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Merge pull request #43 from martinghunt/spades_3.6.2
Spades 3.6.2
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,5 +1,6 @@ | ||
| __all__ = [ | ||
| 'assemble', | ||
| 'assembly', | ||
| 'bamfilter', | ||
| 'clean', | ||
| 'common', | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,153 @@ | ||
| import os | ||
| import pyfastaq | ||
|
|
||
| class Error (Exception): pass | ||
|
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| class Assembly: | ||
| def __init__(self, path): | ||
| '''path can be a directory or a filename. If directory, assumes the name of a SPAdes | ||
| output directory. If a file, assumes it is a fasta file of contigs''' | ||
| if not os.path.exists(path): | ||
| raise Error('Input path to Assembly.__init__ not found: ' + path) | ||
| elif os.path.isdir(path): | ||
| self.spades_dir = os.path.abspath(path) | ||
| else: | ||
| self.contigs_fasta = os.path.abspath(path) | ||
| self.spades_dir = None | ||
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| self._set_filenames() | ||
|
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| @staticmethod | ||
| def _file_exists(filename): | ||
| if os.path.exists(filename): | ||
| return filename | ||
| else: | ||
| return None | ||
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|
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| def _set_filenames(self): | ||
| self.contigs_fastg = None | ||
| self.contigs_paths = None | ||
| self.assembly_graph_fastg = None | ||
|
|
||
| if self.spades_dir is None: | ||
| return | ||
|
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| contigs_fasta = os.path.join(self.spades_dir, 'contigs.fasta') | ||
| self.contigs_fasta = self._file_exists(os.path.join(contigs_fasta)) | ||
|
|
||
| if self.contigs_fasta is None: | ||
| raise Error('Error finding SPAdes contigs file: ' + contigs_fasta) | ||
|
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| self.contigs_fastg = self._file_exists(os.path.join(self.spades_dir, 'contigs.fastg')) | ||
| self.contigs_paths = self._file_exists(os.path.join(self.spades_dir, 'contigs.paths')) | ||
| self.assembly_graph_fastg = self._file_exists(os.path.join(self.spades_dir, 'assembly_graph.fastg')) | ||
|
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| if None == self.contigs_fastg == self.contigs_paths == self.assembly_graph_fastg or \ | ||
| ( self.contigs_fastg is None and (None in {self.contigs_paths, self.assembly_graph_fastg}) ) or \ | ||
| ( self.contigs_fastg is not None and (self.contigs_paths is not None or self.assembly_graph_fastg is not None) ): | ||
| error_message = '\n'.join([ | ||
| 'Error finding SPAdes graph files in the directory ' + self.spades_dir, | ||
| 'Expected either:', | ||
| ' contigs.fastg (SPAdes <3.6.1)', | ||
| 'or:', | ||
| ' contigs.paths and assembly_graph.fastg (SPAdes >3.6.1)' | ||
| ]) | ||
| raise Error(error_message) | ||
|
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|
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| def get_contigs(self): | ||
| '''Returns a dictionary of contig_name -> pyfastaq.Sequences.Fasta object''' | ||
| contigs = {} | ||
| pyfastaq.tasks.file_to_dict(self.contigs_fasta, contigs) | ||
| return contigs | ||
|
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| @classmethod | ||
| def _circular_contigs_from_spades_before_3_6_1(cls, fastg_file): | ||
| seq_reader = pyfastaq.sequences.file_reader(fastg_file) | ||
| names = set([x.id.rstrip(';') for x in seq_reader if ':' in x.id]) | ||
| found_fwd = set() | ||
| found_rev = set() | ||
| for name in names: | ||
| l = name.split(':') | ||
| if len(l) != 2: | ||
| continue | ||
| if l[0] == l[1]: | ||
| if l[0][-1] == "'": | ||
| found_rev.add(l[0][:-1]) | ||
| else: | ||
| found_fwd.add(l[0]) | ||
|
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| return found_fwd.intersection(found_rev) | ||
|
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|
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| @classmethod | ||
| def _spades_contigs_paths_to_dict(cls, filename): | ||
| d = {} | ||
| node = None | ||
|
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| with open(filename) as f: | ||
| for line in f: | ||
| if node is None: | ||
| if not line.startswith('NODE_'): | ||
| raise Error('Error loading info from SPAdes contigs path file ' + filename) | ||
| node = line.rstrip() | ||
| else: | ||
| if line.startswith('NODE_') or node in d: | ||
| raise Error('Error loading info from SPAdes contigs path file ' + filename) | ||
| d[node] = line.rstrip() | ||
| node = None | ||
|
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| return d | ||
|
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| @classmethod | ||
| def _circular_edges_to_edge_numbers_dict(cls, circular_edges): | ||
| '''Edge names are like this: EDGE_1_length_44766_cov_16.555. | ||
| This returns dict of edge number -> edge name. | ||
| eg 1 -> EDGE_1_length_44766_cov_16.555.''' | ||
| return {x.split('_')[1]: x for x in circular_edges} | ||
|
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| @staticmethod | ||
| def _circular_contigs_from_spades_after_3_6_1(assembly_graph_fastg, contigs_paths): | ||
| circular_graph_edges = Assembly._circular_contigs_from_spades_before_3_6_1(assembly_graph_fastg) | ||
| circular_edge_dict = Assembly._circular_edges_to_edge_numbers_dict(circular_graph_edges) | ||
| paths_dict = Assembly._spades_contigs_paths_to_dict(contigs_paths) | ||
| circular_nodes = set() | ||
|
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| for node in paths_dict: | ||
| if node.endswith("'"): | ||
| continue | ||
|
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| edges = paths_dict[node].split(',') | ||
| rev_node = node + "'" | ||
|
|
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| if len(edges) != 1 or rev_node not in paths_dict: | ||
| continue | ||
|
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| rev_edges = paths_dict[rev_node].split(',') | ||
|
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| if len(rev_edges) != 1: | ||
| continue | ||
|
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| edge = list(edges)[0][:-1] | ||
| edge_strand = list(edges)[0][-1] | ||
| rev_edge = list(rev_edges)[0][:-1] | ||
| rev_edge_strand = list(rev_edges)[0][-1] | ||
| if {'-', '+'} == {edge_strand, rev_edge_strand} and edge == rev_edge and edge in circular_edge_dict: | ||
| circular_nodes.add(node) | ||
|
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| return circular_nodes | ||
|
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| def circular_contigs(self): | ||
| '''Returns a set of the contig names that are circular''' | ||
| if self.contigs_fastg is not None: | ||
| return self._circular_contigs_from_spades_before_3_6_1(self.contigs_fastg) | ||
| elif None not in [self.contigs_paths, self.assembly_graph_fastg]: | ||
| return self._circular_contigs_from_spades_after_3_6_1(self.assembly_graph_fastg, self.contigs_paths) | ||
| else: | ||
| return set() |
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