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How to use the gtdbtk.tools.symlink_f function in gtdbtk

To help you get started, we’ve selected a few gtdbtk examples, based on popular ways it is used in public projects.

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github Ecogenomics / GTDBTk / gtdbtk / main.py View on Github external
taxonomy,
              options.output_tree)

        self.logger.info('Done.')

        # symlink to the decorated tree file, if not run independently
        if hasattr(options, 'suffix'):
            if options.suffix == 'bac120':
                symlink_f(PATH_BAC120_DECORATED_TREE.format(prefix=options.prefix),
                          os.path.join(options.out_dir,
                                       os.path.basename(PATH_BAC120_DECORATED_TREE.format(prefix=options.prefix))))
                symlink_f(PATH_BAC120_DECORATED_TREE.format(prefix=options.prefix) + '-table',
                          os.path.join(options.out_dir,
                                       os.path.basename(PATH_BAC120_DECORATED_TREE.format(prefix=options.prefix)  + '-table')))
            elif options.suffix == 'ar122':
                symlink_f(PATH_AR122_DECORATED_TREE.format(prefix=options.prefix),
                          os.path.join(options.out_dir,
                                       os.path.basename(PATH_AR122_DECORATED_TREE.format(prefix=options.prefix))))
                symlink_f(PATH_AR122_DECORATED_TREE.format(prefix=options.prefix) + '-table',
                          os.path.join(options.out_dir,
                                       os.path.basename(PATH_AR122_DECORATED_TREE.format(prefix=options.prefix)  + '-table')))
            else:
                raise GenomeMarkerSetUnknown(
                    'There was an error determining the marker set.')
github Ecogenomics / GTDBTk / gtdbtk / main.py View on Github external
else:
            output_tree = os.path.join(options.out_dir,
                                       PATH_UNROOTED_TREE.format(prefix=options.prefix))
            tree_log = os.path.join(options.out_dir,
                                    PATH_TREE_LOG.format(prefix=options.prefix))
            fasttree_log = os.path.join(options.out_dir,
                                        PATH_FASTTREE_LOG.format(prefix=options.prefix))

        fasttree = FastTree()
        fasttree.run(output_tree, tree_log, fasttree_log, options.prot_model,
                     options.no_support, options.gamma, options.msa_file,
                     options.cpus)
        self.logger.info(f'FastTree version: {fasttree.version}')

        if hasattr(options, 'subparser_name') and options.subparser_name == 'infer':
            symlink_f(output_tree[len(options.out_dir) + 1:],
                      os.path.join(options.out_dir,
                                   os.path.basename(output_tree)))

        self.logger.info('Done.')
github Ecogenomics / GTDBTk / gtdbtk / classify.py View on Github external
symlink_f(PATH_BAC120_TREE_FILE.format(prefix=prefix),
                      os.path.join(out_dir, os.path.basename(PATH_BAC120_TREE_FILE.format(prefix=prefix))))
        elif marker_set_id == 'ar122':
            symlink_f(PATH_AR122_TREE_FILE.format(prefix=prefix),
                      os.path.join(out_dir, os.path.basename(PATH_AR122_TREE_FILE.format(prefix=prefix))))
        else:
            self.logger.error('There was an error determining the marker set.')
            raise GenomeMarkerSetUnknown

        # Symlink to the tree summary file
        if marker_set_id == 'bac120':
            if levelopt is None:
                symlink_f(PATH_BAC120_TREE_FILE.format(prefix=prefix),
                          os.path.join(out_dir, os.path.basename(PATH_BAC120_TREE_FILE.format(prefix=prefix))))
            elif levelopt == 'high':
                symlink_f(PATH_HIGH_BAC120_TREE_FILE.format(prefix=prefix),
                          os.path.join(out_dir, os.path.basename(PATH_HIGH_BAC120_TREE_FILE.format(prefix=prefix))))
            elif levelopt == 'low':
                symlink_f(PATH_LOW_BAC120_TREE_FILE.format(iter=tree_iter, prefix=prefix),
                          os.path.join(out_dir, os.path.basename(PATH_LOW_BAC120_TREE_FILE.format(iter=tree_iter, prefix=prefix))))
        elif marker_set_id == 'ar122':
            symlink_f(PATH_AR122_TREE_FILE.format(prefix=prefix),
                      os.path.join(out_dir, os.path.basename(PATH_AR122_TREE_FILE.format(prefix=prefix))))
        else:
            self.logger.error('There was an error determining the marker set.')
            raise GenomeMarkerSetUnknown

