Switch types=["file"] to filename=True in app wrapper parameters (pri…

…vate API change)

Bio/Align/Applications/_Clustalw.py

@@ -39,13 +39,13 @@ def __init__(self, cmd="clustalw", **kwargs):
             [
             _Option(["-infile", "-INFILE", "INFILE", "infile"],
                     "Input sequences.",
-                    types=["file"]),
+                    filename=True),
             _Option(["-profile1", "-PROFILE1", "PROFILE1", "profile1"],
                     "Profiles (old alignment).",
-                    types=["file"]),
+                    filename=True),
             _Option(["-profile2", "-PROFILE2", "PROFILE2", "profile2"],
                     "Profiles (old alignment).",
-                    types=["file"]),
+                    filename=True),
             ################## VERBS (do things) #############################
             _Switch(["-options", "-OPTIONS", "OPTIONS", "options"],
                     "List the command line parameters"),
@@ -83,7 +83,7 @@ def __init__(self, cmd="clustalw", **kwargs):
                     "Protein alignment with negative values in matrix"),
             _Option(["-outfile", "-OUTFILE", "OUTFILE", "outfile"],
                     "Output sequence alignment file name",
-                    types=["file"]),
+                    filename=True),
             _Option(["-output", "-OUTPUT", "OUTPUT", "output"],
                     "Output format: GCG, GDE, PHYLIP, PIR or NEXUS",
                     checker_function=lambda x: x in ["GCG", "GDE", "PHYLIP",
@@ -145,13 +145,13 @@ def __init__(self, cmd="clustalw", **kwargs):
                                                      "blosum", "pam",
                                                      "gonnet", "id"] or \
                                                 os.path.exists(x),
-                    types=["file"]),
+                    filename=True),
             _Option(["-pwdnamatrix", "-PWDNAMATRIX", "PWDNAMATRIX", "pwdnamatrix"],
                     "DNA weight matrix=IUB, CLUSTALW or filename",
                     checker_function=lambda x: x in ["IUB", "CLUSTALW",
                                                      "iub", "clustalw"] or \
                                                os.path.exists(x),
-                    types=["file"]),
+                    filename=True),
             _Option(["-pwgapopen", "-PWGAPOPEN", "PWGAPOPEN", "pwgapopen"],
                     "Gap opening penalty",
                     checker_function=lambda x: isinstance(x, int) or \
@@ -163,25 +163,25 @@ def __init__(self, cmd="clustalw", **kwargs):
             # ***Multiple Alignments:***
             _Option(["-newtree", "-NEWTREE", "NEWTREE", "newtree"],
                     "Output file name for newly created guide tree",
-                    types=["file"]),
+                    filename=True),
             _Option(["-usetree", "-USETREE", "USETREE", "usetree"],
                     "File name of guide tree",
                     checker_function=lambda x: os.path.exists,
-                    types=["file"]),
+                    filename=True),
             _Option(["-matrix", "-MATRIX", "MATRIX", "matrix"],
                     "Protein weight matrix=BLOSUM, PAM, GONNET, ID or filename",
                     checker_function=lambda x: x in ["BLOSUM", "PAM",
                                                      "GONNET", "ID",
                                                      "blosum", "pam",
                                                      "gonnet", "id"] or \
                                                os.path.exists(x),
-                    types=["file"]),
+                    filename=True),
             _Option(["-dnamatrix", "-DNAMATRIX", "DNAMATRIX", "dnamatrix"],
                     "DNA weight matrix=IUB, CLUSTALW or filename",
                     checker_function=lambda x: x in ["IUB", "CLUSTALW",
                                                      "iub", "clustalw"] or \
                                                os.path.exists(x),
-                    types=["file"]),
+                    filename=True),
             _Option(["-gapopen", "-GAPOPEN", "GAPOPEN", "gapopen"],
                     "Gap opening penalty",
                     checker_function=lambda x: isinstance(x, int) or \
@@ -226,18 +226,18 @@ def __init__(self, cmd="clustalw", **kwargs):
                     "Merge two alignments by profile alignment"),
             _Option(["-newtree1", "-NEWTREE1", "NEWTREE1", "newtree1"],
                     "Output file name for new guide tree of profile1",
-                    types=["file"]),
+                    filename=True),
             _Option(["-newtree2", "-NEWTREE2", "NEWTREE2", "newtree2"],
                     "Output file for new guide tree of profile2",
-                    types=["file"]),
+                    filename=True),
             _Option(["-usetree1", "-USETREE1", "USETREE1", "usetree1"],
                     "File name of guide tree for profile1",
                     checker_function=lambda x: os.path.exists,
-                    types=["file"]),
+                    filename=True),
             _Option(["-usetree2", "-USETREE2", "USETREE2", "usetree2"],
                     "File name of guide tree for profile2",
                     checker_function=lambda x: os.path.exists,
-                    types=["file"]),
+                    filename=True),
             # ***Sequence to Profile Alignments:***
             _Switch(["-sequences", "-SEQUENCES", "SEQUENCES", "sequences"],
                     "Sequentially add profile2 sequences to profile1 alignment"),

