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Commit 8fa94535 authored by Mikael Boden's avatar Mikael Boden
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added_regex_search_in_gappy_sequences

parent 9889428a
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      annotation_test.py
      View file @ 8fa94535
      import annotations
      import phylo
      tree = phylo.parseNewick("(Paenibacillus_thiaminolyticus:4.0,(((bacterium_endosymbiont_of_Mortierella_elongata_FMR23_6:4.0,(Pandoraea_faecigallinarum:4.0,Pandoraea_vervacti:4.0,Pandoraea_oxalativorans:4.0):4.0,(Burkholderia_sp_b14:4.0,Burkholderia_sp_b13:4.0,(Burkholderia_pseudomallei_406e:4.0,Burkholderia_pseudomallei_1710a:4.0):4.0):4.0):4.0,(Chromobacterium_amazonense:4.0,(Microvirgula_sp_AG722:4.0,Microvirgula_aerodenitrificans:4.0):4.0):4.0):4.0,(Candidatus_Endobugula:4.0,Moritella_sp_PE36:4.0,(Enterovibrio_nigricans:4.0,Photobacterium_iliopiscarium:4.0,Vibrio_campbellii:4.0):4.0,(((Pantoea_sp_AMG_501:4.0,Pantoea_wallisii:4.0,Pantoea_rodasii:4.0):4.0,(Erwinia_sp_ErVv1:4.0,Erwinia_toletana:4.0,Erwinia_mallotivora:4.0):4.0):4.0,(Candidatus_Fukatsuia:4.0,Rahnella_aquatilis:4.0,(Yersinia_pekkanenii:4.0,Yersinia_entomophaga:4.0,Yersinia_mollaretii:4.0,(Yersinia_wautersii:4.0,Yersinia_similis:4.0,Yersinia_pseudotuberculosis:4.0,Yersinia_pestis:4.0):4.0,Yersinia_enterocolitica:4.0):4.0):4.0,(Cosenzaea_myxofaciens:4.0,(Photorhabdus_laumondii:4.0,Photorhabdus_bodei:4.0,Photorhabdus_sp_HUG-39:4.0,Photorhabdus_sp_CRCIA-P01:4.0,Photorhabdus_namnaonensis:4.0,Photorhabdus_khanii:4.0,Photorhabdus_heterorhabditis:4.0,Photorhabdus_temperata:4.0,Photorhabdus_asymbiotica:4.0,Photorhabdus_australis:4.0,Photorhabdus_thracensis:4.0,Photorhabdus_luminescens:4.0):4.0,(Xenorhabdus_ishibashii:4.0,Xenorhabdus_khoisanae:4.0,Xenorhabdus_mauleonii:4.0,Xenorhabdus_miraniensis:4.0,Xenorhabdus_vietnamensis:4.0,Xenorhabdus_stockiae:4.0,Xenorhabdus_szentirmaii:4.0,Xenorhabdus_budapestensis:4.0,Xenorhabdus_bovienii:4.0,Xenorhabdus_nematophila:4.0):4.0,(Proteus_sp_TJ1640:4.0,Proteus_sp_TJ1636:4.0,Proteus_sp_FJ2001126-3:4.0,Proteus_columbae:4.0,Proteus_alimentorum:4.0,Proteus_genomosp_6_str._ATCC_51471:4.0,Proteus_genomosp_4_str._ATCC_51469:4.0,Proteus_cibarius:4.0,Proteus_hauseri:4.0,Proteus_penneri:4.0,Proteus_vulgaris:4.0):4.0,(Morganella_sp_HMSC11D09:4.0,Morganella_sp_EGD-HP17:4.0,Morganella_morganii:4.0):4.0):4.0,(Escherichia_sp_ESNIH1:4.0,Mangrovibacter_phragmitis:4.0,(Enterobacter_sp_DC4:4.0,Enterobacter_sp_BIDMC_26:4.0):4.0,Kosakonia_sacchari:4.0,Pseudescherichia_vulneris:4.0):4.0):4.0,(Pseudomonas_kribbensis:4.0,Pseudomonas_lactis:4.0,Pseudomonas_paralactis:4.0,Pseudomonas_helleri:4.0,Pseudomonas_weihenstephanensis:4.0,Pseudomonas_coleopterorum:4.0,Pseudomonas_endophytica:4.0,Pseudomonas_granadensis:4.0,Pseudomonas_prosekii:4.0,Pseudomonas_brassicacearum:4.0,Pseudomonas_deceptionensis:4.0,Pseudomonas_baetica:4.0,Pseudomonas_simiae:4.0,Pseudomonas_moraviensis:4.0,Pseudomonas_batumici:4.0,Pseudomonas_antarctica:4.0,Pseudomonas_rhizosphaerae:4.0,Pseudomonas_lini:4.0,Pseudomonas_kilonensis:4.0,Pseudomonas_psychrophila:4.0,Pseudomonas_abietaniphila:4.0,Pseudomonas_thivervalensis:4.0,Pseudomonas_jessenii:4.0,Pseudomonas_plecoglossicida:4.0,Pseudomonas_agarici:4.0,(Pseudomonas_cichorii:4.0,Pseudomonas_syringae:4.0):4.0,Pseudomonas_sp:4.0,(Pseudomonas_lundensis:4.0,Pseudomonas_fragi:4.0):4.0,(Pseudomonas_poae:4.0,Pseudomonas_mediterranea:4.0,Pseudomonas_extremorientalis:4.0,Pseudomonas_orientalis:4.0,Pseudomonas_libanensis:4.0,Pseudomonas_synxantha:4.0,Pseudomonas_corrugata:4.0,Pseudomonas_fluorescens:4.0):4.0):4.0):4.0):4.0);")
      # tree = phylo.readNewick("/Users/gabefoley/Dropbox/PhD/Projects/Phylo Island/Species trees/species_tree.nwk")
      # tree = phylo.readNewick("/Users/gabefoley/Dropbox/PhD/Smaller Projects/GRASP tree/non_unique.nwk")
      ......@@ -10,17 +12,17 @@ import phylo
      working_dir = "/Users/gabefoley/Dropbox/PhD/Smaller Projects/Nexus_colouring/Read_annotations/"
      tree = phylo.read_nexus(working_dir + "annotation_simple.nexus")
      print (tree)
      print (tree.nexus_annotations.annotations)
      tree.swap_annotations("PDB")
      print (tree)
      print (tree.nexus_annotations.annotations)
      # working_dir = "/Users/gabefoley/Dropbox/PhD/Smaller Projects/Nexus_colouring/Read_annotations/"
      #
      # tree = phylo.read_nexus(working_dir + "annotation_simple.nexus")
      #
      # print (tree)
      # print (tree.nexus_annotations.annotations)
      #
      # tree.swap_annotations("PDB")
      #
      # print (tree)
      # print (tree.nexus_annotations.annotations)
      #
      # tree.write_to_nexus(working_dir + "output.nexus")
      ......
