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Separating GO wr-hierarchy from general wr-hierarchy
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,72 @@ | ||
| """Print a GO term's lower-level hierarchy.""" | ||
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| __copyright__ = "Copyright (C) 2016-2018, DV Klopfenstein, H Tang. All rights reserved." | ||
| __author__ = "DV Klopfenstein" | ||
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| import sys | ||
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| # pylint: disable=too-many-instance-attributes,too-few-public-methods | ||
| class WrHierPrt(object): | ||
| """Print GO hierarchy.""" | ||
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| def __init__(self, id2obj, id2nt, cfg, prt=sys.stdout): | ||
| self.id2obj = id2obj # Contains children (and parents) | ||
| self.id2nt = id2nt # Contains fields for printing | ||
| self.nm2prtfmt = cfg['name2prtfmt'] | ||
| self.max_indent = cfg['max_indent'] | ||
| self.include_only = cfg['include_only'] | ||
| self.go_marks = cfg['go_marks'] | ||
| self.concise_prt = cfg['concise_prt'] | ||
| self.indent = cfg['indent'] | ||
| # vars | ||
| self.prt = prt | ||
| self.gos_printed = set() | ||
| self.dash_len = cfg['dash_len'] + 12 | ||
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| def prt_hier_rec(self, goid, depth=1): | ||
| """Write hierarchy for a GO Term record and all GO IDs down to the leaf level.""" | ||
| ntgo = self.id2nt[goid] | ||
| ntobj = self.id2obj[goid] | ||
| # Shortens hierarchy report by only printing the hierarchy | ||
| # for the sub-set of user-specified GO terms which are connected. | ||
| if self.include_only and goid not in self.include_only: | ||
| return | ||
| nrp = self.concise_prt and goid in self.gos_printed | ||
| if self.go_marks: | ||
| self.prt.write('{MARK} '.format(MARK='>' if goid in self.go_marks else ' ')) | ||
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| # '-' is default character indicating hierarchy level | ||
| # '=' is used to indicate a hierarchical path printed in detail previously. | ||
| dct = ntgo._asdict() | ||
| self.prt.write('{DASHGO:{N}}'.format( | ||
| DASHGO=self._str_dashgoid(dct, depth, not nrp or not ntobj.children), | ||
| N=self.dash_len)) | ||
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| self.prt.write("{INFO}\n".format(INFO=self.nm2prtfmt['ITEM'].format(**dct))) | ||
| self.gos_printed.add(goid) | ||
| # Do not print hierarchy below this turn if it has already been printed | ||
| if nrp: | ||
| return | ||
| depth += 1 | ||
| if self.max_indent is not None and depth > self.max_indent: | ||
| return | ||
| for child in ntobj.children: | ||
| self.prt_hier_rec(child.id, depth) | ||
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| @staticmethod | ||
| def _str_dash(depth, single_or_double): | ||
| """Return a string containing dashes (optional) and GO ID.""" | ||
| # '-' is default character indicating hierarchy level | ||
| # '=' is used to indicate a hierarchical path printed in detail previously. | ||
| letter = '-' if single_or_double else '=' | ||
| return ''.join([letter]*depth) | ||
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| def _str_dashgoid(self, dct, depth, single_or_double): | ||
| """Return a string containing dashes (optional) and GO ID.""" | ||
| return "{DASHES} {ID}".format( | ||
| DASHES=self._str_dash(depth, single_or_double) if self.indent else "", | ||
| ID=self.nm2prtfmt['ID'].format(**dct)) | ||
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| # Copyright (C) 2016-2018, DV Klopfenstein, H Tang. All rights reserved. |