Skip to content

Commit

Permalink
Make name and description mandatory in app wrappers
Browse files Browse the repository at this point in the history 
Note this changes the private API to the Bio.Application wrapper parameter classes.
  • Loading branch information
@peterjc
peterjc committed Dec 3, 2010
1 parent 3fa22e9 commit 6957dd5
Show file tree
Hide file tree
Showing 11 changed files with 1,616 additions and 1,505 deletions.
330 changes: 103 additions & 227 deletions Bio/Align/Applications/_Clustalw.py
View file

Large diffs are not rendered by default.

148 changes: 78 additions & 70 deletions Bio/Align/Applications/_Mafft.py
View file
Expand Up @@ -88,69 +88,69 @@ def __init__(self, cmd="mafft", **kwargs):
"Automatically select strategy. Default off."),
#Distance is calculated based on the number of shared 6mers. Default: on
_Switch(["--6merpair", "6merpair", "sixmerpair"],
"Distance is calculated based on the number of shared "
"6mers. Default: on"),
"Distance is calculated based on the number of shared "
"6mers. Default: on"),
#All pairwise alignments are computed with the Needleman-Wunsch
#algorithm. More accurate but slower than --6merpair. Suitable for a
#set of globally alignable sequences. Applicable to up to ~200
#sequences. A combination with --maxiterate 1000 is recommended (G-
#INS-i). Default: off (6mer distance is used)
_Switch(["--globalpair", "globalpair"],
"All pairwise alignments are computed with the "
"Needleman-Wunsch algorithm. Default: off"),
"All pairwise alignments are computed with the "
"Needleman-Wunsch algorithm. Default: off"),
#All pairwise alignments are computed with the Smith-Waterman
#algorithm. More accurate but slower than --6merpair. Suitable for a
#set of locally alignable sequences. Applicable to up to ~200
#sequences. A combination with --maxiterate 1000 is recommended (L-
#INS-i). Default: off (6mer distance is used)
_Switch(["--localpair", "localpair"],
"All pairwise alignments are computed with the "
"Smith-Waterman algorithm. Default: off"),
"All pairwise alignments are computed with the "
"Smith-Waterman algorithm. Default: off"),
#All pairwise alignments are computed with a local algorithm with
#the generalized affine gap cost (Altschul 1998). More accurate but
#slower than --6merpair. Suitable when large internal gaps are
#expected. Applicable to up to ~200 sequences. A combination with --
#maxiterate 1000 is recommended (E-INS-i). Default: off (6mer
#distance is used)
_Switch(["--genafpair", "genafpair"],
"All pairwise alignments are computed with a local "
"algorithm with the generalized affine gap cost "
"(Altschul 1998). Default: off"),
"All pairwise alignments are computed with a local "
"algorithm with the generalized affine gap cost "
"(Altschul 1998). Default: off"),
#All pairwise alignments are computed with FASTA (Pearson and Lipman
#1988). FASTA is required. Default: off (6mer distance is used)
_Switch(["--fastapair", "fastapair"],
"All pairwise alignments are computed with FASTA "
"(Pearson and Lipman 1988). Default: off"),
"All pairwise alignments are computed with FASTA "
"(Pearson and Lipman 1988). Default: off"),
#Weighting factor for the consistency term calculated from pairwise
#alignments. Valid when either of --blobalpair, --localpair, --
#genafpair, --fastapair or --blastpair is selected. Default: 2.7
_Option(["--weighti", "weighti"], [],
lambda x: isinstance(x, float), 0,
"Weighting factor for the consistency term calculated "
"from pairwise alignments. Default: 2.7",
0),
_Option(["--weighti", "weighti"],
"Weighting factor for the consistency term calculated "
"from pairwise alignments. Default: 2.7",
checker_function=lambda x: isinstance(x, float),
equate=False),
#Guide tree is built number times in the progressive stage. Valid
#with 6mer distance. Default: 2
_Option(["--retree", "retree"], [],
lambda x: isinstance(x, int), 0,
"Guide tree is built number times in the progressive "
"stage. Valid with 6mer distance. Default: 2",
0),
_Option(["--retree", "retree"],
"Guide tree is built number times in the progressive "
"stage. Valid with 6mer distance. Default: 2",