      annotations.py
      View file @ 8fa94535
      from collections import defaultdict
      from phylo import *
      import phylo
      import matplotlib
      import random
      ......@@ -146,3 +147,5 @@ class NexusAnnotations():
      def generate_colour_list(self, num):
      return num
      # tree = phylo.readNewick("/Users/gabefoley/Dropbox/PhD/Projects/Phylo Island/Species trees/species_tree_115.nwk")
      gtf.py
      View file @ 8fa94535
      ......@@ -242,7 +242,7 @@ def writeGtfFile(entries, filename, header = None):
      f.close()
      if __name__ == '__main__':
      bf = GtfFile('/Users/mikael/simhome/NFIX/WT1677.gtf')
      bf = GtfFile('/Users/mikael/simhome/NFIX/WT1689.gtf')
      print(bf.chroms.keys())
      g = bf.generate('chr12')
      print(next(g))
      ......
      phylo.py
      View file @ 8fa94535
      '''
      Module with methods and classes for phylogeny.
      Extended to handle n-ary trees (Jan 2019).
      @author: mikael
      '''
      import sequence
      from collections import defaultdict
      import annotations
      class PhyloTree:
      """ Rooted, binary (bifurcating) tree for representing phylogenetic relationships.
      """ Rooted, n-ary tree for representing phylogenetic relationships.
      Functionality includes labelling and traversing nodes; reading and writing to Newick format;
      association with sequence alignment; maximum parsimony inference of ancestral sequence;
      generation of single, bifurcating rooted tree by UPGMA.
      Known issues: Binary only; Parsimony does not handle gaps in alignment.
      generation of rooted tree by UPGMA.
      Known issues: Parsimony does not handle gaps in alignment.
      Programmers should note that almost all functionality is implemented through recursion. """
      def __init__(self, root):
      ......@@ -27,7 +27,6 @@ class PhyloTree:
      def putAnnotations(self, nexus_annotations):
      self.nexus_annotations = nexus_annotations
      # Update the annotations dictionary so that it contains PhyloNode objects as keys, not text labels
      for node in self.getNodes():
      if node.label in self.nexus_annotations.leaf_annotations:
      ......@@ -60,10 +59,18 @@ class PhyloTree:
      node = queue.pop()
      nodes.append(node)
      # if strategy.upper().startswith('DEPTH'):
      if node.left: queue.append(node.left)
      if node.right: queue.append(node.right)
      if not node.isLeaf():
      queue.extend(node.children)
      return nodes
      def getLeaves(self):
      all = self.getNodes()
      leaves = []
      for n in all:
      if n.isLeaf():
      leaves.append(n)
      return leaves
      def getDescendantsOf(self, node, transitive=False):
      """ Retrieve and return the (list of) descendants (children) of a specified node.
      Node can be the label or the instance.
      ......@@ -86,28 +93,7 @@ class PhyloTree:
      if not isinstance(node, PhyloNode):
      node = self.findLabel(node)
      if node:
      myroot = self.root
      found = False
      branching = []
      while not found and myroot != None:
      branching.append(myroot)
      # check if "myroot" is a leaf node, i.e. does not have children
      if myroot.left == node or myroot.right == node:
      found = True
      break
      if myroot.left != None: # myroot has a "left" child
      # check if the "left" child of "myroot" is the ancestor of "node"
      if myroot.left.isAncestorOf(node, transitive=True): # if yes,
      myroot = myroot.left # move to the "left" child
      else: # if not,
      myroot = myroot.right # move to the "right" child
      else: # myroot does NOT have a "left" child, so let's move "right"
      myroot = myroot.right
      if found and transitive:
      return branching
      elif found and len(branching) > 0:
      return branching[len(branching) - 1]
      return None
      return node.getAncestors(transitive)
      def parsimony(self):
      """ Solve the "small parsimony problem",
      ......@@ -117,12 +103,8 @@ class PhyloTree:
      self.root._backwardParsimony(self.aln) # use scores to determine sequences
      return self.root.getSequence() # return the sequence found at the root
      def canonise(self):
      self.root._canonise()
      def swap_annotations(self, annotation_key):
      try:
      for node in self.getNodes():
      if node.isLeaf():
      node.label = self.nexus_annotations.leaf_annotations[node][annotation_key]
      ......@@ -135,103 +117,91 @@ class PhyloTree:
      :param out_path: The path to write the NEXUS file to
      :param nexus_annotations: The NexusAnnotations containing the annotations
      """
      if write_annotations and not nexus_annotations:
      if not self.nexus_annotations:
      raise RuntimeError("This tree file has no associated annotation file. Either associate or supply one as a parameter.")
      nexus_annotations = self.nexus_annotations
      if nexus_annotations:
      for node in self.getNodes():
      if node in self.nexus_annotations.node_annotations:
      node.annotate_node(self.nexus_annotations.node_annotations, self.nexus_annotations.annotation_symbols, exclude_annotations, use_symbols)
      tree_annotation = str(self) + ";"
      self.swap_annotations("Original")
      for node in self.getNodes():
      if node in self.nexus_annotations.leaf_annotations:
      node.annotate_node(self.nexus_annotations.leaf_annotations, exclude_annotations)
      leaves = []
      for node in self.getNodes():
      if node.isLeaf():
      leaves.append(node.label)
      leaf_annotation = ""
      for leaf in leaves:
      leaf_annotation += "\n\t%s" % (leaf)
      with open(out_path, "w+") as file:
      file.write(
      "#NEXUS\nbegin taxa;\n\tdimensions ntax=%d;\n\ttaxlabels%s\n;\nend;\n\nbegin trees;\n\ttree tree_1 = "
      "[&R] %s\nend;" % (len(leaves), leaf_annotation, tree_annotation))
      class PhyloNode:
      """ A class for a node in a rooted, binary (bifurcating) tree.
      Contains pointers to descendants/daughters (left and right),
      """ A class for a node in a rooted, n-ary tree.
      Contains pointers to multiple descendants/daughters,
      optional fields include data, label, sequence and dist.
      If parsimony is used scores and traceback pointers are available.
      A number of methods are named with a _ prefix. These can be, but
      are not intended to be used from outside the class. """
      def __init__(self, label=''):
      """ Initialise an initially unlinked node.
      Populate fields left and right to link it with other nodes.
      def __init__(self, parent = None, label=''):
      """ Initialise a node.
      Set its parent (another PhyloNode), parent can be None.
      Set label to name it.
      Use field data for any type of information associated with node.
      Use dist to indicate the distance to its parent (if any).