Bio/Align/Applications/_Dialign.py

@@ -171,7 +171,7 @@ def __init__(self, cmd="dialign2-2", **kwargs):
                     "specified that are NOT considered for pairwise alignment"),
             _Argument(["input"],
                       "Input file name. Must be FASTA format",
-                      types=["file"],
+                      filename=True,
                       is_required=True),
             ]
         AbstractCommandline.__init__(self, cmd, **kwargs)

Bio/Align/Applications/_Mafft.py

@@ -260,7 +260,7 @@ def __init__(self, cmd="mafft", **kwargs):
                     "Transmembrane PAM number (Jones et al. 1994) "
                     "matrix is used. number>0. Default: BLOSUM62",
                     checker_function=os.path.exists,
-                    types=["file"],
+                    filename=True,
                     equate=False),
             #Use a user-defined AA scoring matrix. The format of matrixfile is
             #the same to that of BLAST. Ignored when nucleotide sequences are
@@ -269,7 +269,7 @@ def __init__(self, cmd="mafft", **kwargs):
                     "Use a user-defined AA scoring matrix. "
                     "Default: BLOSUM62",
                     checker_function=os.path.exists,
-                    types=["file"],
+                    filename=True,
                     equate=False),
             #Incorporate the AA/nuc composition information into the scoring
             #matrix. Default: off
@@ -314,7 +314,7 @@ def __init__(self, cmd="mafft", **kwargs):
                     "Seed alignments given in alignment_n (fasta format) "
                     "are aligned with sequences in input.",
                     checker_function=os.path.exists,
-                    types=["file"],
+                    filename=True,
                     equate=False),
             #The old solution of also defining extra parameters with
             #["--seed", "seed1"] etc worked, but clashes with the recent
@@ -328,15 +328,15 @@ def __init__(self, cmd="mafft", **kwargs):
             _Argument(["input"],
                       "Input file name",
                       checker_function=os.path.exists,
-                      types=["file"],
+                      filename=True,
                       is_required=True),
             ###################################################################
             #mafft-profile takes a second alignment input as an argument:
             #mafft-profile align1 align2
             _Argument(["input1"],
                       "Second input file name for the mafft-profile command",
                       checker_function=os.path.exists,
-                      types=["file"]),
+                      filename=True),
             ]
         AbstractCommandline.__init__(self, cmd, **kwargs)
 

Bio/Align/Applications/_Muscle.py

@@ -51,23 +51,23 @@ def __init__(self, cmd="muscle", **kwargs):
             #Can't use "in" as the final alias as this is a reserved word in python:
             _Option(["-in", "in", "input"],
                     "Input filename",
-                    types=["file"],
+                    filename=True,
                     equate=False),
             _Option(["-out", "out"],
                     "Output filename",
-                    types=["file"],
+                    filename=True,
                     equate=False),
             _Switch(["-diags", "diags"],
                     "Find diagonals (faster for similar sequences)"),
             _Switch(["-profile", "profile"],
                     "Perform a profile alignment"),
             _Option(["-in1", "in1"],
                     "First input filename for profile alignment",
-                    types=["file"],
+                    filename=True,
                     equate=False),
             _Option(["-in2", "in2"],
                     "Second input filename for a profile alignment",
-                    types=["file"],
+                    filename=True,
                     equate=False),
             #anchorspacing   Integer              32                 Minimum spacing between
             _Option(["-anchorspacing", "anchorspacing"],
@@ -149,13 +149,13 @@ def __init__(self, cmd="muscle", **kwargs):
             #                                                        existing file).
             _Option(["-log", "log"],
                     "Log file name",
-                    types=["file"],
+                    filename=True,
                     equate=False),
             #loga            File name            None.              Log file name (append
             #                                                        to existing file).
             _Option(["-loga", "loga"],
                     "Log file name (append to existing file)",
-                    types=["file"],
+                    filename=True,
                     equate=False),
             #maxdiagbreak    Integer              1                  Maximum distance
             #                                                        between two diagonals
@@ -349,31 +349,31 @@ def __init__(self, cmd="muscle", **kwargs):
             ################## Additional specified output files #########
             _Option(["-phyiout", "phyiout"],
                     "Write PHYLIP interleaved output to specified filename",
-                    types=["file"],
+                    filename=True,
                     equate=False),
             _Option(["-physout", "physout"],"Write PHYLIP sequential format to specified filename",
-                    types=["file"],
+                    filename=True,
                     equate=False),
             _Option(["-htmlout", "htmlout"],"Write HTML output to specified filename",
-                    types=["file"],
+                    filename=True,
                     equate=False),
             _Option(["-clwout", "clwout"],
                     "Write CLUSTALW output (with MUSCLE header) to specified "
                     "filename",
-                    types=["file"],
+                    filename=True,
                     equate=False),
             _Option(["-clwstrictout", "clwstrictout"],
                     "Write CLUSTALW output (with version 1.81 header) to "
                     "specified filename",
-                    types=["file"],
+                    filename=True,
                     equate=False),
             _Option(["-msfout", "msfout"],
                     "Write MSF format output to specified filename",
-                    types=["file"],
+                    filename=True,
                     equate=False),
             _Option(["-fastaout", "fastaout"],
                     "Write FASTA format output to specified filename",
-                    types=["file"],
+                    filename=True,
                     equate=False),
             ############## END FORMATS ###################################
             #anchors            yes             Use anchor optimization in tree dependent

