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opensource
binfpy
Commits
ac6c5d6b
Commit
ac6c5d6b
authored
Feb 14, 2017
by
Mikael Boden
Browse files
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python3_5
parent
934c2bff
Changes
16
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Showing
16 changed files
with
860 additions
and
1533 deletions
+860
-1533
binomial.py
binomial.py
+3
-3
genome.py
genome.py
+32
-43
gibbs.py
gibbs.py
+2
-2
godata.py
godata.py
+41
-43
guide.py
guide.py
+172
-844
ml.py
ml.py
+2
-2
phylo.py
phylo.py
+19
-5
prob.py
prob.py
+6
-8
sam.py
sam.py
+44
-44
seqdata.py
seqdata.py
+38
-35
sequence.py
sequence.py
+31
-32
spred.py
spred.py
+3
-3
sstruct.py
sstruct.py
+2
-2
sym.py
sym.py
+1
-1
webservice.py
webservice.py
+447
-449
wordcount.py
wordcount.py
+17
-17
No files found.
binomial.py
View file @
ac6c5d6b
...
@@ -95,8 +95,8 @@ def betacf(a, b, x):
...
@@ -95,8 +95,8 @@ def betacf(a, b, x):
h
*=
delta
h
*=
delta
if
(
abs
(
delta
-
1.0
)
<
EPS
):
break
if
(
abs
(
delta
-
1.0
)
<
EPS
):
break
if
(
m
>
MAXIT
):
print
>>
sys
.
stderr
,
(
"a or b too big or MAXIT too small "
if
(
m
>
MAXIT
):
print
(
(
"a or b too big or MAXIT too small "
"in betacf"
)
"in betacf"
)
,
file
=
sys
.
stderr
)
return
h
return
h
...
@@ -118,5 +118,5 @@ def gammaln(x):
...
@@ -118,5 +118,5 @@ def gammaln(x):
def
die
(
string
):
def
die
(
string
):
print
>>
sys
.
stderr
,
string
print
(
string
,
file
=
sys
.
stderr
)
genome.py
View file @
ac6c5d6b
...
@@ -105,7 +105,7 @@ class GeneExpression:
...
@@ -105,7 +105,7 @@ class GeneExpression:
{'G2': array([ 4.1, -0.9]), 'G3': array([ 2.1, -2.1])}
{'G2': array([ 4.1, -0.9]), 'G3': array([ 2.1, -2.1])}
"""
"""
if
names
==
None
:
if
names
==
None
:
return
self
.
genes
.
keys
(
)
return
list
(
self
.
genes
.
keys
()
)
elif
isinstance
(
names
,
str
):
elif
isinstance
(
names
,
str
):
return
self
.
matrix
[
self
.
genes
[
names
],:]
return
self
.
matrix
[
self
.
genes
[
names
],:]
else
:
else
:
...
@@ -148,7 +148,7 @@ class GeneExpression:
...
@@ -148,7 +148,7 @@ class GeneExpression:
except
:
except
:
index
=
samples
index
=
samples
mygenes
=
{}
mygenes
=
{}
for
(
name
,
ndx
)
in
self
.
genes
.
items
(
):
for
(
name
,
ndx
)
in
list
(
self
.
genes
.
items
()
):
mygenes
[
name
]
=
self
.
matrix
[
ndx
,
index
]
mygenes
[
name
]
=
self
.
matrix
[
ndx
,
index
]
return
mygenes
return
mygenes
...
@@ -165,7 +165,7 @@ class GeneExpression:
...
@@ -165,7 +165,7 @@ class GeneExpression:
sort_ndx
=
np
.
nan_to_num
(
self
.
matrix
[:,
index
])
.
argsort
()
sort_ndx
=
np
.
nan_to_num
(
self
.
matrix
[:,
index
])
.
argsort
()
except
:
except
:
sort_ndx
=
np
.
nan_to_num
(
self
.
matrix
[:,
sample
])
.
argsort
()
sort_ndx
=
np
.
nan_to_num
(
self
.
matrix
[:,
sample
])
.
argsort
()
name_tuples
=
sorted
(
self
.
genes
.
items
(
),
key
=
lambda
v
:
v
[
1
])
# put all gene names in order of the matrix of profiles
name_tuples
=
sorted
(
list
(
self
.
genes
.
items
()
),
key
=
lambda
v
:
v
[
1
])
# put all gene names in order of the matrix of profiles
names
=
[]
names
=
[]
if
descending
:
if
descending
:
for
(
name
,
index
)
in
[
name_tuples
[
index
]
for
index
in
sort_ndx
[::
-
1
]]:
# reverse the order
for
(
name
,
index
)
in
[
name_tuples
[
index
]
for
index
in
sort_ndx
[::
-
1
]]:
# reverse the order
...
