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modified to define default moltype for functions used in QIIME #19

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Apr 21, 2014
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modified to define default moltype for functions used in QIIME #19

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13 changes: 6 additions & 7 deletions brokit/cd_hit.py
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Original file line number Diff line number Diff line change
Expand Up @@ -108,7 +108,7 @@ class CD_HIT(CommandLineApplication):
'-p':ValuedParameter('-',Name='p',Delimiter=' '),

# 1 or 0, default 0
# by cd-hit's default algorithm, a sequence is clustered to the first
# by cd-hit's default algorithm, a sequence is clustered to the first
# cluster that meet the threshold (fast cluster). If set to 1, the program
# will cluster it into the most similar cluster that meet the threshold
# (accurate but slow mode)
Expand All @@ -119,7 +119,7 @@ class CD_HIT(CommandLineApplication):
'-h':ValuedParameter('-',Name='h',Delimiter=' ')
}
_synonyms = {'Similarity':'-c'}

def getHelp(self):
"""Method that points to documentation"""
help_str =\
Expand All @@ -129,12 +129,12 @@ def getHelp(self):

The following papers should be cited if this resource is used:

Clustering of highly homologous sequences to reduce thesize of large
Clustering of highly homologous sequences to reduce thesize of large
protein database", Weizhong Li, Lukasz Jaroszewski & Adam Godzik
Bioinformatics, (2001) 17:282-283

Tolerating some redundancy significantly speeds up clustering of large
protein databases", Weizhong Li, Lukasz Jaroszewski & Adam Godzik
protein databases", Weizhong Li, Lukasz Jaroszewski & Adam Godzik
Bioinformatics, (2002) 18:77-82
"""
return help_str
Expand Down Expand Up @@ -213,7 +213,7 @@ class CD_HIT_EST(CD_HIT):
'-r':ValuedParameter('-',Name='r',Delimiter=' ')
})

def cdhit_clusters_from_seqs(seqs, moltype, params=None):
def cdhit_clusters_from_seqs(seqs, moltype=DNA, params=None):
"""Returns the CD-HIT clusters given seqs

seqs : dict like collection of sequences
Expand All @@ -230,7 +230,7 @@ def cdhit_clusters_from_seqs(seqs, moltype, params=None):
int_map, int_keys = seqs.getIntMap()
#Create SequenceCollection from int_map.
int_map = SequenceCollection(int_map,MolType=moltype)

# setup params and make sure the output argument is set
if params is None:
params = {}
Expand Down Expand Up @@ -332,4 +332,3 @@ def parse_cdhit_clstr_file(lines):
clusters.append(curr_cluster)

return clusters

97 changes: 48 additions & 49 deletions brokit/clearcut.py
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Original file line number Diff line number Diff line change
Expand Up @@ -22,10 +22,10 @@


class Clearcut(CommandLineApplication):
""" clearcut application controller
The parameters are organized by function to give some idea of how the
program works. However, no restrictions are put on any combinations
""" clearcut application controller

The parameters are organized by function to give some idea of how the
program works. However, no restrictions are put on any combinations
of parameters. Misuse of parameters can lead to errors or otherwise
strange results.
"""
Expand All @@ -43,16 +43,16 @@ class Clearcut(CommandLineApplication):
'-S':FlagParameter('-',Name='S'),
#--neighbor. Use traditional Neighbor-Joining algorithm. (Default: OFF)
'-N':FlagParameter('-',Name='N'),

}


# Input file is distance matrix or alignment. Default expects distance
# matrix. Output file is tree created by clearcut.
_input = {\
# --in=<infilename>. Input file
'--in':ValuedParameter('--',Name='in',Delimiter='=',IsPath=True),
# --stdin. Read input from STDIN.
# --stdin. Read input from STDIN.
'-I':FlagParameter('-',Name='I'),
# --distance. Input file is a distance matrix. (Default: ON)
'-d':FlagParameter('-',Name='d',Value=True),
Expand All @@ -64,17 +64,17 @@ class Clearcut(CommandLineApplication):
# --protein. Input alignment are protein sequences.
'-P':FlagParameter('-',Name='P'),
}