      Other fields are used internally, including sequence for associated alignment,
      seqscores, backleft and backright for maximum parsimony. """
      self.left = None
      self.right = None
      seqscores, back for maximum parsimony. """
      self.parent = parent
      self.children = None
      self.data = None
      self.label = label
      self.dist = None
      self.sequence = None # The sequence after an alignment have been mapped (leaf) or the most parsimonous sequence (ancestral)
      self.seqscores = None # The scores propagated from leaves via children
      self.backleft = None # Pointers back to left child: what symbol rendered current/parent symbols
      self.backright = None # Pointers back to right child: what symbol rendered current/parent symbols
      self.seqscores = None # The scores propagated from leaves via children
      self.backptr = None # Pointers back to children: what symbol rendered current/parent symbols
      def isLeaf(self):
      return self.left == self.right == None
      return self.nChildren() == 0
      def nChildren(self):
      if self.children == None:
      return 0
      else:
      return len(self.children)
      def __str__(self):
      """ Returns string with node (incl descendants) in a Newick style. """
      left = right = label = dist = ''
      if self.left:
      left = str(self.left)
      if self.right:
      right = str(self.right)
      stubs = ['' for _ in range(self.nChildren())]
      label = dist = ''
      for i in range(self.nChildren()):
      stubs[i] = str(self.children[i])
      if self.dist or self.dist == 0.0:
      dist = ':' + str(self.dist)
      if self.label != None:
      label = str(self.label)
      if not self.left and not self.right:
      return label + dist
      else:
      return '(' + left + ',' + right + ')' + label + dist
      else: # there is no label
      if self.nChildren() == 0:
      return label + dist
      else:
      stubstr = '('
      for i in range(len(stubs) - 1):
      stubstr += stubs[i] + ','
      return stubstr + stubs[-1] + ')' + label + dist
      # there is no label
      '''
      if not self.left and self.right:
      return ',' + right
      elif self.left and not self.right:
      return left + ','
      elif self.left and self.right:
      return '(' + left + ',' + right + ')' + dist
      '''
      # def __le__(self, other):
      # """ Returns indication of less than other node. """
      ......@@ -247,38 +217,31 @@ class PhyloNode:
      def _printSequences(self, start, end):
      """ Returns string with node (incl descendants) in a Newick style. """
      left = right = label = dist = ''
      if self.left:
      left = self.left._printSequences(start, end)
      if self.right:
      right = self.right._printSequences(start, end)
      if self.dist:
      stubs = ['' for _ in range(self.nChildren())]
      label = dist = ''
      for i in range(self.nChildren()):
      stubs[i] = self._printSequences(self.children[i], start, end)
      if self.dist or self.dist == 0.0:
      dist = ':' + str(self.dist)
      if self.sequence != None:
      label = "".join(self.sequence[start:end]) + ""
      if not self.left and not self.right:
      return label + dist
      else:
      return '(' + left + ',' + right + ')' + label + dist
      else: # there is no label
      if not self.left and self.right:
      return ',' + right
      elif self.left and not self.right:
      return left + ','
      elif self.left and self.right:
      return '(' + left + ',' + right + ')' + dist
      if self.label != None:
      label = str(self.label)
      if self.nChildren() == 0:
      return label + dist
      else:
      stubstr = '('
      for i in range(len(stubs) - 1):
      stubstr += stubs[i] + ','
      return stubstr + stubs[-1] + ')' + label + dist
      def _findLabel(self, label):
      """ Find a node by label at this node or in any descendants (recursively). """
      if self.label == label:
      return self
      else:
      if self.left:
      foundLeft = self.left._findLabel(label)
      if foundLeft:
      return foundLeft
      if self.right:
      return self.right._findLabel(label)
      for i in range(self.nChildren()):
      found = self.children[i]._findLabel(label)
      if found:
      return found
      return None
      def _propagateDistance(self, parent_dist):
      ......@@ -286,24 +249,21 @@ class PhyloNode:
      The only parameter is the absolute distance to the parent of this node. """
      travelled = self.dist # absolute distance to this node
      self.dist = parent_dist - self.dist # relative distance to this node
      if self.left != None: # if there is a child node...
      self.left._propagateDistance(travelled) # pass absolute distance to this node
      if self.right != None:
      self.right._propagateDistance(travelled)
      for i in range(self.nChildren()):
      self.children[i]._propagateDistance(travelled) # pass absolute distance to this node
      def _assignAlignment(self, aln):
      """ Assign an alignment to the node, which implies assigning a sequence to it if one is
      available in the alignment. """
      self.sequence = None
      if self.left != None:
      self.left._assignAlignment(aln)
      if self.right != None:
      self.right._assignAlignment(aln)
      for i in range(self.nChildren()):
      self.children[i]._assignAlignment(aln)
      for seq in aln.seqs:
      if seq.name == self.label:
      self.sequence = seq
      break
      """ # Not sure if this is required (putting nodes into a canonical ordering)
      def _canonise(self):
      if self.left == None and self.right == None: # at leaf
      return self.label
      ......@@ -315,52 +275,38 @@ class PhyloNode:
      self.right = tmpnode
      return myright
      return myleft
      """
      def _forwardParsimony(self, aln):
      """ Internal function that operates recursively to first initialise each node (forward),
      stopping only once a sequence has been assigned to the node,
      then to propagate scores from sequence assigned nodes to root (backward). """
      if self.sequence == None: # no sequence has been assigned
      if self.left == None and self.right == None: # no children, so terminal, cannot propagate scores
      if self.nChildren() == 0: # no children, so terminal, cannot propagate scores
      raise RuntimeError("No sequence assigned to leaf node:", self.label)
      scoresleft = scoresright = None
      if self.left != None:
      scoresleft = self.left._forwardParsimony(aln)
      if self.right != None:
      scoresright = self.right._forwardParsimony(aln)
      scores = [None for _ in range(self.nChildren())]
      for i in range(self.nChildren()):