checker_function=lambda x: isinstance(x, int),
equate=False),
#Number cycles of iterative refinement are performed. Default: 0
_Option(["--maxiterate", "maxiterate"], [],
lambda x: isinstance(x, int), 0,
"Number cycles of iterative refinement are performed. "
"Default: 0",
0),
_Option(["--maxiterate", "maxiterate"],
"Number cycles of iterative refinement are performed. "
"Default: 0",
checker_function=lambda x: isinstance(x, int),
equate=False),
#Use FFT approximation in group-to-group alignment. Default: on
_Switch(["--fft", "fft"],
"Use FFT approximation in group-to-group alignment. "
"Default: on"),
#Do not use FFT approximation in group-to-group alignment. Default:
#off
_Switch(["--nofft", "nofft"],
"Do not use FFT approximation in group-to-group "
"alignment. Default: off"),
"Do not use FFT approximation in group-to-group "
"alignment. Default: off"),
#Alignment score is not checked in the iterative refinement stage.
#Default: off (score is checked)
_Switch(["--noscore", "noscore"],
Expand Down Expand Up @@ -182,94 +182,95 @@ def __init__(self, cmd="mafft", **kwargs):
"The PartTree algorithm is used with distances based "
"on FASTA. Default: off"),
#The number of partitions in the PartTree algorithm. Default: 50
_Option(["--partsize", "partsize"], [],
lambda x: isinstance(x, int), 0,
_Option(["--partsize", "partsize"],
"The number of partitions in the PartTree algorithm. "
"Default: 50",
0),
checker_function=lambda x: isinstance(x, int),
equate=False),
#Do not make alignment larger than number sequences. Valid only with
#the --*parttree options. Default: the number of input sequences
_Switch(["--groupsize", "groupsize"],
"Do not make alignment larger than number sequences. "
"Default: the number of input sequences"),
#**** Parameter ****
#Gap opening penalty at group-to-group alignment. Default: 1.53
_Option(["--op", "op"], [],
lambda x: isinstance(x, float), 0,
_Option(["--op", "op"],
"Gap opening penalty at group-to-group alignment. "
"Default: 1.53",
0),
checker_function=lambda x: isinstance(x, float),
equate=False),
#Offset value, which works like gap extension penalty, for group-to-
#group alignment. Deafult: 0.123
_Option(["--ep", "ep"], [],
lambda x: isinstance(x, float), 0,
_Option(["--ep", "ep"],
"Offset value, which works like gap extension penalty, "
"for group-to- group alignment. Default: 0.123",
0),
checker_function=lambda x: isinstance(x, float),
equate=False),
#Gap opening penalty at local pairwise alignment. Valid when the --
#localpair or --genafpair option is selected. Default: -2.00
_Option(["--lop", "lop"], [],
lambda x: isinstance(x, float), 0,
_Option(["--lop", "lop"],
"Gap opening penalty at local pairwise alignment. "
"Default: 0.123",
0),
checker_function=lambda x: isinstance(x, float),
equate=False),
#Offset value at local pairwise alignment. Valid when the --
#localpair or --genafpair option is selected. Default: 0.1
_Option(["--lep", "lep"], [],
lambda x: isinstance(x, float), 0,
_Option(["--lep", "lep"],
"Offset value at local pairwise alignment. "
"Default: 0.1",
0),
checker_function=lambda x: isinstance(x, float),
equate=False),
#Gap extension penalty at local pairwise alignment. Valid when the -
#-localpair or --genafpair option is selected. Default: -0.1
_Option(["--lexp", "lexp"], [],
lambda x: isinstance(x, float), 0,
_Option(["--lexp", "lexp"],
"Gap extension penalty at local pairwise alignment. "
"Default: -0.1",
0),
checker_function=lambda x: isinstance(x, float),
equate=False),
#Gap opening penalty to skip the alignment. Valid when the --
#genafpair option is selected. Default: -6.00
_Option(["--LOP", "LOP"], [],
lambda x: isinstance(x, float), 0,
_Option(["--LOP", "LOP"],
"Gap opening penalty to skip the alignment. "
"Default: -6.00",
0),
checker_function=lambda x: isinstance(x, float),
equate=False),
#Gap extension penalty to skip the alignment. Valid when the --
#genafpair option is selected. Default: 0.00
_Option(["--LEXP", "LEXP"], [],
lambda x: isinstance(x, float),
0,
_Option(["--LEXP", "LEXP"],
"Gap extension penalty to skip the alignment. "
"Default: 0.00",
0),
checker_function=lambda x: isinstance(x, float),
equate=False),