@@ -199,7 +199,7 @@ class GeneExpression:
...
@@ -199,7 +199,7 @@ class GeneExpression:
Creates and returns a gene dictionary with the corresponding ratios. """
Creates and returns a gene dictionary with the corresponding ratios. """
mygenes
=
{}
mygenes
=
{}
mdiv
=
self
.
matrix
[:,
index1
]
/
self
.
matrix
[:,
index2
]
mdiv
=
self
.
matrix
[:,
index1
]
/
self
.
matrix
[:,
index2
]
for
(
name
,
ndx
)
in
self
.
genes
.
items
(
):
for
(
name
,
ndx
)
in
list
(
self
.
genes
.
items
()
):
mygenes
[
name
]
=
mdiv
[
ndx
]
mygenes
[
name
]
=
mdiv
[
ndx
]
return
mygenes
return
mygenes
...
@@ -208,7 +208,7 @@ class GeneExpression:
...
@@ -208,7 +208,7 @@ class GeneExpression:
Creates and returns a gene dictionary with the corresponding log-ratios. """
Creates and returns a gene dictionary with the corresponding log-ratios. """
mygenes
=
{}
mygenes
=
{}
mlr
=
np
.
log2
(
self
.
matrix
[:,
index1
]
/
self
.
matrix
[:,
index2
])
mlr
=
np
.
log2
(
self
.
matrix
[:,
index1
]
/
self
.
matrix
[:,
index2
])
for
(
name
,
ndx
)
in
self
.
genes
.
items
(
):
for
(
name
,
ndx
)
in
list
(
self
.
genes
.
items
()
):
mygenes
[
name
]
=
mlr
[
ndx
]
mygenes
[
name
]
=
mlr
[
ndx
]
return
mygenes
return
mygenes
...
@@ -218,7 +218,7 @@ class GeneExpression:
...
@@ -218,7 +218,7 @@ class GeneExpression:
index
=
self
.
genes
[
probeID
]
index
=
self
.
genes
[
probeID
]
profile
=
self
.
matrix
[
index
,
:]
profile
=
self
.
matrix
[
index
,
:]
mygenes
=
{}
mygenes
=
{}
for
(
name
,
ndx
)
in
self
.
genes
.
items
(
):
for
(
name
,
ndx
)
in
list
(
self
.
genes
.
items
()
):
other
=
self
.
matrix
[
ndx
,
:]
other
=
self
.
matrix
[
ndx
,
:]
mygenes
[
name
]
=
pearson
(
profile
,
other
)
mygenes
[
name
]
=
pearson
(
profile
,
other
)
return
mygenes
return
mygenes
...
@@ -252,7 +252,7 @@ class GeneExpression:
...
@@ -252,7 +252,7 @@ class GeneExpression:
# Calculate Z-score for the given column for each gene
# Calculate Z-score for the given column for each gene
zscore
=
(
self
.
matrix
[:,
index
]
-
mu
)
/
sd
zscore
=
(
self
.
matrix
[:,
index
]
-
mu
)
/
sd
mygenes
=
{}
mygenes
=
{}
for
(
name
,
ndx
)
in
self
.
genes
.
items
(
):
for
(
name
,
ndx
)
in
list
(
self
.
genes
.
items
()
):
try
:
try
:
mygenes
[
name
]
=
zscore
[
ndx
,
:]
mygenes
[
name
]
=
zscore
[
ndx
,
:]
except
IndexError
:
except
IndexError
:
...
@@ -331,9 +331,9 @@ def readGEOFile(filename, id_column=0):
...
@@ -331,9 +331,9 @@ def readGEOFile(filename, id_column=0):
genes
[
name
]
=
values
genes
[
name
]
=
values
if
len
(
genes
)
==
0
:
if
len
(
genes
)
==
0
:
raise
RuntimeError
(
'No data in file'
)
raise
RuntimeError
(
'No data in file'
)
print
'Data set
%
s contains
%
d entries'
%
(
dataset
,
len
(
genes
))
print
(
'Data set
%
s contains
%
d genes'
%
(
dataset
,
len
(
genes
)
))
if
cnt_null
>
0
:
if
cnt_null
>
0
:
print
'Data set has
%
d null-values'
%
(
cnt_null
)
print
(
'Data set has
%
d null-values'
%
(
cnt_null
)
)
return
GeneExpression
(
dataset
,
headers
[
2
:],
genes
)
return
GeneExpression
(
dataset
,
headers
[
2
:],
genes
)
...
@@ -357,40 +357,29 @@ def pearson(X, Y):
...
