Python workaround_phylografter_export_diffs示例

示例#1

文件： migrate_testing_phylesystem.py 项目： OpenTreeOfLife/peyotl

        if not os.path.exists(scratch_dir):
            os.makedirs(scratch_dir)
        full_source = os.path.join(old_phylesystem_study, source_study, source_study + '.json')
        dest_dir = os.path.split(dest_full)[0]
        assert(os.path.exists(full_source))
        if os.path.exists(dest_full):
            debug('Skipping {} because output exists'.format(f))
            continue
        # read input and do the phylografter_workaround to valid 0.0.0 syntax
        # store in scratch.
        valid_bf = os.path.join(scratch_dir, 'v0.0.0-' + source_study + '.json')
        debug('Raw phylografter from "{}" to valid 0.0.0 NexSON at "{}" ...'.format(full_source, valid_bf))
        with codecs.open(full_source, mode='rU', encoding='utf-8') as inp:
            obj = json.load(inp)
        try:
            workaround_phylografter_export_diffs(obj, valid_bf)
        except:
            _LOG.exception('Exception in workaround_phylografter_export_diffs for study ' + f)
            failed.append(f)
            continue

        # Convert to 1.2.1
        unchecked_hbf = os.path.join(scratch_dir, 'v1.2.1-' + source_study + '.json')
        debug('Converting cleaned 0.0.0 NexSON from "{}" to unchecked 1.2.1 NexSON at "{}" ...'.format(valid_bf, unchecked_hbf))
        invoc = [sys.executable,
                 conversion_script, 
                '-s',
                '-e',
                '1.2.1',
                '-o',
                unchecked_hbf,

示例#2

文件： migrate_testing_phylesystem.py 项目： mtholder/peyotl

                                   source_study + '.json')
        dest_dir = os.path.split(dest_full)[0]
        assert (os.path.exists(full_source))
        if os.path.exists(dest_full):
            debug('Skipping {} because output exists'.format(f))
            continue
        # read input and do the phylografter_workaround to valid 0.0.0 syntax
        # store in scratch.
        valid_bf = os.path.join(scratch_dir,
                                'v0.0.0-' + source_study + '.json')
        debug('Raw phylografter from "{}" to valid 0.0.0 NexSON at "{}" ...'.
              format(full_source, valid_bf))
        with codecs.open(full_source, mode='rU', encoding='utf-8') as inp:
            obj = json.load(inp)
        try:
            workaround_phylografter_export_diffs(obj, valid_bf)
        except:
            _LOG.exception(
                'Exception in workaround_phylografter_export_diffs for study '
                + f)
            failed.append(f)
            continue

        # Convert to 1.2.1
        unchecked_hbf = os.path.join(scratch_dir,
                                     'v1.2.1-' + source_study + '.json')
        debug(
            'Converting cleaned 0.0.0 NexSON from "{}" to unchecked 1.2.1 NexSON at "{}" ...'
            .format(valid_bf, unchecked_hbf))
        invoc = [
            sys.executable, conversion_script, '-s', '-e', '1.2.1', '-o',

示例#3

文件： phylografter_workaround.py 项目： pombredanne/peyotl

#!/usr/bin/env python
import sys, json, codecs
from peyotl.phylografter.nexson_workaround import workaround_phylografter_export_diffs
inpfn = sys.argv[1]
outfn = sys.argv[2]
inp = codecs.open(inpfn, mode='rU', encoding='utf-8')
obj = json.load(inp)
workaround_phylografter_export_diffs(obj, outfn)

示例#4

#!/usr/bin/env python
import sys, json, codecs
from peyotl.phylografter.nexson_workaround import workaround_phylografter_export_diffs
inpfn = sys.argv[1]
outfn = sys.argv[2]
with codecs.open(inpfn, mode='rU', encoding='utf-8') as inp:
    obj = json.load(inp)
workaround_phylografter_export_diffs(obj, outfn)