      scores[i] = self.children[i]._forwardParsimony(aln)
      # for each position in the alignment,
      # introduce (initially zero) score for each symbol in alphabet
      self.seqscores = [[0 for _ in aln.alphabet] for col in range(aln.alignlen)]
      # for each position in the alignment,
      # allocate a position to put the left child symbol from which each current node symbol score was determined
      self.backleft = [[None for _ in aln.alphabet] for _ in range(aln.alignlen)]
      # allocate a position to put the right child symbol from which each current node symbol score was determined
      self.backright = [[None for _ in aln.alphabet] for _ in range(aln.alignlen)]
      # allocate a position to put the each child symbol from which each current node symbol score was determined
      self.backptr = [[[None for _ in aln.alphabet] for _ in range(aln.alignlen)] for _ in range(self.nChildren())]
      for col in range(aln.alignlen):
      # left child will contribute first
      for a_parent in range(len(aln.alphabet)):
      best_score_left = +9999999
      best_symb_left = 0
      for a in range(len(aln.alphabet)):
      score = (scoresleft[col][a] + (
      1 if a != a_parent else 0)) # if we want to weight scores, this would need to change
      if score < best_score_left:
      best_symb_left = a
      best_score_left = score
      self.seqscores[col][a_parent] = best_score_left
      self.backleft[col][a_parent] = best_symb_left
      # right child will contribute next
      for a_parent in range(len(aln.alphabet)):
      best_score_right = +9999999
      best_symb_right = 0
      for a in range(len(aln.alphabet)):
      score = (scoresright[col][a] + (
      1 if a != a_parent else 0)) # if we want to weight scores, this would need to change
      if score < best_score_right:
      best_symb_right = a
      best_score_right = score
      self.seqscores[col][a_parent] += best_score_right
      self.backright[col][a_parent] = best_symb_right
      for i in range(self.nChildren()):
      # left child will contribute first
      for a_parent in range(len(aln.alphabet)):
      best_score = +9999999
      best_symb = 0
      for a in range(len(aln.alphabet)):
      score = (scores[i][col][a] + (
      1 if a != a_parent else 0)) # if we want to weight scores, this would need to change
      if score < best_score:
      best_symb = a
      best_score = score
      self.seqscores[col][a_parent] += best_score
      self.backptr[i][col][a_parent] = best_symb
      else:
      self.seqscores = [[0 if a == sym else 999999 for a in aln.alphabet] for sym in
      self.sequence] # if we want to weight scores, this would need to change
      ......@@ -370,39 +316,37 @@ class PhyloNode:
      """ Internal function that operates recursively to inspect scores to determine
      most parsimonious sequence, from root to leaves. """
      if self.sequence == None: # no sequence has been assigned
      leftbuf = []
      rightbuf = []
      if self.left == None and self.right == None: # no children, so terminal, cannot propagate scores
      childbuf = [[] for _ in range(self.nChildren())]
      if self.nChildren() == 0: # no children, so terminal, cannot propagate scores
      raise RuntimeError("No sequence assigned to leaf node:", self.label)
      if seq == None: # Only root can do this, no parents to consider, so we pick the lowest scoring symbol
      currbuf = []
      for col in range(aln.alignlen):
      min_score = 999999
      min_symb = None
      left_symb = None
      right_symb = None
      child_symb = [None for _ in range(self.nChildren())]
      for a_parent in range(len(aln.alphabet)):
      if self.seqscores[col][a_parent] < min_score:
      min_score = self.seqscores[col][a_parent]
      min_symb = a_parent
      left_symb = self.backleft[col][a_parent]
      right_symb = self.backright[col][a_parent]
      for i in range(self.nChildren()):
      child_symb[i] = self.backptr[i][col][a_parent]
      currbuf.append(aln.alphabet[min_symb])
      leftbuf.append(aln.alphabet[left_symb])
      rightbuf.append(aln.alphabet[right_symb])
      for i in range(self.nChildren()):
      childbuf[i].append(aln.alphabet[child_symb[i]])
      self.sequence = sequence.Sequence(currbuf, aln.alphabet, self.label, gappy=True)
      else: # Non-root, but not leaf
      self.sequence = seq
      col = 0
      for sym_parent in self.sequence:
      a_parent = aln.alphabet.index(sym_parent)
      left_symb = self.backleft[col][a_parent]
      right_symb = self.backright[col][a_parent]
      leftbuf.append(aln.alphabet[left_symb])
      rightbuf.append(aln.alphabet[right_symb])
      child_symb = [None for _ in range(self.nChildren())]
      for i in range(self.nChildren()):
      child_symb[i] = self.backptr[i][col][a_parent]
      childbuf.append(aln.alphabet[child_symb[i]])
      col += 1
      self.left._backwardParsimony(aln, sequence.Sequence(leftbuf, aln.alphabet, self.label, gappy=True))
      self.right._backwardParsimony(aln, sequence.Sequence(rightbuf, aln.alphabet, self.label, gappy=True))
      for i in range(self.nChildren()):
      self.children[i]._backwardParsimony(aln, sequence.Sequence(childbuf[i], aln.alphabet, self.label, gappy=True))
      return self.sequence
      def getSequence(self):
      ......@@ -418,26 +362,35 @@ class PhyloNode:
      """ Decide if this node is the ancestor of specified node.
      If transitive is True (default), all descendants are included.
      If transitive is False, only direct descendants are included. """
      if node == self.left or node == self.right:
      return True
      elif transitive:
      if self.left:
      statusLeft = self.left.isAncestorOf(node, transitive)
      if statusLeft: return True
      if self.right:
      return self.right.isAncestorOf(node, transitive)
      for i in range(self.nChildren()):
      if node == self.children[i]:
      return True
      elif transitive:
      status = self.children[i].isAncestorOf(node, transitive)
      if status: return True
      else:
      return False
      def getAncestors(self, transitive=False):
      """ Retrieve and return (list of) parent nodes.
      If transitive is False (default), only the direct parent is included.
      If transitive is True, all parents (parents of parents etc) are included. """
      if self.parent == None:
      return []
      if not transitive:
      return [self.parent]
      else:
      parents = self.parent.getAncestors(transitive)
      parents.append(self.parent)
      return parents
      def getDescendants(self, transitive=False):
      """ Retrieve and return (list of) nodes descendant of this.
      If transitive is False (default), only direct descendants are included.