#BLOSUM number matrix (Henikoff and Henikoff 1992) is used.
#number=30, 45, 62 or 80. Default: 62
_Option(["--bl", "bl"], [],
lambda x: x in BLOSUM_MATRICES, 0,
_Option(["--bl", "bl"],
"BLOSUM number matrix is used. Default: 62",
0),
checker_function=lambda x: x in BLOSUM_MATRICES,
equate=False),
#JTT PAM number (Jones et al. 1992) matrix is used. number>0.
#Default: BLOSUM62
_Option(["--jtt", "jtt"], [], None, 0,
_Option(["--jtt", "jtt"],
"JTT PAM number (Jones et al. 1992) matrix is used. "
"number>0. Default: BLOSUM62",
0),
equate=False),
#Transmembrane PAM number (Jones et al. 1994) matrix is used.
#number>0. Default: BLOSUM62
_Option(["--tm", "tm"], [],
os.path.exists, 0,
_Option(["--tm", "tm"],
"Transmembrane PAM number (Jones et al. 1994) "
"matrix is used. number>0. Default: BLOSUM62",
0),
checker_function=os.path.exists,
types=["file"],
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
#input. Default: BLOSUM62
_Option(["--aamatrix", "aamatrix"], [],
os.path.exists, 0,
_Option(["--aamatrix", "aamatrix"],
"Use a user-defined AA scoring matrix. "
"Default: BLOSUM62",
0),
checker_function=os.path.exists,
types=["file"],
equate=False),
#Incorporate the AA/nuc composition information into the scoring
#matrix. Default: off
_Switch(["--fmodel", "fmodel"],
Expand Down Expand Up @@ -309,10 +310,12 @@ def __init__(self, cmd="mafft", **kwargs):
# form: "mafft --seed align1 --seed align2 [etc] input"
# Effectively for n number of seed alignments. Here we're going to
# assume 6 extra are enough
_Option(["--seed", "seed"], ["file"], os.path.exists, 0,
_Option(["--seed", "seed"],
"Seed alignments given in alignment_n (fasta format) "
"are aligned with sequences in input.",
0),
checker_function=os.path.exists,
types=["file"],
equate=False),
#The old solution of also defining extra parameters with
#["--seed", "seed1"] etc worked, but clashes with the recent
#code in the base class to look for duplicate paramters and raise
Expand All @@ -322,13 +325,18 @@ def __init__(self, cmd="mafft", **kwargs):
#assigned to the value?
####################### END SEEDS ################################
#The input (must be FASTA format)
_Argument(["input"], ["file"], os.path.exists, 1,
"Input file name"),
_Argument(["input"],
"Input file name",
checker_function=os.path.exists,
types=["file"],
is_required=True),
###################################################################
#mafft-profile takes a second alignment input as an argument:
#mafft-profile align1 align2
_Argument(["input1"], ["file"], os.path.exists, 0,
"Second input file name for the mafft-profile command")
_Argument(["input1"],
"Second input file name for the mafft-profile command",
checker_function=os.path.exists,
types=["file"]),
]
AbstractCommandline.__init__(self, cmd, **kwargs)

Expand Down

0 comments on commit 6957dd5

Please sign in to comment.