@@ -357,40 +357,29 @@ def pearson(X, Y):
return
0
return
0
return
(
sum
-
n
*
(
Xmu
*
Ymu
))
/
(
n
*
math
.
sqrt
(
Xvar
)
*
math
.
sqrt
(
Yvar
))
return
(
sum
-
n
*
(
Xmu
*
Ymu
))
/
(
n
*
math
.
sqrt
(
Xvar
)
*
math
.
sqrt
(
Yvar
))
# ------------------- Example ---------------------
# ------------------- Example
(basically exercise 7 in prac 9)
---------------------
ge3716
=
readGEOFile
(
'/Users/mikael/workspace/COSC2000/GDS3716.soft'
)
if
__name__
==
'__main__'
:
ratio
=
GeneExpression
(
'GDS3716_ratio'
)
g
=
readGEOFile
(
'GDS3198.soft'
,
id_column
=
1
)
ratio
.
addSamples
(
'S1_ER+/Healthy'
,
ge3716
.
getRatio
(
33
,
0
))
meanfold
=
{}
ratio
.
addSamples
(
'S2_ER+/Healthy'
,
ge3716
.
getRatio
(
34
,
1
))
for
gene
in
g
.
genes
:
ratio
.
addSamples
(
'S3_ER+/Healthy'
,
ge3716
.
getRatio
(
35
,
2
))
profile
=
g
.
getGenes
(
gene
)
ratio
.
addSamples
(
'S4_ER+/Healthy'
,
ge3716
.
getRatio
(
36
,
3
))
meanfold
[
gene
]
=
(
np
.
log2
(
profile
[
0
]
/
profile
[
3
])
+
np
.
log2
(
profile
[
1
]
/
profile
[
4
])
+
np
.
log2
(
profile
[
2
]
/
profile
[
5
]))
/
3
ratio
.
addSamples
(
'S5_ER+/Healthy'
,
ge3716
.
getRatio
(
37
,
4
))
ratio
.
addSamples
(
'S6_ER+/Healthy'
,
ge3716
.
getRatio
(
38
,
5
))
import
matplotlib.pyplot
as
plt
ratio
.
addSamples
(
'S7_ER+/Healthy'
,
ge3716
.
getRatio
(
39
,
6
))
scores
=
[
y
for
y
in
list
(
meanfold
.
values
())
if
not
np
.
isnan
(
y
)]
ratio
.
addSamples
(
'S8_ER+/Healthy'
,
ge3716
.
getRatio
(
40
,
7
))
hist
,
bins
=
np
.
histogram
(
scores
,
bins
=
50
)
ratio
.
addSamples
(
'S9_ER+/Healthy'
,
ge3716
.
getRatio
(
41
,
8
))
width
=
0.7
*
(
bins
[
1
]
-
bins
[
0
])
ratio
.
addSamples
(
'S1_ER-/Healthy'
,
ge3716
.
getRatio
(
24
,
9
))
center
=
(
bins
[:
-
1
]
+
bins
[
1
:])
/
2
ratio
.
addSamples
(
'S2_ER-/Healthy'
,
ge3716
.
getRatio
(
25
,
10
))
plt
.
bar
(
center
,
hist
,
align
=
'center'
,
width
=
width
)
ratio
.
addSamples
(
'S3_ER-/Healthy'
,
ge3716
.
getRatio
(
26
,
11
))
plt
.
show
()
ratio
.
addSamples
(
'S4_ER-/Healthy'
,
ge3716
.
getRatio
(
27
,
12
))
ratio
.
addSamples
(
'S5_ER-/Healthy'
,
ge3716
.
getRatio
(
28
,
13
))
ratio
.
addSamples
(
'S6_ER-/Healthy'
,
ge3716
.
getRatio
(
29
,
14
))
ratio
.
addSamples
(
'S7_ER-/Healthy'
,
ge3716
.
getRatio
(
30
,
15
))
ratio
.
addSamples
(
'S8_ER-/Healthy'
,
ge3716
.
getRatio
(
31
,
16
))
ratio
.
addSamples
(
'S9_ER-/Healthy'
,
ge3716
.
getRatio
(
32
,
17
))
ratio
.
writeGEOFile
(
'/Users/mikael/workspace/COSC2000/GDS3716_ratios.soft'
)
print
ge3716
.
getHeaders
()
z
=
ratio
.
getZScore
(
0
)
# NOT recommended! Ratios are NOT normally distributed! Use log-ratios instead.
ge38
=
readGEOFile
(
'/Users/mikael/workspace/COSC2000/GDS38.soft'
,
id_column
=
1
)
cln2_profile
=
ge38
.