#Correction model for computing distance matrix (Default: NO Correction):
_correction={\
# --jukes. Use Jukes-Cantor correction for computing distance matrix.
'-j':FlagParameter('-',Name='j'),
# --kimura. Use Kimura correction for distance matrix.
'-k':FlagParameter('-',Name='k'),

}

_output={\
# --out=<outfilename>. Output file
'--out':ValuedParameter('--',Name='out',Delimiter='=',IsPath=True),
Expand All @@ -88,10 +88,10 @@ class Clearcut(CommandLineApplication):
'-e':FlagParameter('-',Name='e'),
# --expdist. Exponential notation in distance output. (Default: OFF)
'-E':FlagParameter('-',Name='E'),

}


#NOT SUPPORTED
#'-h':FlagParameter('-','h'), #Help
#'-V':FlagParameter('-','V'), #Version
Expand All @@ -102,9 +102,9 @@ class Clearcut(CommandLineApplication):
_parameters.update(_input)
_parameters.update(_correction)
_parameters.update(_output)

_command = 'clearcut'

def getHelp(self):
"""Method that points to the Clearcut documentation."""
help_str =\
Expand All @@ -113,7 +113,7 @@ def getHelp(self):
http://bioinformatics.hungry.com/clearcut/
"""
return help_str

def _input_as_multiline_string(self, data):
"""Writes data to tempfile and sets -infile parameter

Expand Down Expand Up @@ -150,17 +150,17 @@ def _input_as_seqs(self,data):

def _input_as_string(self,data):
"""Makes data the value of a specific parameter

This method returns the empty string. The parameter will be printed
automatically once set.
"""
if data:
self.Parameters['--in'].on(data)
return ''

def _tree_filename(self):
"""Return name of file containing the alignment

prefix -- str, prefix of alignment file.
"""
if self.Parameters['--out']:
Expand All @@ -176,32 +176,32 @@ def _get_result_paths(self,data):
if self.Parameters['--out'].isOn():
out_name = self._tree_filename()
result['Tree'] = ResultPath(Path=out_name,IsWritten=True)
return result
return result




#SOME FUNCTIONS TO EXECUTE THE MOST COMMON TASKS


def align_unaligned_seqs(seqs, moltype, params=None):
def align_unaligned_seqs(seqs, moltype=DNA, params=None):
"""Returns an Alignment object from seqs.

seqs: SequenceCollection object, or data that can be used to build one.

moltype: a MolType object. DNA, RNA, or PROTEIN.

params: dict of parameters to pass in to the Clearcut app controller.

Result will be an Alignment object.
"""
#Clearcut does not support alignment
raise NotImplementedError, """Clearcut does not support alignment."""

def align_and_build_tree(seqs, moltype, best_tree=False, params={}):
"""Returns an alignment and a tree from Sequences object seqs.

seqs: SequenceCollection object, or data that can be used to build one.

best_tree: if True (default:False), uses a slower but more accurate
algorithm to build the tree.

Expand All @@ -213,19 +213,19 @@ def align_and_build_tree(seqs, moltype, best_tree=False, params={}):
"""
#Clearcut does not support alignment
raise NotImplementedError, """Clearcut does not support alignment."""
def build_tree_from_alignment(aln, moltype, best_tree=False, params={},\

def build_tree_from_alignment(aln, moltype=DNA, best_tree=False, params={},\
working_dir='/tmp'):
"""Returns a tree from Alignment object aln.

aln: an cogent.core.alignment.Alignment object, or data that can be used
to build one.
- Clearcut only accepts aligned sequences. Alignment object used to
handle unaligned sequences.

moltype: a cogent.core.moltype object.
- NOTE: If moltype = RNA, we must convert to DNA since Clearcut v1.0.8
gives incorrect results if RNA is passed in. 'U' is treated as an
gives incorrect results if RNA is passed in. 'U' is treated as an
incorrect character and is excluded from distance calculations.

best_tree: if True (default:False), uses a slower but more accurate
Expand All @@ -237,7 +237,7 @@ def build_tree_from_alignment(aln, moltype, best_tree=False, params={},\
fails.
"""
params['--out'] = get_tmp_filename(working_dir)