      If transitive is True, all descendants are (recursively) included. """
      children = []
      if self.left:
      children.append(self.left)
      if self.right:
      children.append(self.right)
      for i in range(self.nChildren()):
      children.append(self.children[i])
      if not transitive:
      return children
      else:
      ......@@ -450,13 +403,11 @@ class PhyloNode:
      return children
      def annotate_node(self, annotations, annotation_symbols= None, exclude_annotations = [], use_symbols=False ):
      annotation_string = "[&"
      for key, val_list in annotations[self].items():
      if type(val_list) != list:
      val_list = [val_list]
      if key not in exclude_annotations:
      # If we are using annotation symbols and the annotation has an associated symbol
      for val in val_list:
      if use_symbols and val in annotation_symbols:
      ......@@ -464,11 +415,8 @@ class PhyloNode:
      annotation_string += '%s="%s",' % (key, ' '.join(['%s' % (val,) for val in sorted_symbols]))
      else:
      annotation_string += '%s="%s",' % (key, ' '.join(['%s' % (val,) for val in val_list]))
      # Remove the final comma and add in a closing bracket
      annotation_string = annotation_string[0: len(annotation_string) - 1] + "]"
      if len(annotation_string) > 2:
      if ":" in self.label:
      self.label = self.label.split(":")[0] + annotation_string + self.label.split(":")[1]
      ......@@ -488,7 +436,7 @@ def runUPGMA(aln, measure, absoluteDistances=False):
      D = {}
      N = {} # The number of sequences in each node
      M = aln.calcDistances(measure) # determine all pairwise distances
      nodes = [PhyloNode(seq.name) for seq in aln.seqs] # construct all leaf nodes
      nodes = [PhyloNode(label=seq.name) for seq in aln.seqs] # construct all leaf nodes
      """ For each node-pair, assign the distance between them. """
      for i in range(len(nodes)):
      nodes[i].sequence = aln.seqs[i]
      ......@@ -525,8 +473,9 @@ def runUPGMA(aln, measure, absoluteDistances=False):
      N[z] = Nx + Ny # total number of sequences in new cluster, insert new cluster in list N
      for w in dz: # we have to run through the nodes again, now not including the removed x and y
      D[frozenset([z, w])] = dz[w] # for each "other" cluster, update distance per EQ8.16 (Z&B p. 278)
      z.left = x # link the phylogenetic tree
      z.right = y
      x.parent = z
      y.parent = z
      z.children = [x, y]
      nodes.append(z)
      if not absoluteDistances:
      x._propagateDistance(z.dist) # convert absolute distances to relative by recursing down left path
      ......@@ -534,24 +483,22 @@ def runUPGMA(aln, measure, absoluteDistances=False):
      z.dist = 0.0 # root z is at distance 0 from merged x and y
      return PhyloTree(z) # make it to tree, return
      """ ----------------------------------------------------------------------------------------
      Methods for processing files of trees on the Newick format
      ----------------------------------------------------------------------------------------"""
      def _findComma(string, level=0):
      """ Find first comma at specified level of embedding """
      """ Find all commas at specified level of embedding """
      mylevel = 0
      commas = []
      for i in range(len(string)):
      if string[i] == '(':
      mylevel += 1
      elif string[i] == ')':
      mylevel -= 1
      elif string[i] == ',' and mylevel == level:
      return i
      return -1
      commas.append(i)
      return commas
      def parseNewickNode(string):
      """ Utility function that recursively parses embedded string using Newick format. """
      ......@@ -559,7 +506,7 @@ def parseNewickNode(string):
      last = string[::-1].find(')') # look from the back
      if first == -1 and last == -1: # we are at leaf
      y = string.split(':')
      node = PhyloNode(y[0])
      node = PhyloNode(label=y[0])
      if len(y) >= 2:
      node.dist = float(y[1])
      return node
      ......@@ -569,17 +516,24 @@ def parseNewickNode(string):
      embed = string[first + 1:last]
      tail = string[last + 1:]
      # find where corresp comma is
      comma = _findComma(embed)
      if comma == -1:
      commas = _findComma(embed)
      if len(commas) < 1:
      raise RuntimeError('Invalid format: invalid placement of "," in sub-string "' + embed + '"')
      left = embed[0:comma].strip()
      right = embed[comma + 1:].strip()
      prev_comma = 0
      child_tokens = []
      for comma in commas:
      child_tokens.append(embed[prev_comma:comma].strip())
      prev_comma = comma + 1
      child_tokens.append(embed[prev_comma:].strip())
      y = tail.split(':')
      node = PhyloNode(y[0]) # node is an instance of the PhyloNode() class
      node = PhyloNode(label=y[0]) # node is an instance of the PhyloNode() class
      if len(y) >= 2:
      node.dist = float(y[1])
      node.left = parseNewickNode(left)
      node.right = parseNewickNode(right)
      node.children = []
      for tok in child_tokens:
      child = parseNewickNode(tok)
      child.parent = node
      node.children.append(child)
      return node
      else:
      raise RuntimeError('Invalid format: unbalanced parentheses in sub-string "' + string + '"')
      ......@@ -628,8 +582,6 @@ def parse_nexus(string):
      taxon_num = num + 1
      while not lines[taxon_num].strip().startswith(";"):
      taxon_name = lines[taxon_num].split("[")[0].strip()
      for annot_line in lines[taxon_num].split("[&")[1].split(","):
      #TODO: Make these regex calls
      # print ("Annotation Key is ", annot_line.split("=")[0])
      ......@@ -641,34 +593,18 @@ def parse_nexus(string):
      annot_val = annot_line.split("=")[1].split("]")[0]
      annotation_dict[taxon_name][annot_key.strip()] = annot_val
      taxon_num +=1
      if line.strip().startswith("begin trees"):
      tree_num = num + 1
      tree = (lines[tree_num].split("[&R]")[1])
      phylo_tree = parseNewick(tree)
      nexus_annotations = annotations.NexusAnnotations(tree=phylo_tree)
      nexus_annotations.add_annotations(annotation_dict)
      # print (nexus_annotations.annotations)
      phylo_tree.putAnnotations(nexus_annotations)
      ## Extract all of the annotations from the tree and add them to the NexusAnnotations object
      print ("Number of taxons is %s " % (taxon_number))
      return phylo_tree
      """ ----------------------------------------------------------------------------------------
      Method for generating a PhyloTree with unique tip names
      ----------------------------------------------------------------------------------------"""
      ......@@ -676,7 +612,6 @@ def parse_nexus(string):
      def get_unique_tree(tree):
      unique_tree = tree
      unique_labels = {}
      for node in unique_tree.getNodes():
      if node.isLeaf() and node.label in unique_labels:
      unique_labels[node.label] = unique_labels[node.label] + 1
      ......@@ -688,3 +623,6 @@ def get_unique_tree(tree):
      def unpack_list(list):
      return (" ".join(["%s"] * len(list)) + "!") % (x for x in list)
      if __name__ == '__main__':
      tree = readNewick('/Users/mikael/simhome/ASR/edge1.nwk')
      print(tree)
      \ No newline at end of file
      sequence.py
      View file @ 8fa94535
      ......@@ -226,9 +226,16 @@ def readFasta(string, alphabet = None, ignore = False, gappy = False, parse_defl
      if parse_defline:
      parsed = parseDefline(seqinfo[0])
      seqname = parsed[0]
      else:
      seqinfo = line[1:]
      else: # we are not parsing the sequence name so no need to duplicate it in the info
      seqname = seqinfo[0]
      seqinfo = line[1:]
      if len(seqinfo) > 0: # more than a name
      edited_info = ''
      for infopart in seqinfo[1:]:
      edited_info += infopart + ' '
      seqinfo = edited_info
      else:
      seqinfo = ''
      except IndexError as errmsg:
      if not ignore:
      raise RuntimeError(errmsg)
      ......@@ -717,60 +724,62 @@ class Alignment():
      distmat[i, j] = distmat[j, i] = dist
      return distmat
      def writeHTML(self, filename = None):
      def writeHTML(self, filename = None, col_start = None, col_end = None):
      """ Generate HTML that displays the alignment in color.