getGenes
(
'CLN2'
)
pcorr
=
ge38
.
getPearson
(
'CLN2'
)
gp
=
GeneExpression
(
'Ex3'
,
'PC_CLN2'
,
pcorr
)
sorted
=
gp
.
sort
(
'PC_CLN2'
,
True
)
print
sorted
[
0
],
ge38
.
getGenes
(
sorted
[
0
])
print
sorted
[
1
],
ge38
.
getGenes
(
sorted
[
1
])
result
=
sorted
(
list
(
meanfold
.
items
()),
key
=
lambda
v
:
v
[
1
])
print
(
'========== Wildtype may down-regulate =========='
)
for
r
in
result
[
0
:
100
]:
print
(
r
[
0
],
r
[
1
])
print
(
'========== Wildtype may up-regulate =========='
)
for
r
in
result
[
-
1
:
-
100
:
-
1
]:
print
(
r
[
0
],
r
[
1
])
gibbs.py
View file @
ac6c5d6b
...
@@ -138,7 +138,7 @@ class GibbsMotif():
...
@@ -138,7 +138,7 @@ class GibbsMotif():
LL
+=
math
.
log
(
Qk
/
Pk
)
LL
+=
math
.
log
(
Qk
/
Pk
)
except
ZeroDivisionError
:
except
ZeroDivisionError
:
pass
pass
print
"LL @
%5
d=
\t
%5.2
f"
%
(
round
,
LL
)
print
(
"LL @
%5
d=
\t
%5.2
f"
%
(
round
,
LL
)
)
# end main for-loop
# end main for-loop
self
.
q
=
q
self
.
q
=
q
...
@@ -312,7 +312,7 @@ class GibbsAlign():
...
@@ -312,7 +312,7 @@ class GibbsAlign():
LL
+=
math
.
log
(
Qk
/
Pk
)
LL
+=
math
.
log
(
Qk
/
Pk
)
except
ZeroDivisionError
:
except
ZeroDivisionError
:
pass
pass
print
"LL @
%5
d=
\t
%5.2
f"
%
(
round
,
LL
)
print
(
"LL @
%5
d=
\t
%5.2
f"
%
(
round
,
LL
)
)
# end main for-loop
# end main for-loop
self
.
q
=
q
self
.
q
=
q
...
...
godata.py
View file @
ac6c5d6b
This diff is collapsed.
Click to expand it.
guide.py
View file @
ac6c5d6b
This diff is collapsed.
Click to expand it.
ml.py
View file @
ac6c5d6b
...
@@ -21,7 +21,7 @@ class NN():
...
@@ -21,7 +21,7 @@ class NN():
self
.
b_hid
=
numpy
.
random
.
randn
(
nHidden
)
# biases hidden layer
self
.
b_hid
=
numpy
.
random
.
randn
(
nHidden
)
# biases hidden layer
self
.
w_out
=
numpy
.
random
.
randn
(
nOutput
,
nHidden
)
# weights hid -> out
self
.
w_out
=
numpy
.
random
.
randn
(
nOutput
,
nHidden
)
# weights hid -> out
self
.
b_out
=
numpy
.
random
.
randn
(
nOutput
)
# biases output layer
self
.
b_out
=
numpy
.
random
.
randn
(
nOutput
)
# biases output layer
print
"Constructed NN with
%
d inputs,
%
d hidden and
%
d output nodes."
%
(
self
.
ninput
,
len
(
self
.
hidden
),
len
(
self
.
output
))
print
(
"Constructed NN with
%
d inputs,
%
d hidden and
%
d output nodes."
%
(
self
.
ninput
,
len
(
self
.
hidden
),
len
(
self
.
output
)
))
def
writeFile
(
self
,
filename
):
def
writeFile
(
self
,
filename
):
""" Save NN to a file. """
""" Save NN to a file. """
...
@@ -110,7 +110,7 @@ class NN():
...
@@ -110,7 +110,7 @@ class NN():
multi_targ
=
[
target
]
multi_targ
=
[
target
]
for
i
in
range
(
niter
):
for
i
in
range
(
niter
):
mse
=
0.0
mse
=
0.0
entries
=
range
(
len
(
multi_input
))
entries
=
list
(
range
(
len
(
multi_input
)
))
if
shuffle
:
if
shuffle
:
random
.
shuffle
(
entries
)
random
.
shuffle
(
entries
)
for
p
in
entries
:
for
p
in
entries
:
...
...
phylo.py
View file @
ac6c5d6b
...
@@ -2,7 +2,7 @@
...
@@ -2,7 +2,7 @@
Module with methods and classes for phylogeny.
