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August 10, 2016 12:27
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Class for searching G-quadruplex motifs. (Part of QuadBase2 webserver)
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| import re | |
| from itertools import groupby | |
| import os | |
| """ | |
| MIT License | |
| Copyright (c) [2016] [Parashar Dhapola] | |
| Permission is hereby granted, free of charge, to any person obtaining a copy | |
| of this software and associated documentation files (the "Software"), to deal | |
| in the Software without restriction, including without limitation the rights | |
| to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | |
| copies of the Software, and to permit persons to whom the Software is | |
| furnished to do so, subject to the following conditions: | |
| 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 OTHERWISE, ARISING FROM, | |
| OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE | |
| SOFTWARE. | |
| """ | |
| __author__ = "Parashar Dhapola" | |
| __email__ = "parashar.dhapola@gmail.com" | |
| class QuadMotifFinder(): | |
| """ | |
| This class allows searching G-quadruplex motifs in given seuqences. | |
| Please see the paper below for details and cite it if you use this code | |
| QuadBase2: web server for multiplexed guanine quadruplex mining and | |
| visualization | |
| doi: 10.1093/nar/gkw425 | |
| """ | |
| def __init__(self, fasta_file, savename, stem=3, loop_start=1, | |
| loop_stop=7, greedy=True, bulge=0): | |
| self.fastaFile = fasta_file | |
| self.saveName = savename | |
| self.stemSize = stem | |
| self.minLoopSize = loop_start | |
| self.maxLoopSize = loop_stop | |
| self.greedySearch = greedy | |
| self.bulgeSize = bulge | |
| self.outHandles = {} | |
| self._sanitize_params() | |
| self.resOv, self.resNov = [], [] | |
| fastaGen = self._read_fasta(self.fastaFile) | |
| for h, s in fastaGen: | |
| for i in ['+', '-']: | |
| signature, motifOv, motifNov = self._make_motif(i) | |
| self.resOv.extend(self._run_regex(s, h, motifOv, signature)) | |
| self.resNov.extend(self._run_regex(s, h, motifNov, signature)) | |
| self.outHandles['ov'].write("\n".join(self.resOv) + "\n") | |
| self.outHandles['nov'].write("\n".join(self.resNov) + "\n") | |
| self.outHandles['ov'].close() | |
| self.outHandles['nov'].close() | |
| def _sanitize_params(self): | |
| try: | |
| self.stemSize = int(self.stemSize) | |
| self.minLoopSize = int(self.minLoopSize) | |
| self.maxLoopSize = int(self.maxLoopSize) | |
| self.bulgeSize = int(self.bulgeSize) | |
| except: | |
| raise TypeError('Please provide only integer values for size paramaters') | |
| try: | |
| self.greedySearch = bool(self.greedySearch) | |
| except: | |
| raise TypeError('Please provide only boolean values for greedySearch') | |
| if self.minLoopSize >= self.maxLoopSize: | |
| raise ValueError('Minimum loop size has to be larger than maximum loop size') | |
| if os.path.isfile(self.fastaFile) is False: | |
| print "File 'fasta_file' not found!." | |
| if self.bulgeSize > 0 and self.stemSize != 3: | |
| print "Bulge search disabled as stem size not equal to 3" | |
| self.bulgeSize = 0 | |
| try: | |
| self.outHandles['ov'] = open('%s_ov.bed' % self.saveName, 'w') | |
| self.outHandles['nov'] = open('%s_nov.bed' % self.saveName, 'w') | |
| except IOError: | |
| raise IOError('Unable to open output file') | |
| def _read_fasta(self, fasta_name): | |
| fh = open(fasta_name) | |
| faiter = (f[1] for f in groupby(fh, lambda line: line[0] == ">")) | |
| for head in faiter: | |
| head = head.next()[1:].strip() | |
| s = "".join(s.strip() for s in faiter.next()) | |
| yield head, s | |
| def _make_base(self, strand): | |
| if strand == "+": | |
| base = 'G' | |
| invert_base = 'C' | |
| else: | |
| base = 'C' | |
| invert_base = 'G' | |
| return base, invert_base | |
| def _make_signature(self, base): | |
| return "".join(map(str, [base, self.stemSize, 'L', | |
| self.minLoopSize, '-', self.maxLoopSize])) | |
| def _make_stem_motif(self, base, invert_base): | |
| if self.bulgeSize > 0: | |
| stem_motif = '(?:%s|%s[AT%sN]{1,%d}%s|%s[AT%sN]{1,%d}%s)' % (base * 3, base, invert_base, | |
| self.bulgeSize, base * 2, base * 2, invert_base, self.bulgeSize, base) | |
| else: | |
| stem_motif = '%s' % (base * self.stemSize) | |
| return stem_motif | |
| def _make_loop_motif(self, base, invert_base): | |
| if self.greedySearch is True: | |
| loop_motif = "[ACTGN]{%d,%d}" % (self.minLoopSize, self.maxLoopSize) | |
| else: | |
| loop_motif = '[ATGCN](?:[ATN%s]|(?!%s{2})%s){%d,%d}' % ( | |
| invert_base, base, base, self.minLoopSize - 1, self.maxLoopSize - 1) | |
| return loop_motif | |
| def _make_motif(self, strand): | |
| base, invert_base = self._make_base(strand) | |
| quad_signature = self._make_signature(base) | |
| stem_motif = self._make_stem_motif(base, invert_base) | |
| loop_motif = self._make_loop_motif(base, invert_base) | |
| quad_motif_nov = (stem_motif + loop_motif) * 3 + stem_motif | |
| quad_motif_nov = "(" + quad_motif_nov + ")" | |
| quad_motif_ov = "(?=(%s))" % quad_motif_nov | |
| return quad_signature, quad_motif_ov, quad_motif_nov | |
| def _run_regex(self, seq, name, pattern, signature): | |
| regex = re.compile(pattern, flags=re.IGNORECASE) | |
| reg_obj = regex.finditer(seq) | |
| res = [] | |
| for match in reg_obj: | |
| temp_res = [name, match.start(), match.start() + len(match.group(1)) + 1, | |
| len(match.group(1)), signature, match.group(1)] | |
| res.append("\t".join(map(str, temp_res))) | |
| return res | |
| if __name__ == "__main__": | |
| with open('testquad.fa', 'w') as OUT: | |
| OUT.write('>hell\nACTGCGGGTACGGGGATCGGGGGATCGTGGGGGGATCGGGGGG') | |
| q = QuadMotifFinder('testquad.fa', 'quads', stem=3, loop_start=2, bulge=1) |
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