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Remove deprecated EMBOSS PHYLIP wrappers

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1 parent 9ac791a commit 53f4841d0577c51acf13872fc93c2ea6e83b9d98 @peterjc peterjc committed Aug 11, 2011
Showing with 5 additions and 245 deletions.
  1. +0 −236 Bio/Emboss/Applications.py
  2. +5 −9 DEPRECATED
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@@ -470,242 +470,6 @@ def __init__(self, cmd="primersearch", **kwargs):
_EmbossCommandLine.__init__(self, cmd, **kwargs)
-class EProtDistCommandline(_EmbossCommandLine):
- """Commandline object for the eprotdist program from EMBOSS (DEPRECATED).
-
- This is an EMBOSS wrapper around protdist from PHYLIP.
-
- It has been replaced by "fprotdist", see FProtDistCommandline.
- """
- def __init__(self, cmd="eprotdist", **kwargs):
- import warnings
- import Bio
- warnings.warn("Bio.Emboss.Application.EProtDistCommandline has been deprecated; please use 'fprotdist' instead (see FProtDistCommandline).", Bio.BiopythonDeprecationWarning)
- self.parameters = [
- _Option(["-msf","msf"],
- "File containing sequences",
- is_required=True),
- _Option(["-method","method"],
- "Choose the method to use",
- is_required=True),
- _Option(["-categ","categ"],
- "Choose the category to use"),
- _Option(["-gencode","gencode"],
- "Which genetic code"),
- _Option(["-prob","prob"],
- "Prob change category (1.0=easy)"),
- _Option(["-tranrate","tranrate"],
- "Transition/transversion ratio"),
- _Option(["-freqa","freqa"],
- "Frequency for A"),
- _Option(["-freqc","freqc"],
- "Frequency for C"),
- _Option(["-freqg","freqg"],
- "Frequency for G"),
- _Option(["-freqt","freqt"],
- "Frequency for T"),
- _Option(["-printdata","printdata"],
- "Print out the data at start of run"),
- _Option(["-progress","progress"],
- "Print indications of progress of run"),
- _Option(["-basefrequency","basefrequency"],
- "Use empirical base frequencies")]
- _EmbossCommandLine.__init__(self, cmd, **kwargs)
-
-
-class ENeighborCommandline(_EmbossCommandLine):
- """Commandline object for the eneighbor program from EMBOSS (DEPRECATED).
-
- This is an EMBOSS wrapper around neighbor from PHYLIP.
-
- It has been replaced by "fneighbor", see FNeighborCommandline.
- """
- def __init__(self, cmd="eneighbor", **kwargs):
- import warnings
- import Bio
- warnings.warn("Bio.Emboss.Application.ENeighborCommandline has been deprecated; please use 'fneighbor' instead (see FNeighborCommandline).", Bio.BiopythonDeprecationWarning)
- self.parameters = [
- _Option(["-infile","infile"],
- "infile value",
- is_required=True),
- _Option(["-trout","trout"],
- "Create a tree file",
- is_required=True),
- _Option(["-treefile","treefile"],
- "Tree file name",
- is_required=True),
- _Option(["-nj","nj"],
- "Neighbor-joining",
- is_required=True), #TODO - Check this
- _Option(["-noog","noog"],
- "Outgroup root",
- is_required=True), #TODO - Check this
- _Option(["-outgnum","outgnum"],
- "number of the outgroup"),
- _Option(["-randseed","randseed"],
- "Random number seed (must be odd)"),
- _Option(["-datasets","datasets"],
- "How many data sets"),
- _Option(["-drawtree","drawtree"],
- "Draw tree"),
- _Option(["-lt","lt"],
- "Lower-triangular data matrix"),
- _Option(["-ut","ut"],
- "Upper-triangular data matrix"),
- _Option(["-sr","sr"],
- "Subreplicates"),
- _Option(["-random","random"],
- "Randomize input order of species"),
- _Option(["-multsets","multsets"],
- "Analyze multiple data sets"),
- _Option(["-printdata","printdata"],
- "Print out the data at start of run"),
- _Option(["-progress","progress"],
- "Print indications of progress of run")]
- _EmbossCommandLine.__init__(self, cmd, **kwargs)
-
-
-class EProtParsCommandline(_EmbossCommandLine):
- """Commandline object for the eprotpars program from EMBOSS (DEPRECATED).
-
- This is an EMBOSS wrapper around protpars from PHYLIP.
-
- It has been replaced by "fprotpars", see FProtParsCommandline.
- """
- def __init__(self, cmd="eprotpars", **kwargs):
- import warnings
- import Bio
- warnings.warn("Bio.Emboss.Application.EProtParsCommandline has been deprecated; please use 'fprotpars' instead (see FProtParsCommandline).", Bio.BiopythonDeprecationWarning)
- self.parameters = [
- _Option(["-msf","msf"],
- "Sequences file to be read in",
- filename=True,
- is_required=True),
- _Option(["-besttree","besttree"],
- "Search for the best tree"),
- _Option(["-random","random"],
- "Randomize input order of species"),
- _Option(["-norandom","norandom"],
- "Do not randomize input order of species"),
- _Option(["-randseed","randseed"],
- "Random number seed (must be odd)"),
- _Option(["-randtimes","randtimes"],
- "How many times to randomize"),
- _Option(["-og","og"],
- "Use an outgroup root"),
- _Option(["-noog","noog"],
- "Do not use an outgroup root"),
- _Option(["-outgnum","outgnum"],
- "Number of the outgroup"),
- _Option(["-thresh","thresh"],
- "Use Threshold parsimony"),
- _Option(["-valthresh","valthresh"],
- "threshold value"),
- _Option(["-printdata","printdata"],
- "Print out the data at start of run"),
- _Option(["-progress","progress"],
- "Print indications of progress of run"),
- _Option(["-steps","steps"],
- "Print out steps in each site"),
- _Option(["-seqatnodes","seqatnodes"],
- "Print sequences at all nodes of tree"),
- _Option(["-drawtree","drawtree"],
- "Draw tree"),
- _Option(["-trout","trout"],
- "Create a tree file"),
- _Option(["-notrout","notrout"],
- "Do not create a tree file"),
- _Option(["-treefile","treefile"],
- "Output treefile name",
- types=["file"])]
- _EmbossCommandLine.__init__(self, cmd, **kwargs)
-
-
-class EConsenseCommandline(_EmbossCommandLine):
- """Commandline object for the econsense program from EMBOSS (DEPRECATED).
