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| Original file line number | Diff line number | Diff line change |
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| """Command-line interface to create an initial Python sections file | ||
| Usage: | ||
| wr_sections.py [GO_FILE] | ||
| wr_sections.py [GO_FILE] [options] | ||
| Options: | ||
| -h --help show this help message and exit | ||
| -i <file.txt>, --ifile=<sections_in.txt> Read or Write file name [default: sections_in.txt] | ||
| -o <file.txt>, --ofile=<sections.txt> write file name [default: sections.txt] | ||
| --txt=<file.txt> Write file name [default: grouped_gos.txt] | ||
| --py=<file.py> Write the sections list into a Python file | ||
| --xlsx=<file.xlsx> Group user GO IDs and write the results into an xlsx file | ||
| --obo=<file.obo> Ontologies in obo file [default: go-basic.obo]. | ||
| --slims=<file.obo> GO slims in obo file [default: goslim_generic.obo]. | ||
| --gaf=<file.gaf> Annotations from a gaf file | ||
| --gene2go=<gene2go> Annotations from a gene2go file downloaded from NCBI | ||
| """ | ||
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| from __future__ import print_function | ||
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| __copyright__ = "Copyright (C) 2016-2018, DV Klopfenstein, H Tang. All rights reserved." | ||
| __author__ = "DV Klopfenstein" | ||
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| import os | ||
| import sys | ||
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| from goatools.base import get_godag | ||
| from goatools.associations import get_tcntobj | ||
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| from goatools.cli.docopt_parse import DocOptParse | ||
| from goatools.cli.gos_get import GetGOs | ||
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| from goatools.gosubdag.gosubdag import GoSubDag | ||
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| from goatools.grouper.read_goids import read_sections | ||
| from goatools.grouper.grprdflts import GrouperDflts | ||
| from goatools.grouper.hdrgos import HdrgosSections | ||
| from goatools.grouper.grprobj import Grouper | ||
| from goatools.grouper.wr_sections import WrSections | ||
| from goatools.grouper.wr_sections import WrPySections | ||
| from goatools.grouper.sorter import Sorter | ||
| from goatools.grouper.wrxlsx import WrXlsxSortedGos | ||
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| # pylint: disable=too-few-public-methods | ||
| class SectionsWr(object): | ||
| """Class for command-line interface for creating GO term diagrams""" | ||
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| kws_dict = set(['GO_FILE', 'obo', 'slims', | ||
| 'ifile', 'ofile', 'txt', | ||
| 'py', 'xlsx', | ||
| 'gaf', 'gene2go', 'taxid']) | ||
| kws_set = set() | ||
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| def __init__(self, gosubdag=None): | ||
| self.objdoc = DocOptParse(__doc__, self.kws_dict, self.kws_set) | ||
| self.gosubdag = None if gosubdag is None else gosubdag | ||
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| def cli(self, prt=sys.stdout): | ||
| """Command-line interface for go_draw script.""" | ||
| kws = self.objdoc.get_docargs(prt=None) | ||
| godag = get_godag(kws['obo'], prt=None, loading_bar=False, optional_attrs=['relationship']) | ||
| usrgos = GetGOs(godag, max_gos=200).get_usrgos(kws.get('GO_FILE'), prt) | ||
| tcntobj = self._get_tcntobj(usrgos, godag, **kws) # Gets TermCounts or None | ||
| self.gosubdag = GoSubDag(usrgos, godag, relationships=True, tcntobj=tcntobj, prt=None) | ||
| grprdflt = GrouperDflts(self.gosubdag, kws['slims']) | ||
| ver_list = [godag.version, grprdflt.ver_goslims] | ||
| prt.write("{VER}\n".format(VER="\n".join(ver_list))) | ||
| sections = read_sections(kws['ifile'], exclude_ungrouped=True, prt=None) | ||
| # print("SECSECSEC", sections) | ||
| hdrobj = HdrgosSections(self.gosubdag, grprdflt.hdrgos_dflt, sections) | ||