Bio/Align/Applications/_Prank.py

@@ -49,11 +49,11 @@ def __init__(self, cmd="prank", **kwargs):
             #-d=sequence_file
             _Option(["-d", "d"],
                     "Input filename",
-                    types=["file"],
+                    filename=True,
                     is_required=True),
             #-t=tree_file [default: no tree, generate approximate NJ tree]
             _Option(["-t", "t"],"Input guide tree filename",
-                    types=["file"]),
+                    filename=True),
             #-tree="tree_string" [tree in newick format; in double quotes]
             _Option(["-tree", "tree"],
                     "Input guide tree as Newick string"),
@@ -66,7 +66,7 @@ def __init__(self, cmd="prank", **kwargs):
                     "Output filenames prefix. Default: 'output'\n "
                     "Will write: output.?.fas (depending on requested "
                     "format), output.?.xml and output.?.dnd",
-                    types=["file"]),
+                    filename=True),
             #-f=output_format [default: 8]
             _Option(["-f", "f"],
                     "Output alignment format. Default: 8 FASTA\n"

Bio/Align/Applications/_Probcons.py

@@ -101,7 +101,7 @@ def __init__(self, cmd="probcons", **kwargs):
             _Argument(["input"],
                       "Input file name. Must be multiple FASTA alignment "+ \
                       "(MFA) format",
-                      types=["file"],
+                      filename=True,
                       is_required=True),
             ]
         AbstractCommandline.__init__(self, cmd, **kwargs)

Bio/Align/Applications/_TCoffee.py

@@ -54,14 +54,14 @@ def __init__(self, cmd="t_coffee", **kwargs):
                    equate=False),
            _Option(["-infile", "infile"],
                    "Specify the input file.",
-                   types=["file"],
+                   filename=True,
                    is_required=True,
                    equate=False),
            #Indicates the name of the alignment output by t_coffee. If the
            #default is used, the alignment is named <your sequences>.aln
            _Option(["-outfile", "outfile"],
                    "Specify the output file. Default: <your sequences>.aln",
-                   types=["file"],
+                   filename=True,
                    equate=False),
            _Switch(["-convert", "convert"],
                    "Specify you want to perform a file conversion"),

Bio/Application/__init__.py

@@ -467,11 +467,8 @@ class _Option(_AbstractParameter):
 
     o description -- a description of the option.
 
-    o param_types -- a list of string describing the type of parameter, 
-    which can help let programs know how to use it. The only supported
-    values for this are the empty list (default), and ['file'] which means
-    these argument values will automatically be escaped if the filename
-    contains spaces.
+    o filename -- True if this argument is a filename and should be
+    automatically quoted if it contains spaces.
 
     o checker_function -- a reference to a function that will determine
     if a given value is valid for this parameter. This function can either
@@ -487,14 +484,12 @@ class _Option(_AbstractParameter):
 
     o value -- the value of a parameter
     """
-    def __init__(self, names, description, types=[], checker_function=None,
+    def __init__(self, names, description, filename=False, checker_function=None,
                  is_required=False, equate=True):
         self.names = names
         assert isinstance(description, basestring), \
                "%r for %s" % (description, names[-1])
-        assert types == [] or types == ["file"], \
-               "%r for %s" % (types, names[0])
-        self.param_types = types
+        self.is_filename = filename
         self.checker_function = checker_function
         self.description = description
         self.equate = equate
@@ -514,7 +509,7 @@ def __str__(self):
         # now made explicitly when setting up the option.
         if self.value is None:
             return "%s " % self.names[0]
-        if "file" in self.param_types:
+        if self.is_filename:
             v = _escape_filename(self.value)
         else:
             v = str(self.value)
@@ -563,14 +558,12 @@ def __str__(self):
 class _Argument(_AbstractParameter):
     """Represent an argument on a commandline.
     """
-    def __init__(self, names, description, types=[], checker_function=None,
-                 is_required=False):
+    def __init__(self, names, description, filename=False,
+                 checker_function=None, is_required=False):
         self.names = names
         assert isinstance(description, basestring), \
                "%r for %s" % (description, names[-1])
-        assert types == [] or types == ["file"], \
-               "%r for %s" % (types, names[0])
-        self.param_types = types
+        self.is_filename = filename
         self.checker_function = checker_function
         self.description = description
         self.is_required = is_required
@@ -580,6 +573,8 @@ def __init__(self, names, description, types=[], checker_function=None,
     def __str__(self):
         if self.value is None:
             return " "
+        elif self.is_filename:
+            return "%s " % _escape_filename(self.value)
         else:
             return "%s " % self.value