire['TargetDist'], repertoire['GermlineDist'], bins=[101-min_identity, max_divergence+1], range=[[min_identity, 101], [-1, max_divergence]], normed=False)
  
      # For alternative interpolations and plots, see http://docs.scipy.org/doc/numpy/reference/generated/numpy.histogram2d.html
      # For colour maps, see http://matplotlib.org/examples/color/colormaps_reference.html
  
      fig = plt.figure()
      
      cm = plt.cm.get_cmap(colourmap)
      
      if args.background:
          cm.set_under(color=args.background)
  
      ax = fig.add_subplot(1,1,1)
      im = plt.imshow(H, interpolation='bilinear', origin='low', extent=[xedges[0], xedges[-1], yedges[0], yedges[-1]], vmin=0.0000001, cmap=cm)
      ax.set_xlim(xedges[0], xedges[-1])
      ax.set_ylim(yedges[0], yedges[-1])
      
      if args.bar:
          cb = plt.colorbar(im, shrink=0.8, extend='neither')
          cb.ax.set_ylabel('sequences', rotation=90)
  
      texts = []
      
      for point in points:
          df, format = point
          markersize = 5
          label = False
          labelcolour = 'black'
          fmt = format.split('/')
          format = fmt[0]
          for f in fmt[1:]:
              if f[0] == 'm':
                  markersize = int(f[1:])
              elif f[0] == 'l':
                  label = True
                  if len(f) > 1:
                      labelcolour = f[1:]
              else:
                  print 'Unrecognised format string: %s' % format
          for index, row in df.iterrows():
              if label:
                  if args.adjust:
                      texts.append(plt.text(row['GermlineDist'], row['TargetDist'], row['SequenceId'], bbox={'pad':0, 'alpha':0}, fontdict={ 'color': labelcolour}))
                  else:
                      texts.append(plt.text(row['GermlineDist'] + 0.2, row['TargetDist'] - 0.2, row['SequenceId'], bbox={'pad':0, 'alpha':0}, fontdict={ 'color': labelcolour}))
              ax.plot(row['GermlineDist'], row['TargetDist'], format, markersize=markersize)
  
      if args.adjust:
          adjust_text(texts)
  
      plt.xlabel('Germline Divergence (%)')
      plt.ylabel('Target Ab Identity (%)')
      
      if savefile:
          plt.savefig(savefile)
      else:
          plt.show()
  
  
  def read_file(file):
      df = pd.read_csv(file, converters={'SequenceId': lambda x: x})
      for key in ("SequenceId", "TargetDist", "GermlineDist"):
          if key not in df.keys():
              print 'File %s does not contain a column "%s"' % (file, key)
              quit()
              
      for index, row in df.iterrows():
          try:
              x = row[1] * row[2]     # check they behave like numbers
          except:
              print 'Error in file %s: malformed row at %s.' % (file, row[0])
  
      if len(df) < 1:
          print '%s: empty file.' % file
          quit()
  
      return df
  
  
  if __name__=="__main__":
      main(sys.argv)
  
  