| grprobj = Grouper("init", usrgos, hdrobj, self.gosubdag) | ||
| # Write sections | ||
| objsecwr = WrSections(grprobj, ver_list) | ||
| if not os.path.exists(kws['ifile']): | ||
| objsecwr.wr_txt_section_hdrgos(kws['ifile']) | ||
| objsecwr.wr_txt_section_hdrgos(kws['ofile']) | ||
| objsecpy = WrPySections(grprobj, ver_list) | ||
| if 'py' in kws: | ||
| objsecpy.wr_py_sections(kws['py'], sections, doc=godag.version) | ||
| # Write user GO IDs in sections | ||
| sortobj = Sorter(grprobj) | ||
| objgowr = WrXlsxSortedGos("init", sortobj, ver_list) | ||
| objgowr.wr_txt_gos(kws['txt'], sortby=objsecpy.fncsortnt) | ||
| #objwr.wr_txt_section_hdrgos(kws['ofile'], sortby=objwr.fncsortnt) | ||
| self._prt_cnt_usrgos(usrgos, sys.stdout) | ||
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| def _prt_cnt_usrgos(self, usrgos_read, prt): | ||
| num_usrgos = len(self.gosubdag.go_sources) | ||
| prt.write("{GOs:6} user GO IDs".format(GOs=num_usrgos)) | ||
| if len(usrgos_read) != num_usrgos: | ||
| prt.write(" of {M} GO IDs read".format(M=len(usrgos_read))) | ||
| prt.write("\n") | ||
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| @staticmethod | ||
| def _get_tcntobj(goids, go2obj, **kws): | ||
| """Get a TermCounts object if the user provides an annotation file, otherwise None.""" | ||
| # kws: gaf (gene2go taxid) | ||
| if 'gaf' in kws or 'gene2go' in kws: | ||
| # Get a reduced go2obj set for TermCounts | ||
| _gosubdag = GoSubDag(goids, go2obj, rcntobj=False, prt=None) | ||
| return get_tcntobj(_gosubdag.go2obj, **kws) # TermCounts | ||
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| # Copyright (C) 2016-2018, DV Klopfenstein, H Tang. All rights reserved. |
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| """Various methods to estimating if a GO term is more specific than another GO term.""" | ||
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| __copyright__ = "Copyright (C) 2016-2018, DV Klopfenstein, H Tang, All rights reserved." | ||
| __author__ = "DV Klopfenstein" | ||
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| def get_most_specific_dcnt(goids, go2nt): | ||
| """Get the GO ID with the lowest descendants count.""" | ||
| # go2nt_usr = {go:go2nt[go] for go in goids} | ||
| # return min(go2nt_usr.items(), key=lambda t: t[1].dcnt)[0] | ||
| return min(_get_go2nt(goids, go2nt), key=lambda t: t[1].dcnt)[0] | ||
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| def get_most_specific_tinfo(goids, go2nt): | ||
| """Get the GO ID with the highest GO term annotation information value.""" | ||
| # go2nt_usr = {go:go2nt[go] for go in goids} | ||
| # return max(go2nt_usr.items(), key=lambda t: t[1].tinfo)[0] | ||
| return max(_get_go2nt(goids, go2nt), key=lambda t: t[1].tinfo)[0] | ||
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| def get_most_specific_tinfo_dcnt(goids, go2nt): | ||
| """Get the GO ID with the highest GO term annotation information value.""" | ||
| # go2nt_usr = {go:go2nt[go] for go in goids} | ||
| # return max(go2nt_usr.items(), key=lambda t: [t[1].tinfo, t[1].dcnt])[0] | ||
| return max(_get_go2nt(goids, go2nt), key=lambda t: [t[1].tinfo, t[1].dcnt])[0] | ||
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| def _get_go2nt(goids, go2nt_all): | ||
| """Get user go2nt using main GO IDs, not alt IDs.""" | ||
| go_nt_list = [] | ||
| goids_seen = set() | ||
| for goid_usr in goids: | ||
| ntgo = go2nt_all[goid_usr] | ||
| goid_main = ntgo.id | ||
| if goid_main not in goids_seen: | ||
| goids_seen.add(goid_main) | ||
| go_nt_list.append((goid_main, ntgo)) | ||
| return go_nt_list | ||
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| # Copyright (C) 2016-2018, DV Klopfenstein, H Tang, All rights reserved. |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1 +1 @@ | ||
| # Group GO Terms under researcher-defined sections | ||
| # Directory for grouper functions and classes |
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