diff --git a/core/pymod/core/pm3argparse.py b/core/pymod/core/pm3argparse.py
index 51f55bca7287eea8c45fd27508eae0ac8b724b44..59cc9485139069166841e3f68650b0ad30064a40 100644
--- a/core/pymod/core/pm3argparse.py
+++ b/core/pymod/core/pm3argparse.py
@@ -121,6 +121,14 @@ def _AssembleTrgTplAln(target, template):
new_aln.SetSequenceOffset(1, start)
return new_aln
+class PM3StoreOnceAction(argparse.Action):
+ """Action for argument parsing to prevent multiple calls to an option.
+ """
+ def __call__(self, parser, namespace, values, option_string=None):
+ if getattr(namespace, self.dest, None) is not None:
+ raise argparse.ArgumentError(self, 'may only be used once.')
+ setattr(namespace, self.dest, values)
+
class PM3ArgumentParser(argparse.ArgumentParser):
"""
This class is a child of :class:`argparse.ArgumentParser`. It provides a
@@ -224,12 +232,18 @@ class PM3ArgumentParser(argparse.ArgumentParser):
Options/ arguments added:
- * ``--fasta trg:<NAME> <FILE>`` - describing a target-template alignment
- with ``trg:`` marking the target sequence inside :file:`<FILE>`
+ * ``-f/ --fasta trg:<NAME> <FILE>`` - describing a target-template
+ alignment with ``trg:`` marking the target sequence inside
+ :file:`<FILE>`. The order of arguments is arbitrary which means file
+ names starting with :file:`trg:` will not work.
+
+ * ``-j/ --json <OBJECT>|<FILE>`` - target-template alignments in JSON
+ format. Either an object string or a file name. The string variant is
+ limited to how many characters your command line can gobble.
Exit codes related to alignment input:
- * 11 - no prefix ``trg:`` found for an argument to '--fasta'
+ * 11 - no prefix ``trg:`` found for an argument to ``--fasta``
* 12 - a given alignment file does not exist
@@ -248,9 +262,12 @@ class PM3ArgumentParser(argparse.ArgumentParser):
Attributes added to the namespace returned by
:meth:`Parse`:
- * :attr:`fasta` - filled with the input of the '--fasta' argument, a
+ * :attr:`fasta` - filled with the input of the ``--fasta`` option, a
:class:`list` with multiple :class:`list` objects
+ * :attr:`json` - argument of the ``--json`` option, :class:`str`. May
+ be a filename of a JSON object string.
+
* :attr:`alignments` - :class:`ost.AlignmentList`, same order as
:attr:`fasta`
@@ -264,17 +281,26 @@ class PM3ArgumentParser(argparse.ArgumentParser):
"""
Actually add alignment arguments/ options
"""
+ aln_grp = self.add_mutually_exclusive_group()
# FastA input: - always pairwise alignments
# - callable multiple times
# - goes by 'trg:<SEQNAME> <FILE>'
# - excludes JSON file/ object
- # - leading whitespaces will be deleted
- self.add_argument('-f', '--fasta', nargs=2, action='append',
- metavar=('trg:<NAME>', '<FILE>'),
- help='Pairwise alignment in FastA format, needs to '+
- 'declare what is the target sequence.')
- # input: FastA/ JSON
- # determined by extension: if we are wrong, the whole loading fails
+ # - leading whitespaces of FastA headers will be deleted
+ aln_grp.add_argument('-f', '--fasta', nargs=2, action='append',
+ metavar=('trg:<NAME>', '<FILE>'),
+ help='Pairwise alignment in FastA format, needs '+
+ 'to declare what is the target sequence.')
+ # JSON input: - right as string or file
+ # - object starts with {, so not allowed for files
+ # - callable only ONCE: should include everything needed
+ # - fields/ objects used: ...