-
- This is an EMBOSS wrapper around consense from PHYLIP.
-
- It has been replaced by "fconsense", see FConsenseCommandline.
- """
- def __init__(self, cmd="econsense", **kwargs):
- import warnings
- import Bio
- warnings.warn("Bio.Emboss.Application.EConsenseCommandline has been deprecated; please use 'fconsense' instead (see FConsenseCommandline).", Bio.BiopythonDeprecationWarning)
- self.parameters = [
- _Option(["-infile","infile"],
- "file to read in (New Hampshire standard form)",
- filename=True,
- is_required=True),
- _Option(["-notrout","notrout"],
- "Do not create a tree file"),
- _Option(["-trout","trout"],
- "Create a tree file"),
- _Option(["-treefile","treefile"],
- "tree file name",
- filename=True),
- _Option(["-noog","noog"],
- "Do not use an outgroup"),
- _Option(["-og","og"],
- "Use an outgroup"),
- _Option(["-outgnum","outgnum"],
- "number of the outgroup"),
- _Option(["-nodrawtree","nodrawtree"],
- "Do not draw a tree"),
- _Option(["-drawtree","drawtree"],
- "Draw tree"),
- _Option(["-root","root"],
- "Trees to be treated as Rooted"),
- _Option(["-progress","progress"],
- "Print indications of the progress of run"),
- _Option(["-noprintsets","noprintsets"],
- "Do not print out the sets of species"),
- _Option(["-printsets","printsets"],
- "Print out the sets of species")]
- _EmbossCommandLine.__init__(self, cmd, **kwargs)
-
-
-class ESeqBootCommandline(_EmbossCommandLine):
- """Commandline object for the eseqboot program from EMBOSS (DEPRECATED).
-
- This is an EMBOSS wrapper around seqboot from PHYLIP.
-
- It has been replaced by "fseqboot", see FSeqBootCommandline.
- """
- def __init__(self, cmd="eseqboot", **kwargs):
- import warnings
- import Bio
- warnings.warn("Bio.Emboss.Application.ESeqBootCommandline has been deprecated; please use 'fseqboot' instead (see FSeqBootCommandline).", Bio.BiopythonDeprecationWarning)
- self.parameters = [
- _Option(["-datafile","datafile"],
- "Input file",
- filename=True,
- is_required=True),
- _Option(["-randseed","randseed"],
- "Random number seed (must be odd)",
- is_required=True),
- _Option(["-method","method"],
- "Choose the method",
- is_required=True), #TODO - Options?
- _Option(["-test","test"],
- "Choose test", #TODO - options?
- is_required=True),
- _Option(["-reps","reps"],
- "How many replicates",
- is_required=True),
- _Option(["-inter","inter"],
- "Interleaved input"),
- _Option(["-enzymes","enzymes"],
- "Present in input file"),
- _Option(["-all","all"],
- "All alleles present at each locus"),
- _Option(["-printdata","printdata"],
- "Print out the data at start of run"),
- _Option(["-progress","progress"],
- "Print indications of progress of run")]
- _EmbossCommandLine.__init__(self, cmd, **kwargs)
-
-
class FDNADistCommandline(_EmbossCommandLine):
"""Commandline object for the fdnadist program from EMBOSS.
View
@@ -68,12 +68,6 @@ BlastpgpCommandline and RpsBlastCommandline were declared obsolete in Release
1.53, having been replace with wrappers for the new NCBI BLAST+ tools (e.g.
NcbiblastpCommandline and NcbipsiblastCommandline).
-Bio.EMBOSS.Applications
-=======================
-The wrappers for the "old" EMBOSS PHYLIP tools (e.g. eneighbor) were declared
-obsolete in Biopython 1.52, please use the wrappers for the "new" EMBOSS
-PHYLIP tools (e.g. fneighbor) instead.
-
Bio.Clustalw
============
Declared obsolete in Release 1.52, deprecated in Release 1.55 final, and
@@ -218,9 +212,11 @@ replaced by Bio.Emboss.Primer3 and Bio.Emboss.PrimerSearch instead.
Bio.Emboss.Applications
=======================
-EProtDistCommandline, ENeighborCommandline, EProtParsCommandline,
-EConsenseCommandline, and ESeqBootCommandline were declared obsolete in
-Release 1.52, and deprecated in Release 1.55 final. These functions were
+The wrappers for the "old" EMBOSS PHYLIP tools (e.g. eneighbor) were declared
+obsolete in Biopython 1.52, deprecated in Release 1.55 final, and removed in
+release 1.58. please use the wrappers for the "new" EMBOSS PHYLIP tools (e.g.
+fneighbor) instead. Specifically, EProtDistCommandline, ENeighborCommandline,
+EProtParsCommandline, EConsenseCommandline, and ESeqBootCommandline are
replaced by FProtDistCommandline, FNeighborCommandline, FProtParsCommandline,
FConsenseCommandline, and FSeqBootCommandline, respectively.

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