      Requires that the alphabet is annotated with the label 'html-color' (see Sequence.annotateSym)
      and that each symbol maps to a text string naming the color, e.g. 'blue'
      """
      col_start = col_start or 0
      col_end = col_end or self.alignlen
      html = '''<html><head><meta content="text/html; charset=ISO-8859-1" http-equiv="Content-Type">\n<title>Sequence Alignment</title>\n</head><body><pre>\n'''
      html += '''<p style="font-size:12px">\n'''
      maxNameLength = self.getnamelen()
      html += ''.ljust(maxNameLength) + ' '
      for i in range(self.alignlen - 1):
      if (i+1) % 10 == 0:
      if (i+1) % 10 == 0 and (i >= col_start and i < col_end):
      html += str(i/10+1)[0]
      else:
      elif (i >= col_start and i < col_end):
      html += ' '
      html += '%s\n' % (self.alignlen)
      # html += '%s\n' % (col_end)
      html += '\n'
      if self.alignlen > 10:
      html += ''.ljust(maxNameLength) + ' '
      for i in range(self.alignlen - 1):
      if (i+1) % 10 == 0:
      if (i+1) % 10 == 0 and (i >= col_start and i < col_end):
      index = len(str(i/10 + 1).split('.')[0])
      html += str(i / 10 + 1).split('.')[0][(index * -1) + 1 ] if (len(str(i / 10 + 1).split('.')[0]) > 1) else '0'
      else:
      elif (i >= col_start and i < col_end):
      html += ' '
      html += '\n'
      if self.alignlen > 100:
      html += ''.ljust(maxNameLength) + ' '
      for i in range(self.alignlen - 1):
      if (i+1) % 10 == 0 and i >= 99:
      if (i+1) % 10 == 0 and i >= 99 and (i >= col_start and i < col_end):
      index = len(str(i/10 + 1).split('.')[0])
      html += str(i / 10 + 1).split('.')[0][-1] if (len(str(i / 10 + 1).split('.')[0]) >2) else '0'
      else:
      elif (i >= col_start and i < col_end):
      html += ' '
      html += '\n'
      if self.alignlen > 1000:
      html += ''.ljust(maxNameLength) + ' '
      for i in range(self.alignlen - 1):
      if (i+1) % 10 == 0:
      if (i+1) % 10 == 0 and (i >= col_start and i < col_end):
      html += '0' if (len(str(i / 10 + 1).split('.')[0]) > 2) else ' '
      else:
      elif (i >= col_start and i < col_end):
      html += ' '
      html += '\n'
      for seq in self.seqs:
      html += seq.name.ljust(maxNameLength) + ' '
      for sym in seq:
      for sym in seq[col_start:col_end]:
      color = self.alphabet.getAnnotation('html-color', sym)
      if not color:
      color = 'white'
      html += '<font style="BACKGROUND-COLOR: %s">%s</font>' % (color, sym)
      html += '\n'
      html += '</pre></body></html>'
      html += '</p></pre></body></html>'
      if filename:
      fh = open(filename, 'w')
      fh.write(html)
      ......@@ -1187,19 +1196,25 @@ class Regexp(object):
      def __str__(self):
      return self.pattern
      def search(self, sequence):
      def search(self, sequence, gappy = False):
      """ Find matches to the motif in the specified sequence. Returns a list
      of triples, of the form (position, matched string, score). Note that
      the score is always 1.0 because a regexp either matches
      or doesn't. """
      if not type(sequence) is Sequence:
      sequence = Sequence(sequence)
      sequenceString = sequence[:]
      results = []
      for match in self.regex.finditer(sequenceString):
      results.append((match.start(), match.group(), 1.0))
      return results
      if gappy == False or sequence.gappy == False:
      sequenceString = sequence[:]
      results = []
      for match in self.regex.finditer(sequenceString):
      results.append((match.start(), match.group(), 1.0))
      return results
      else: # if the sequence is gappy AND the function is called with gappy = True THEN run the regex matching on the de-gapped sequence
      degapped, idxs = sequence.getDegapped()
      results = []
      for match in self.regex.finditer(''.join(degapped)):
      results.append((idxs[match.start()], match.group(), 1.0))
      return results
      class PWM(object):
      ......
      sym.py
      View file @ 8fa94535
      ......@@ -138,15 +138,46 @@ predefAlphabets = {'Bool_Alphabet': Bool_Alphabet,
      'Protein': Protein_Alphabet,
      'ProteinwX': Protein_wX,
      'ProteinwSTOP' : Protein_wSTOP,
      'ProteinwGAP': Protein_wGAP,
      'DSSP_Alphabet' : DSSP_Alphabet,
      'DSSP3_Alphabet' : DSSP3_Alphabet}
      # The preferred order in which a predefined alphabet is assigned to a sequence
      # (e.g., we'd want to assign DNA to 'AGCT', even though Protein is also valid)
      preferredOrder = ['Bool_Alphabet', 'DNA', 'RNA', 'DNAwN', 'RNAwN', 'Protein', 'ProteinwX', 'ProteinwSTOP', 'DSSP_Alphabet', 'DSSP3_Alphabet']
      preferredOrder = ['Bool_Alphabet', 'DNA', 'RNA', 'DNAwN', 'RNAwN', 'Protein', 'ProteinwX', 'ProteinwSTOP',
      'ProteinwGAP', 'DSSP_Alphabet', 'DSSP3_Alphabet']
      # Useful annotations
      DNA_Alphabet.annotateAll('html-color', {'A':'green','C':'orange','G':'red','T':'#66bbff'})
      RNA_Alphabet.annotateAll('html-color', {'A':'green','C':'orange','G':'red','U':'#66bbff'})
      Protein_Alphabet.annotateAll('html-color', {'G':'orange','P':'orange','S':'orange','T':'orange','H':'red','K':'red','R':'red','F':'#66bbff','Y':'#66bbff','W':'#66bbff','I':'green','L':'green','M':'green','V':'green'})
      #Protein_Alphabet.annotateAll('html-color', {'G':'orange','P':'orange','S':'orange','T':'orange','H':'red','K':'red','R':'red','F':'#66bbff','Y':'#66bbff','W':'#66bbff','I':'green','L':'green','M':'green','V':'green'})
      Protein_Alphabet.annotateAll('html-color', {
      #orange*/
      'G': "#F5A259",
      #green*/
      'N':"#00f900",
      'Q':"#00f900",
      'S': "#00f900",
      'T': "#00f900",
      #red*/
      'K': "#f62f00",
      'R': "#f62f00",
      #blue/purple*/
      'A':"#92b2f3",
      'I': "#92b2f3",
      'L': "#92b2f3",
      'M': "#92b2f3",
      'V': "#92b2f3",
      'W': "#92b2f3",
      'F': "#92b2f3",
      #yellow*/
      'P': "#FFFB00",
      #pink*/
      'C':"#F59692",
      #aqua*/
      'H': "#04B2B3",
      'Y': "#04B2B3",
      #purple*/
      'D':"#CE64CB",
      'E':"#CE64CB"})
      # ------------------ Substitution Matrix ------------------
      ......