+ # - goes by '--json <OBJECT>|<FILE>'
+ # - excludes '--fasta'
+ # - leading whitespaces of sequence names will be deleted
+ aln_grp.add_argument('-j', '--json', metavar='<OBJECT>|<FILE>',
+ help='Alignments provided as JSON file/ object.',
+ action=PM3StoreOnceAction)
# possibility to add JSON: mention limitation!
class PM3OptionsNamespace(object):
diff --git a/core/tests/test_pm3argparse.py b/core/tests/test_pm3argparse.py
index 8bd20a84b36636fc702c63119a7d5d0e7537e686..271dfc26e683ae1a8591791f8d2cab681b41df6c 100644
--- a/core/tests/test_pm3argparse.py
+++ b/core/tests/test_pm3argparse.py
@@ -87,8 +87,9 @@ class PM3ArgParseTests(unittest.TestCase):
self.assertEqual(ecd.exception.code, 2)
self.assertEqual(self.log.messages['ERROR'],
['usage: test_pm3argparse.py [-h] [-f trg:<NAME> '+
- '<FILE>]', 'test_pm3argparse.py: error: argument '+
- '-f/--fasta: expected 2 argument(s)'])
+ '<FILE> | -j <OBJECT>|<FILE>]',
+ 'test_pm3argparse.py: error: argument -f/--fasta: '+
+ 'expected 2 argument(s)'])
def testAddAlignmentNoFileArg(self):
# check failure on missing file argument
@@ -100,8 +101,9 @@ class PM3ArgParseTests(unittest.TestCase):
self.assertEqual(ecd.exception.code, 2)
self.assertEqual(self.log.messages['ERROR'],
['usage: test_pm3argparse.py [-h] [-f trg:<NAME> '+
- '<FILE>]', 'test_pm3argparse.py: error: argument '+
- '-f/--fasta: expected 2 argument(s)'])
+ '<FILE> | -j <OBJECT>|<FILE>]',
+ 'test_pm3argparse.py: error: argument -f/--fasta: '+
+ 'expected 2 argument(s)'])
def testAddAlignemntNoTrgPfx(self):
# checking that we fail on missing 'trg:' prefix for arguments of
@@ -272,6 +274,38 @@ class PM3ArgParseTests(unittest.TestCase):
self.assertEqual(opts.alignments[0].GetSequence(1).name, '1AKE.B')
self.assertEqual(opts.aln_sources[0], 'data/fasta/1ake.fas')
+ def testAddAlignmentFastaAndJson(self):
+ # testing that --fasta and --json DO NOT work together
+ parser = pm3argparse.PM3ArgumentParser(__doc__, action=False)
+ parser.AddAlignment()
+ parser.AssembleParser()
+ with self.assertRaises(SystemExit) as ecd:
+ opts = parser.Parse(['--fasta', 'trg:target',
+ 'data/fasta/1ake.fas', '--json', 'foo'])
+ self.assertEqual(ecd.exception.code, 2)
+ self.assertEqual(self.log.messages['ERROR'][0],
+ 'usage: test_pm3argparse.py [-h] [-f trg:<NAME> '+
+ '<FILE> | -j <OBJECT>|<FILE>]',
+ 'test_pm3argparse.py: error: argument -j/--json: '+
+ 'not allowed with argument -f/--fasta')
+
+ def testAddAlignmentJsonMulti(self):
+ # passing --json multiple times is not allowed
+ # also serves as a unit test for PM3StoreOnceAction
+ parser = pm3argparse.PM3ArgumentParser(__doc__, action=False)
+ parser.AddAlignment()
+ parser.AssembleParser()
+ with self.assertRaises(SystemExit) as ecd:
+ opts = parser.Parse(['--json', 'foo', '--json', 'bar'])
+ self.assertEqual(ecd.exception.code, 2)
+ self.assertEqual(self.log.messages['ERROR'][0],
+ 'usage: test_pm3argparse.py [-h] [-f trg:<NAME> '+
+ '<FILE> | -j <OBJECT>|<FILE>]',
+ 'test_pm3argparse.py: error: argument -j/--json: '+
+ 'may only be used once.')
+
+# test no multiple --json
+
if __name__ == "__main__":
from ost import testutils
testutils.RunTests()