Module with methods and classes for phylogeny.
@author: mikael
@author: mikael
'''
'''
##
import sequence
import
sequence
class
PhyloTree
:
class
PhyloTree
:
""" Rooted, binary (bifurcating) tree for representing phylogenetic relationships.
""" Rooted, binary (bifurcating) tree for representing phylogenetic relationships.
...
@@ -140,7 +140,19 @@ class PhyloNode:
...
@@ -140,7 +140,19 @@ class PhyloNode:
return
left
+
','
return
left
+
','
elif
self
.
left
and
self
.
right
:
elif
self
.
left
and
self
.
right
:
return
'('
+
left
+
','
+
right
+
')'
+
dist
return
'('
+
left
+
','
+
right
+
')'
+
dist
def
__le__
(
self
,
other
):
""" Returns indication of less than other node. """
return
other
and
self
.
__hash__
()
<=
other
.
__hash__
()
def
__eq__
(
self
,
other
):
""" Returns indication of equivalence to other node. """
return
other
and
self
.
__hash__
()
==
other
.
__hash__
()
def
__hash__
(
self
):
""" Returns hash of object. """
return
hash
((
self
.
label
,
self
.
dist
,
self
.
sequence
))
def
_printSequences
(
self
,
start
,
end
):
def
_printSequences
(
self
,
start
,
end
):
""" Returns string with node (incl descendants) in a Newick style. """
""" Returns string with node (incl descendants) in a Newick style. """
left
=
right
=
label
=
dist
=
''
left
=
right
=
label
=
dist
=
''
...
@@ -352,12 +364,12 @@ def runUPGMA(aln, measure, absoluteDistances = False):
...
@@ -352,12 +364,12 @@ def runUPGMA(aln, measure, absoluteDistances = False):
find the *closest* pair of clusters, and
find the *closest* pair of clusters, and
merge that pair into a new cluster (to replace the two that merged).
merge that pair into a new cluster (to replace the two that merged).
In each case, the new cluster is represented by the (phylo)node that is formed. """
In each case, the new cluster is represented by the (phylo)node that is formed. """
while
len
(
N
)
>
1
:
# N will contain all "live" clusters, to be reduced to a si
gn
le below
while
len
(
N
)
>
1
:
# N will contain all "live" clusters, to be reduced to a si
ng
le below
closest_pair
=
(
None
,
None
)
# The two nodes that are closest to one another according to supplied metric
closest_pair
=
(
None
,
None
)
# The two nodes that are closest to one another according to supplied metric
closest_dist
=
None
# The distance between them
closest_dist
=
None
# The distance between them
for
pair
in
D
:
# check all pairs which should be merged
for
pair
in
D
:
# check all pairs which should be merged
dist
=
D
[
pair
]
dist
=
D
[
pair
]
if
dist
<
closest_dist
or
closest_dist
==
None
:
if
closest_dist
==
None
or
dist
<
closest_dist
:
closest_dist
=
dist
closest_dist
=
dist
closest_pair
=
pair
closest_pair
=
pair
# So we know the closest, now we need to merge...
# So we know the closest, now we need to merge...
...
@@ -365,8 +377,10 @@ def runUPGMA(aln, measure, absoluteDistances = False):
...
@@ -365,8 +377,10 @@ def runUPGMA(aln, measure, absoluteDistances = False):
y
=
closest_pair
[
1
]
y
=
closest_pair
[
1
]
z
=
PhyloNode
()
# create a new node for the cluster z
z
=
PhyloNode
()
# create a new node for the cluster z
z
.
dist
=
D
.
pop
(
_getkey
(
x
,
y
))
/
2.0
# assign the absolute distance, travelled so far, note: this will change to relative distance later
z
.
dist
=
D
.
pop
(
_getkey
(
x
,
y
))
/
2.0
# assign the absolute distance, travelled so far, note: this will change to relative distance later
Nx
=
N
.
pop
(
x
)
# find number of sequences in x, remove the cluster from list N
Nx
=
N
.
pop
(
x
,
None
)
# find number of sequences in x, remove the cluster from list N
Ny
=
N
.
pop
(
y
)
# find number of sequences in y, remove the cluster from list N
Ny
=
N
.
pop
(
y
,
None
)
# find number of sequences in y, remove the cluster from list N
if
Nx
==
None
or
Ny
==
None
:
continue
dz
=
{}
# new distances to cluster z
dz
=
{}
# new distances to cluster z
for
w
in
N
:
# for each node w ...
for
w
in
N
:
# for each node w ...
# we will merge x and y into a new cluster z, so need to consider w (which is not x or y)
# we will merge x and y into a new cluster z, so need to consider w (which is not x or y)
...
