Move ucsc_encode_submission code out of extra so nose will autodiscover it.

[htsworkflow.git] / extra / ucsc_encode_submission / scan_extension.py

diff --git a/extra/ucsc_encode_submission/scan_extension.py b/extra/ucsc_encode_submission/scan_extension.py
deleted file mode 100644 (file)
index 39f19c6..0000000
--- a/extra/ucsc_encode_submission/scan_extension.py
+++ /dev/null
@@ -1,76 +0,0 @@
-from optparse import OptionParser
-import os
-import sys
-from pprint import pprint
-
-def main(cmdline=None):
-    parser = make_parser()
-    opts, args = parser.parse_args(cmdline)
-
-    extensions = scan(args)
-    common_extensions = find_common_suffix(extensions)
-
-    if opts.rdf:
-        print_rdf(common_extensions)
-    else:
-        print common_extensions
-        
-def make_parser():
-    parser = OptionParser("%prog: directory [directory...]")
-    parser.add_option('--rdf', action="store_true", default=False,
-                      help="Produce rdf configuration file for ucsc_gather")
-    return parser
-
-def scan(toscan):
-    index = {}
-    for cur_scan_dir in toscan:
-        for path, dirnames, filenames in os.walk(cur_scan_dir):
-            for filename in filenames:
-                base, ext = os.path.splitext(filename)
-                if ext in ('.daf', 'ddf'):
-                    continue
-                next_index = index
-                for c in filename[::-1]:
-                    next_index = next_index.setdefault(c, {})
-    return index
-
-def find_common_suffix(index, tail=[]):
-    if len(tail) > 0 and len(index) > 1:
-        return "".join(tail[::-1])
-
-    results = []
-    for key, choice in index.items():
-        r = find_common_suffix(choice, tail+[key])
-        if r is not None:
-            results.append (r)
-        
-    if len(results) == 0:
-        return None
-    elif len(results) == 1:
-        return results[0]
-    else:
-        return results
-
-def print_rdf(common_extensions):
-    import RDF
-    from htsworkflow.util import rdfhelp
-    model = rdfhelp.get_model()
-
-    viewName = 'http://jumpgate.caltech.edu/wiki/SubmissionsLog/NAME/view/'
-    subView = RDF.NS(viewName)
-    fileReTerm = rdfhelp.dafTermOntology['filename_re']
-
-    count = 1
-    for ext in common_extensions:
-        s = RDF.Statement(subView['VIEW{0}'.format(count)],
-                          fileReTerm,
-                          '.*{0}$'.format(ext.replace('.', '\\.')))
-        model.add_statement(s)
-        count += 1
-        
-    writer = rdfhelp.get_serializer()
-    writer.set_namespace('thisSubmissionView', subView._prefix)
-    print writer.serialize_model_to_string(model)
-
-if __name__ == "__main__":
-    main()