        return tree_file
github Ecogenomics / GTDBTk / gtdbtk / classify.py View on Github external
out_dir, PATH_HIGH_BAC120_TREE_FILE.format(prefix=prefix))
            elif levelopt == 'low':
                tree_file = os.path.join(
                    out_dir, PATH_LOW_BAC120_TREE_FILE.format(prefix=prefix, iter=tree_iter))
        elif marker_set_id == 'ar122':
            tree_file = os.path.join(
                out_dir, PATH_AR122_TREE_FILE.format(prefix=prefix))
        else:
            self.logger.error('There was an error determining the marker set.')
            raise GenomeMarkerSetUnknown

        pplacer.tog(pplacer_json_out, tree_file)

        # Symlink to the tree summary file
        if marker_set_id == 'bac120':
            symlink_f(PATH_BAC120_TREE_FILE.format(prefix=prefix),
                      os.path.join(out_dir, os.path.basename(PATH_BAC120_TREE_FILE.format(prefix=prefix))))
        elif marker_set_id == 'ar122':
            symlink_f(PATH_AR122_TREE_FILE.format(prefix=prefix),
                      os.path.join(out_dir, os.path.basename(PATH_AR122_TREE_FILE.format(prefix=prefix))))
        else:
            self.logger.error('There was an error determining the marker set.')
            raise GenomeMarkerSetUnknown

        # Symlink to the tree summary file
        if marker_set_id == 'bac120':
            if levelopt is None:
                symlink_f(PATH_BAC120_TREE_FILE.format(prefix=prefix),
                          os.path.join(out_dir, os.path.basename(PATH_BAC120_TREE_FILE.format(prefix=prefix))))
            elif levelopt == 'high':
                symlink_f(PATH_HIGH_BAC120_TREE_FILE.format(prefix=prefix),
                          os.path.join(out_dir, os.path.basename(PATH_HIGH_BAC120_TREE_FILE.format(prefix=prefix))))
github Ecogenomics / GTDBTk / gtdbtk / classify.py View on Github external
symlink_f(PATH_AR122_TREE_FILE.format(prefix=prefix),
                      os.path.join(out_dir, os.path.basename(PATH_AR122_TREE_FILE.format(prefix=prefix))))
        else:
            self.logger.error('There was an error determining the marker set.')
            raise GenomeMarkerSetUnknown

        # Symlink to the tree summary file
        if marker_set_id == 'bac120':
            if levelopt is None:
                symlink_f(PATH_BAC120_TREE_FILE.format(prefix=prefix),
                          os.path.join(out_dir, os.path.basename(PATH_BAC120_TREE_FILE.format(prefix=prefix))))
            elif levelopt == 'high':
                symlink_f(PATH_HIGH_BAC120_TREE_FILE.format(prefix=prefix),
                          os.path.join(out_dir, os.path.basename(PATH_HIGH_BAC120_TREE_FILE.format(prefix=prefix))))
            elif levelopt == 'low':
                symlink_f(PATH_LOW_BAC120_TREE_FILE.format(iter=tree_iter, prefix=prefix),
                          os.path.join(out_dir, os.path.basename(PATH_LOW_BAC120_TREE_FILE.format(iter=tree_iter, prefix=prefix))))
        elif marker_set_id == 'ar122':
            symlink_f(PATH_AR122_TREE_FILE.format(prefix=prefix),
                      os.path.join(out_dir, os.path.basename(PATH_AR122_TREE_FILE.format(prefix=prefix))))
        else:
            self.logger.error('There was an error determining the marker set.')
            raise GenomeMarkerSetUnknown

        return tree_file
github Ecogenomics / GTDBTk / gtdbtk / markers.py View on Github external
trimmed_user_msa = {
                k: v for k, v in trimmed_seqs.items() if k in user_msa}
            if len(trimmed_user_msa) > 0:
                self.logger.info(
                    'Creating concatenated alignment for {:,} {} user genomes.'.format(
                        len(trimmed_user_msa),
                        domain_str))
                self._write_msa(trimmed_user_msa,
                                marker_user_msa_path, gtdb_taxonomy)
            else:
                self.logger.info(f'All {domain_str} user genomes have been filtered out.')