...
prob.py
View file @
ac6c5d6b
...
@@ -277,7 +277,7 @@ def _readDistrib(linelist):
...
@@ -277,7 +277,7 @@ def _readDistrib(linelist):
if
len
(
d
)
==
0
:
if
len
(
d
)
==
0
:
return
None
return
None
alpha
=
Alphabet
(
symstr
)
alpha
=
Alphabet
(
symstr
)
if
'*'
in
d
.
keys
(
):
# tot provided
if
'*'
in
list
(
d
.
keys
()
):
# tot provided
for
sym
in
d
:
for
sym
in
d
:
if
sym
!=
'*'
:
if
sym
!=
'*'
:
d
[
sym
]
=
d
[
sym
]
*
d
[
'*'
]
d
[
sym
]
=
d
[
sym
]
*
d
[
'*'
]
...
@@ -338,7 +338,7 @@ def _readMultiCount(linelist, format = 'JASPAR'):
...
@@ -338,7 +338,7 @@ def _readMultiCount(linelist, format = 'JASPAR'):
ncol
=
len
(
counts
)
ncol
=
len
(
counts
)
if
len
(
name
)
==
1
:
# proper symbol
if
len
(
name
)
==
1
:
# proper symbol
symcount
[
name
]
=
counts
symcount
[
name
]
=
counts
alpha
=
Alphabet
(
''
.
join
(
symcount
.
keys
(
)))
alpha
=
Alphabet
(
''
.
join
(
list
(
symcount
.
keys
()
)))
distribs
=
[]
distribs
=
[]
for
col
in
range
(
ncol
):
for
col
in
range
(
ncol
):
d
=
dict
([(
sym
,
symcount
[
sym
][
col
])
for
sym
in
symcount
])
d
=
dict
([(
sym
,
symcount
[
sym
][
col
])
for
sym
in
symcount
])
...
@@ -412,7 +412,7 @@ def readMultiCount(filename, format = 'JASPAR'):
...
@@ -412,7 +412,7 @@ def readMultiCount(filename, format = 'JASPAR'):
"""
"""
d
=
readMultiCounts
(
filename
,
format
=
format
)
d
=
readMultiCounts
(
filename
,
format
=
format
)
if
len
(
d
)
>
0
:
if
len
(
d
)
>
0
:
return
d
.
values
(
)[
0
]
return
list
(
d
.
values
()
)[
0
]
#################################################################################################
#################################################################################################
# Joint class
# Joint class
...
@@ -628,12 +628,12 @@ class IndepJoint(Joint):
...
@@ -628,12 +628,12 @@ class IndepJoint(Joint):
def
displayMatrix
(
self
,
count
=
False
):
def
displayMatrix
(
self
,
count
=
False
):
""" Pretty-print matrix """
""" Pretty-print matrix """
print
"
\t
%
s"
%
(
''
.
join
(
"
\t
%5
d"
%
(
i
+
1
)
for
i
in
range
(
len
(
self
.
alphas
))))
print
((
"
\t
%
s"
%
(
''
.
join
(
"
\t
%5
d"
%
(
i
+
1
)
for
i
in
range
(
len
(
self
.
alphas
))
))))
for
a
in
self
.
alphas
[
0
]:
for
a
in
self
.
alphas
[
0
]:
if
count
:
if
count
:
print
"
%
s
\t
%
s"
%
(
a
,
''
.
join
(
"
\t
%5
d"
%
(
y
)
for
y
in
self
.
getRow
(
a
,
True
)))
print
((
"
%
s
\t
%
s"
%
(
a
,
''
.
join
(
"
\t
%5
d"
%
(
y
)
for
y
in
self
.
getRow
(
a
,
True
))
)))
else
:
else
:
print
"
%
s
\t
%
s"
%
(
a
,
''
.
join
(
"
\t
%5.3
f"
%
(
y
)
for
y
in
self
.
getRow
(
a
)))
print
((
"
%
s
\t
%
s"
%
(
a
,
''
.
join
(
"
\t
%5.3
f"
%
(
y
)
for
y
in
self
.
getRow
(
a
))
)))
def
__str__
(
self
):
def
__str__
(
self
):
""" Text representation of the table. Note that size is an issue so big tables
""" Text representation of the table. Note that size is an issue so big tables
...
@@ -718,5 +718,3 @@ class NaiveBayes():
...
@@ -718,5 +718,3 @@ class NaiveBayes():
prob
*=
condprob
[
i
][
key
[
i
]]
or
0.0
prob
*=
condprob
[
i
][
key
[
i
]]
or
0.0
out
.
observe
(
outsym
,
prob
)
out
.
observe
(
outsym
,
prob
)
return
out
return
out
sam.py
View file @
ac6c5d6b
This diff is collapsed.