      webservice.py
      View file @ 8fa94535
      import urllib.request
      import urllib.parse
      import os
      from time import sleep
      import stats
      ......@@ -16,10 +17,11 @@ import json
      http://www.ebi.ac.uk/Tools/webservices/tutorials
      """
      __ebiUrl__ = 'http://www.ebi.ac.uk/Tools/'
      __ebiGOUrl__ = 'https://www.ebi.ac.uk/QuickGO/services/'
      __uniprotUrl__ = 'http://www.uniprot.org/'
      __ebiSearchUrl__ = 'http://www.ebi.ac.uk/ebisearch/'
      __ebiUrl__ = 'http://www.ebi.ac.uk/Tools/'
      __ebiGOUrl__ = 'https://www.ebi.ac.uk/QuickGO/services/'
      __uniprotUrl__ = 'http://www.uniprot.org/'
      __ebiSearchUrl__ = 'http://www.ebi.ac.uk/ebisearch/'
      def fetch(entryId, dbName='uniprotkb', format='fasta'):
      """
      ......@@ -31,7 +33,7 @@ def fetch(entryId, dbName='uniprotkb', format='fasta'):
      http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=uniprotkb&id=P63166&format=fasta&style=raw&Retrieve=Retrieve
      """
      # Construct URL
      # Construct URL
      url = __ebiUrl__ + 'dbfetch/dbfetch?style=raw&Retrieve=Retrieve&db=' + dbName + '&format=' + format + '&id=' + entryId
      # Get the entry
      try:
      ......@@ -42,6 +44,7 @@ def fetch(entryId, dbName='uniprotkb', format='fasta'):
      except urllib.error.HTTPError as ex:
      raise RuntimeError(ex.read())
      def search(query, dbName='uniprot', format='list', limit=100, columns=""):
      """
      Retrieve multiple entries matching query from a database currently only via UniProtKB
      ......@@ -54,10 +57,14 @@ def search(query, dbName='uniprot', format='list', limit=100, columns=""):
      """
      if dbName.startswith('uniprot'):
      # Construct URL
      if limit == None: # no limit to number of results returned
      url = __uniprotUrl__ + dbName + '/?format=' + format + '&query=' + query + '&columns='+ columns
      if limit == None: # no limit to number of results returned
      url = "{}{}/?format={}&query={}&columns={}".format(__uniprotUrl__, dbName, format,
      urllib.parse.quote(query),
      columns)
      else:
      url = __uniprotUrl__ + dbName + '/?format=' + format + '&limit=' + str(limit) + '&query=' + query + '&columns='+ columns
      url = "{}{}/?format={}&limit={}&query={}&columns={}".format(__uniprotUrl__, dbName, format, str(limit),
      urllib.parse.quote(query), columns)
      # Get the entries
      try:
      ......@@ -72,13 +79,20 @@ def search(query, dbName='uniprot', format='list', limit=100, columns=""):
      dbs = dbName.split(":")
      if len(dbs) > 1:
      dbName = dbs[1]
      base = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/'
      url = base + "esearch.fcgi?db=" + dbName + "&term=" + query + "&retmax=" + str(limit)
      url = base + "esearch.fcgi?db={}&term={}+AND+srcdb_refseq[" \
      "prop]&retmax={}".format(dbName, urllib.parse.quote(query), str(limit))
      print (url)
      # Get the entries
      try:
      data = urllib.request.urlopen(url).read().decode("utf-8")
      words = data.split("</Id>")
      words = [w[w.find("<Id>")+4:] for w in words[:-1]]
      words = [w[w.find("<Id>") + 4:] for w in words[:-1]]
      if format == 'list':
      return words
      elif format == 'fasta' and len(words) > 0:
      ......@@ -93,9 +107,10 @@ def search(query, dbName='uniprot', format='list', limit=100, columns=""):
      raise RuntimeError(ex.read())
      return
      authorised_database_tag = {9606: ['Homo sapiens', 'ACC', 'ID'],
      3702: ['Arabidopsis thaliana', 'TAIR_ID'],
      4932: ['Saccharomyces cerevisiae', 'SGD_ID', 'CYGD_ID'],
      authorised_database_tag = {9606: ['Homo sapiens', 'ACC', 'ID'],
      3702: ['Arabidopsis thaliana', 'TAIR_ID'],
      4932: ['Saccharomyces cerevisiae', 'SGD_ID', 'CYGD_ID'],
      10090: ['Mus musculus', 'MGI_ID']}
      """
      ......@@ -104,7 +119,8 @@ http://www.ebi.ac.uk/QuickGO/WebServices.html
      Note that this service can be slow for queries involving a large number of entries.
      """
      def getGOReport(positives, background = None):
      def getGOReport(positives, background=None):
      """ Generate a complete GO term report for a set of genes (positives).
      Each GO term is also assigned an enrichment p-value (on basis of background, if provided).
      Returns a list of tuples (GO_Term_ID[str], Foreground_no[int], Term_description[str]) with no background, OR
      ......@@ -135,7 +151,7 @@ def getGOReport(positives, background = None):
      for t in term_set:
      term_cnt[t] = fg_list.count(t)
      sorted_cnt = sorted(list(term_cnt.items()), key=lambda v: v[1], reverse=True)
      else: # a background is provided
      else: # a background is provided
      for t in term_set:
      fg_hit = fg_list.count(t)
      bg_hit = bg_list.count(t)
      ......@@ -148,11 +164,12 @@ def getGOReport(positives, background = None):
      for t in sorted_cnt:
      defin = getGODef(t[0])
      if background != None:
      ret.append((t[0], t[1][2] * len(term_set), t[1][0], t[1][0]+t[1][1], defin['name']))
      ret.append((t[0], t[1][2] * len(term_set), t[1][0], t[1][0] + t[1][1], defin['name']))
      else:
      ret.append((t[0], t[1], defin['name']))
      return ret
      def getGODef(goterm):
      """
      Retrieve information about a GO term
      ......@@ -165,7 +182,7 @@ def getGODef(goterm):
      url = __ebiGOUrl__ + 'ontology/go/search?query=' + goterm
      # Get the entry: fill in the fields specified below
      try:
      entry={'id': None, 'name': None, 'aspect': None}
      entry = {'id': None, 'name': None, 'aspect': None}
      data = urllib.request.urlopen(url).read().decode("utf-8")
      ret = json.loads(data)
      for row in ret['results']:
      ......@@ -179,6 +196,7 @@ def getGODef(goterm):
      except urllib.error.HTTPError as ex:
      raise RuntimeError(ex.read())
      def getGOTerms(genes):
      """
      Retrieve all GO terms for a given set of genes (or single gene).
