def dendropy_read_treefile(treefiles, quiet=False, preserve_underscores=False, **kwargs):
out_stream = kwargs.pop('writer', sys.stderr)
intrees = TreeList()
if not treefiles:
if not quiet:
sys.stderr.write('NOTE: reading trees from stdin\n')
trees = sys.stdin.read()
#try two input formats
try:
intrees.extend(TreeList.get_from_string(trees, "nexus", case_sensitive_taxon_labels=True, preserve_underscores=preserve_underscores, **kwargs))
except (DataParseError, NexusReader.NotNexusFileError) as e:
sys.stderr.write('%s\n' % e.message)
intrees.extend(TreeList.get_from_string(trees, "newick", case_sensitive_taxon_labels=True, preserve_underscores=preserve_underscores, **kwargs))
except (DataParseError, Tokenizer.UnexpectedEndOfStreamError, AttributeError) as e:
if not quiet:
sys.stderr.write('%s\n' % e.message)
sys.exit('Could not read file %s in nexus or newick format ...\n' % tf)
else:
for tf in treefiles:
if not os.path.isfile(tf):
out_stream.write('TreeFile %s does not exist' % tf)
sys.exit()
#try two input formats
try:
if not quiet:
out_stream.write('Reading file %s in nexus format ...\n' % tf)
intrees.extend(TreeList.get_from_path(tf, "nexus", case_sensitive_taxon_labels=True, preserve_underscores=preserve_underscores, **kwargs))
#except (DataParseError, dendropy.dataio.nexusreader.NotNexusFileError) as e:
except (DataParseError, NexusReader.NotNexusFileError, AttributeError) as e:
try:
if not quiet:
out_stream.write('Reading file %s in newick format ...\n' % tf)
intrees.extend(TreeList.get_from_path(tf, "newick", case_sensitive_taxon_labels=True, preserve_underscores=preserve_underscores, **kwargs))
except (DataParseError, Tokenizer.UnexpectedEndOfStreamError, AttributeError) as e:
if not quiet:
sys.stderr.write('%s\n' % e.message)
sys.exit('Could not read file %s in nexus or newick format ...\n' % tf)
return intrees