Click to expand it.
seqdata.py
View file @
ac6c5d6b
This diff is collapsed.
Click to expand it.
sequence.py
View file @
ac6c5d6b
...
@@ -55,10 +55,11 @@ class Sequence(object):
...
@@ -55,10 +55,11 @@ class Sequence(object):
['A', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L', 'M', 'N', 'P', 'Q',
['A', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L', 'M', 'N', 'P', 'Q',
'R', 'S', 'T', 'V', 'W', 'Y'] """
'R', 'S', 'T', 'V', 'W', 'Y'] """
try
:
# convert sequence data into a compact array representation
#try: # convert sequence data into a compact array representation
self
.
sequence
=
array
.
array
(
'c'
,
''
.
join
([
s
.
upper
()
for
s
in
sequence
]))
# self.sequence = sequence.encode("utf-8") #array.array('b', ''.join([s.upper() for s in sequence]))
except
TypeError
:
#except TypeError:
raise
RuntimeError
(
'Sequence data is not specified correctly: must be iterable'
)
# raise RuntimeError('S"""""""""""""""""""""""""""""""equence data is not specified correctly: must be iterable')
self
.
sequence
=
sequence
# Assign an alphabet
# Assign an alphabet
self
.
alphabet
=
None
self
.
alphabet
=
None
...
@@ -133,15 +134,15 @@ class Sequence(object):
...
@@ -133,15 +134,15 @@ class Sequence(object):
Calling self.__getitem__(3) is equivalent to self[3]
Calling self.__getitem__(3) is equivalent to self[3]
"""
"""
if
type
(
ndx
)
is
slice
:
if
type
(
ndx
)
is
slice
:
return
self
.
sequence
[
ndx
]
.
tostring
(
)
return
''
.
join
(
self
.
sequence
[
ndx
]
)
else
:
else
:
return
self
.
sequence
[
ndx
]
return
self
.
sequence
[
ndx
]
def
writeFasta
(
self
):
def
writeFasta
(
self
):
""" Write one sequence in FASTA format to a string and return it. """
""" Write one sequence in FASTA format to a string and return it. """
fasta
=
'>'
+
self
.
name
+
' '
+
self
.
info
+
'
\n
'
fasta
=
'>'
+
self
.
name
+
' '
+
self
.
info
+
'
\n
'
data
=
self
.
sequence
.
tostring
(
)
data
=
''
.
join
(
self
.
sequence
)
nlines
=
(
len
(
self
.
sequence
)
-
1
)
/
60
+
1
nlines
=
int
(
math
.
ceil
((
len
(
self
.
sequence
)
-
1
)
/
60
+
1
))
for
i
in
range
(
nlines
):
for
i
in
range
(
nlines
):
lineofseq
=
''
.
join
(
data
[
i
*
60
:
(
i
+
1
)
*
60
])
+
'
\n
'
lineofseq
=
''
.
join
(
data
[
i
*
60
:
(
i
+
1
)
*
60
])
+
'
\n
'
fasta
+=
lineofseq
fasta
+=
lineofseq
...
@@ -164,7 +165,7 @@ class Sequence(object):
...
@@ -164,7 +165,7 @@ class Sequence(object):
def
find
(
self
,
findme
):
def
find
(
self
,
findme
):
""" Find the position of the specified symbol or sub-sequence """
""" Find the position of the specified symbol or sub-sequence """
return
self
.
sequence
.
tostring
(
)
.
find
(
findme
)
return
''
.
join
(
self
.
sequence
)
.
find
(
findme
)
"""
"""
Below are some useful methods for loading data from strings and files.
Below are some useful methods for loading data from strings and files.
...
@@ -438,8 +439,8 @@ class Alignment():
...
@@ -438,8 +439,8 @@ class Alignment():
column index, entropy, number of gaps, and symbols in order of decreasing probability.
column index, entropy, number of gaps, and symbols in order of decreasing probability.
theta1 is the threshold for displaying symbols in upper case,
theta1 is the threshold for displaying symbols in upper case,
theta2 is the threshold for showing symbols at all, and in lower case. """
theta2 is the threshold for showing symbols at all, and in lower case. """
print
"Alignment of
%
d sequences, with
%
d columns"
%
(
len
(
self
.
seqs
),
self
.
alignlen
)
print
((
"Alignment of
%
d sequences, with
%
d columns"
%
(
len
(
self
.
seqs
),
self
.
alignlen
))
)
print
"Column
\t
Entropy
\t
Gaps
\t
Prob
\t
Conserv
\t
Symbols (Up>=
%.2
f;Low>=
%.2
f)
\n
"
%
(
theta1
,
theta2
)
print
((
"Column
\t
Entropy
\t
Gaps
\t
Prob
\t
Conserv
\t
Symbols (Up>=
%.2
f;Low>=
%.2
f)
\n
"
%
(
theta1
,
theta2
))
)
for
col
in
range
(
self
.
alignlen
):
for
col
in
range
(
self
.
alignlen
):
d
=
Distrib
(
self
.
alphabet
)
d
=
Distrib
(
self
.
alphabet
)
gaps
=
0
gaps
=
0
...