# Create instance of app controller, enable tree, disable alignment
app = Clearcut(InputHandler='_input_as_multiline_string', params=params, \
WorkingDir=working_dir, SuppressStdout=True,\
Expand All @@ -246,17 +246,17 @@ def build_tree_from_alignment(aln, moltype, best_tree=False, params={},\
app.Parameters['-a'].on()
#Turn off input as distance matrix
app.Parameters['-d'].off()

#If moltype = RNA, we must convert to DNA.
if moltype == RNA:
moltype = DNA

if best_tree:
app.Parameters['-N'].on()

#Turn on correct moltype
moltype_string = moltype.label.upper()
app.Parameters[MOLTYPE_MAP[moltype_string]].on()
app.Parameters[MOLTYPE_MAP[moltype_string]].on()

# Setup mapping. Clearcut clips identifiers. We will need to remap them.
# Clearcut only accepts aligned sequences. Let Alignment object handle
Expand All @@ -269,7 +269,7 @@ def build_tree_from_alignment(aln, moltype, best_tree=False, params={},\

# Collect result
result = app(int_map.toFasta())

# Build tree
tree = DndParser(result['Tree'].read(), constructor=PhyloNode)
for node in tree.tips():
Expand All @@ -280,7 +280,7 @@ def build_tree_from_alignment(aln, moltype, best_tree=False, params={},\
del(seq_aln, app, result, int_map, int_keys, params)

return tree

def add_seqs_to_alignment(seqs, aln, params=None):
"""Returns an Alignment object from seqs and existing Alignment.

Expand All @@ -306,13 +306,13 @@ def align_two_alignments(aln1, aln2, params=None):
#Clearcut does not support alignment
raise NotImplementedError, """Clearcut does not support alignment."""


def build_tree_from_distance_matrix(matrix, best_tree=False, params={},\
working_dir='/tmp'):
"""Returns a tree from a distance matrix.

matrix: a square Dict2D object (cogent.util.dict2d)

best_tree: if True (default:False), uses a slower but more accurate
algorithm to build the tree.

Expand All @@ -322,7 +322,7 @@ def build_tree_from_distance_matrix(matrix, best_tree=False, params={},\
fails.
"""
params['--out'] = get_tmp_filename(working_dir)

# Create instance of app controller, enable tree, disable alignment
app = Clearcut(InputHandler='_input_as_multiline_string', params=params, \
WorkingDir=working_dir, SuppressStdout=True,\
Expand All @@ -331,16 +331,16 @@ def build_tree_from_distance_matrix(matrix, best_tree=False, params={},\
app.Parameters['-a'].off()
#Input is a distance matrix
app.Parameters['-d'].on()

if best_tree:
app.Parameters['-N'].on()

# Turn the dict2d object into the expected input format
matrix_input, int_keys = _matrix_input_from_dict2d(matrix)

# Collect result
result = app(matrix_input)

# Build tree
tree = DndParser(result['Tree'].read(), constructor=PhyloNode)

Expand All @@ -356,9 +356,9 @@ def build_tree_from_distance_matrix(matrix, best_tree=False, params={},\

def _matrix_input_from_dict2d(matrix):
"""makes input for running clearcut on a matrix from a dict2D object"""
#clearcut truncates names to 10 char- need to rename before and
#clearcut truncates names to 10 char- need to rename before and
#reassign after

#make a dict of env_index:full name
int_keys = dict([('env_' + str(i), k) for i,k in \
enumerate(sorted(matrix.keys()))])
Expand All @@ -374,7 +374,7 @@ def _matrix_input_from_dict2d(matrix):
for env2 in matrix[env1]:
new_dists.append((int_map[env1], int_map[env2], matrix[env1][env2]))
int_map_dists = Dict2D(new_dists)

#names will be fed into the phylipTable function - it is the int map names
names = sorted(int_map_dists.keys())
rows = []
Expand All @@ -388,6 +388,5 @@ def _matrix_input_from_dict2d(matrix):
input_matrix = phylipMatrix(rows, names)
#input needs a trailing whitespace or it will fail!
input_matrix += '\n'

return input_matrix, int_keys

return input_matrix, int_keys
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