            # Create symlinks to the summary files
            if marker_set_id == 'bac120':
                symlink_f(PATH_BAC120_FILTERED_GENOMES.format(prefix=prefix),
                          os.path.join(out_dir, os.path.basename(PATH_BAC120_FILTERED_GENOMES.format(prefix=prefix))))
                if len(trimmed_user_msa) > 0:
                    symlink_f(PATH_BAC120_USER_MSA.format(prefix=prefix),
                              os.path.join(out_dir, os.path.basename(PATH_BAC120_USER_MSA.format(prefix=prefix))))
                if not skip_gtdb_refs:
                    symlink_f(PATH_BAC120_MSA.format(prefix=prefix),
                              os.path.join(out_dir, os.path.basename(PATH_BAC120_MSA.format(prefix=prefix))))
            elif marker_set_id == 'ar122':
                symlink_f(PATH_AR122_FILTERED_GENOMES.format(prefix=prefix),
                          os.path.join(out_dir, os.path.basename(PATH_AR122_FILTERED_GENOMES.format(prefix=prefix))))
                if len(trimmed_user_msa) > 0:
                    symlink_f(PATH_AR122_USER_MSA.format(prefix=prefix),
                              os.path.join(out_dir, os.path.basename(PATH_AR122_USER_MSA.format(prefix=prefix))))
                if not skip_gtdb_refs:
                    symlink_f(PATH_AR122_MSA.format(prefix=prefix),
                              os.path.join(out_dir, os.path.basename(PATH_AR122_MSA.format(prefix=prefix))))
github Ecogenomics / GTDBTk / gtdbtk / classify.py View on Github external
self.logger.error('There was an error determining the marker set.')
            raise GenomeMarkerSetUnknown

        # Symlink to the tree summary file
        if marker_set_id == 'bac120':
            if levelopt is None:
                symlink_f(PATH_BAC120_TREE_FILE.format(prefix=prefix),
                          os.path.join(out_dir, os.path.basename(PATH_BAC120_TREE_FILE.format(prefix=prefix))))
            elif levelopt == 'high':
                symlink_f(PATH_HIGH_BAC120_TREE_FILE.format(prefix=prefix),
                          os.path.join(out_dir, os.path.basename(PATH_HIGH_BAC120_TREE_FILE.format(prefix=prefix))))
            elif levelopt == 'low':
                symlink_f(PATH_LOW_BAC120_TREE_FILE.format(iter=tree_iter, prefix=prefix),
                          os.path.join(out_dir, os.path.basename(PATH_LOW_BAC120_TREE_FILE.format(iter=tree_iter, prefix=prefix))))
        elif marker_set_id == 'ar122':
            symlink_f(PATH_AR122_TREE_FILE.format(prefix=prefix),
                      os.path.join(out_dir, os.path.basename(PATH_AR122_TREE_FILE.format(prefix=prefix))))
        else:
            self.logger.error('There was an error determining the marker set.')
            raise GenomeMarkerSetUnknown

        return tree_file
github Ecogenomics / GTDBTk / gtdbtk / main.py View on Github external
self.logger.info('Done.')

        # symlink to the decorated tree file, if not run independently
        if hasattr(options, 'suffix'):
            if options.suffix == 'bac120':
                symlink_f(PATH_BAC120_DECORATED_TREE.format(prefix=options.prefix),
                          os.path.join(options.out_dir,
                                       os.path.basename(PATH_BAC120_DECORATED_TREE.format(prefix=options.prefix))))
                symlink_f(PATH_BAC120_DECORATED_TREE.format(prefix=options.prefix) + '-table',
                          os.path.join(options.out_dir,
                                       os.path.basename(PATH_BAC120_DECORATED_TREE.format(prefix=options.prefix)  + '-table')))
            elif options.suffix == 'ar122':
                symlink_f(PATH_AR122_DECORATED_TREE.format(prefix=options.prefix),
                          os.path.join(options.out_dir,
                                       os.path.basename(PATH_AR122_DECORATED_TREE.format(prefix=options.prefix))))
                symlink_f(PATH_AR122_DECORATED_TREE.format(prefix=options.prefix) + '-table',
                          os.path.join(options.out_dir,
                                       os.path.basename(PATH_AR122_DECORATED_TREE.format(prefix=options.prefix)  + '-table')))
            else:
                raise GenomeMarkerSetUnknown(
                    'There was an error determining the marker set.')

gtdbtk

A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

GitHub
GPL-3.0
Latest version published 3 months ago

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70 / 100
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