      ......@@ -187,9 +205,9 @@ def getGOTerms(genes):
      if type(genes) != list and type(genes) != set and type(genes) != tuple:
      genes = [genes]
      map = dict()
      batchsize = 100 # size of query batch
      batchsize = 100 # size of query batch
      genecnt = 0
      limitpage = 100 # number of record on each returned page
      limitpage = 100 # number of record on each returned page
      while genecnt < len(genes):
      genebatch = []
      for index in range(batchsize):
      ......@@ -237,6 +255,7 @@ def getGOTerms(genes):
      raise RuntimeError(ex.read())
      return map
      def getGenes(goterms, taxo=None):
      """
      Retrieve all genes/proteins for a given set of GO terms (or single GO term).
      ......@@ -247,9 +266,9 @@ def getGenes(goterms, taxo=None):
      if type(goterms) != list and type(goterms) != set and type(goterms) != tuple:
      goterms = [goterms]
      map = dict()
      batchsize = 10 # size of query batch
      batchsize = 10 # size of query batch
      termcnt = 0
      limitpage = 100 # number of record on each returned page
      limitpage = 100 # number of record on each returned page
      while termcnt < len(goterms):
      termbatch = []
      for index in range(batchsize):
      ......@@ -258,7 +277,8 @@ def getGenes(goterms, taxo=None):
      else:
      break
      termcnt += 1
      uri_string = 'annotation/search?limit=' + str(limitpage) + '&taxonId=' + taxo + "&goId=" if taxo else 'annotation/search?goId='
      uri_string = 'annotation/search?limit=' + str(
      limitpage) + '&taxonId=' + taxo + "&goId=" if taxo else 'annotation/search?goId='
      for i in range(len(termbatch)):
      term = termbatch[i]
      uri_string += term + "," if i < len(termbatch) - 1 else term
      ......@@ -295,11 +315,11 @@ def getGenes(goterms, taxo=None):
      raise RuntimeError(ex.read())
      return map
      class EBI(object):
      __email__ = 'anon@uq.edu.au' # to whom emails about jobs should go
      __ebiServiceUrl__ = 'http://www.ebi.ac.uk/Tools/services/rest/' # Use UQ mirror when available
      __checkInterval__ = 2 # how long to wait between checking job status
      class EBI(object):
      __email__ = 'anon@uq.edu.au' # to whom emails about jobs should go
      __ebiServiceUrl__ = 'http://www.ebi.ac.uk/Tools/services/rest/' # Use UQ mirror when available
      __checkInterval__ = 2 # how long to wait between checking job status
      def __init__(self, service=None):
      """ Initialise service session.
      ......@@ -349,7 +369,8 @@ class EBI(object):
      if self.isLocked():
      raise RuntimeError("""You currently have a %s job running. You must
      wait until it is complete before submitting another job. Go to
      %sstatus/%s to check the status of the job.""" % (self.service, self.__ebiServiceUrl__, self.jobId))
      %sstatus/%s to check the status of the job.""" % (
      self.service, self.__ebiServiceUrl__, self.jobId))
      url = self.__ebiServiceUrl__ + self.service + '/run/'
      # ncbiblast database parameter needs special handling
      if self.service == 'ncbiblast':
      ......@@ -423,8 +444,8 @@ class EBI(object):
      else:
      return results
      def getUniProtDict(ids, cols="", db='uniprot', identities=None):
      def getUniProtDict(ids, cols="", db='uniprot', identities=None):
      """
      :param ids: The list of UniProt IDs
      ......@@ -439,11 +460,11 @@ def getUniProtDict(ids, cols="", db='uniprot', identities=None):
      *** EXAMPLE USAGE ***
      Get a list of UniProt IDs and a list of UniProt columns you're interested in.
      Full list of UniProt column names - https://www.uniprot.org/help/uniprotkb_column_names
      uniprot_names = ['Q9LIR4', 'Q1JUQ1', 'P05791', 'P0ADF6']
      cols = ["lineage(SUPERKINGDOM)", "genes", "lineage(KINGDOM)"]
      up_dict = getUniProtDict(uniprot_names, cols)
      for record in up_dict:
      print (record, up_dict[record].get("lineage(SUPERKINGDOM)"))
      ......@@ -452,22 +473,21 @@ def getUniProtDict(ids, cols="", db='uniprot', identities=None):
      for record in up_dict:
      print (record, up_dict[record].get("genes"))
      If a record doesn't have an entry in UniProt for that column it'll just return None
      print (up_dict['Q1JUQ1'])
      print (up_dict['Q1JUQ1']['lineage(KINGDOM)'])
      *** EXAMPLE USAGE FOR UNIREF SEARCHING ***
      up_dict = getUniProtDict(["Q9LIR4", "P99999"], cols=["members"], db="uniref", identities = 1.0)
      You can either pass a list of identities for each UniProt identifier (in which case the list of identities must be
      the same size as the list of identifiers. Or you can just pass a single identity to search Uniref at.
      """
      # Format the lists of IDs and columns correctly
      cols = ",".join(cols)
      ......@@ -481,12 +501,14 @@ def getUniProtDict(ids, cols="", db='uniprot', identities=None):
      if type(identities) != list:
      identities = [identities] * len(ids)
      elif len(identities) != len(ids):
      raise RuntimeError('Either supply a single identity threshold or supply one for each identifier in the list')
      raise RuntimeError(
      'Either supply a single identity threshold or supply one for each identifier in the list')
      # Check that the identity thresholds are valid values
      for x in identities:
      if x not in [1.0, 0.9, 0.5]:
      raise RuntimeError("UniRef threshold values must be either 1.0, 0.9, or 0.5. Supplied value was - " + str(x))
      raise RuntimeError(
      "UniRef threshold values must be either 1.0, 0.9, or 0.5. Supplied value was - " + str(x))
      # Add the query syntax around the identifiers
      updated_ids = ""
      ......@@ -500,8 +522,6 @@ def getUniProtDict(ids, cols="", db='uniprot', identities=None):
      url = 'https://www.uniprot.org/' + db + '/'
      params = {
      'format': 'tab',
      'query': updated_ids,
      ......@@ -518,12 +538,12 @@ def getUniProtDict(ids, cols="", db='uniprot', identities=None):
      # For each record we retrieve, split the line by tabs and build up the UniProt dict
      for line in page.split("\n")[1:]:
      if line:
      splitlines= line.split("\t")
      splitlines = line.split("\t")
      id_dict = {}
      pos = 1
      for col in cols.split(","):
      id_dict[col] = None if splitlines[pos] == "" else splitlines[pos]
      pos +=1
      pos += 1
      up_dict[splitlines[0]] = id_dict
      return up_dict
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