@@ -448,21 +449,21 @@ class Alignment():
...
@@ -448,21 +449,21 @@ class Alignment():
d
.
observe
(
seq
[
col
])
d
.
observe
(
seq
[
col
])
else
:
else
:
gaps
+=
1
gaps
+=
1
print
(
col
+
1
),
"
\t
%5.3
f"
%
d
.
entropy
(),
"
\t
%4
d
\t
"
%
gaps
,
print
(((
col
+
1
),
"
\t
%5.3
f"
%
d
.
entropy
(),
"
\t
%4
d
\t
"
%
gaps
,))
symprobs
=
d
.
getProbsort
()
symprobs
=
d
.
getProbsort
()
(
_
,
maxprob
)
=
symprobs
[
0
]
(
_
,
maxprob
)
=
symprobs
[
0
]
if
maxprob
>=
theta1
:
if
maxprob
>=
theta1
:
print
"
%
d
\t
TRUE
\t
"
%
int
(
maxprob
*
100
),
print
((
"
%
d
\t
TRUE
\t
"
%
int
(
maxprob
*
100
),))
else
:
else
:
print
"
%
d
\t\t
"
%
int
(
maxprob
*
100
),
print
((
"
%
d
\t\t
"
%
int
(
maxprob
*
100
),))
for
(
sym
,
prob
)
in
symprobs
:
for
(
sym
,
prob
)
in
symprobs
:
if
prob
>=
theta1
:
if
prob
>=
theta1
:
print
sym
,
"
%
d
%%
"
%
int
(
prob
*
100
),
print
((
sym
,
"
%
d
%%
"
%
int
(
prob
*
100
),))
elif
prob
>=
theta2
and
lowercase
:
elif
prob
>=
theta2
and
lowercase
:
print
sym
.
lower
(),
"
%
d
%%
"
%
int
(
prob
*
100
),
print
((
sym
.
lower
(),
"
%
d
%%
"
%
int
(
prob
*
100
),))
elif
prob
>=
theta2
:
elif
prob
>=
theta2
:
print
sym
,
"
%
d
%%
"
%
int
(
prob
*
100
),
print
((
sym
,
"
%
d
%%
"
%
int
(
prob
*
100
),))
print
print
()
def
saveConsensus
(
self
,
myseq
,
filename
,
theta1
=
0.2
,
theta2
=
0.05
,
lowercase
=
True
,
compact
=
False
):
def
saveConsensus
(
self
,
myseq
,
filename
,
theta1
=
0.2
,
theta2
=
0.05
,
lowercase
=
True
,
compact
=
False
):
""" Display a table with rows for each alignment column, showing
""" Display a table with rows for each alignment column, showing
...
@@ -644,7 +645,7 @@ class Alignment():
...
@@ -644,7 +645,7 @@ class Alignment():
return
distmat
return
distmat
def
writeHTML
(
self
,
filename
=
None
):
def
writeHTML
(
self
,
filename
=
None
):
""" Generate HTML that displays the alignment in color.
""" Generate HTML that displays the alignment in color.
Requires that the alphabet is annotated with the label 'html-color' (see Sequence.annotateSym)
Requires that the alphabet is annotated with the label 'html-color' (see Sequence.annotateSym)
and that each symbol maps to a text string naming the color, e.g. 'blue'
and that each symbol maps to a text string naming the color, e.g. 'blue'
"""
"""
...
@@ -681,10 +682,9 @@ class Alignment():
...
@@ -681,10 +682,9 @@ class Alignment():
htmlstr
+=
html
htmlstr
+=
html
htmlstr
+=
'<pre>'
htmlstr
+=
'<pre>'
if
filename
:
if
filename
:
fh
=
open
(
filename
,
'w'
)
with
open
(
filename
,
'w+'
)
as
fh
:
fh
.
write
(
htmlstr
)
fh
.
write
(
htmlstr
)
fh
.
write
(
'</body></html>
\n
'
)
fh
.
write
(
'</body></html>
\n
'
)
fh
.
close
()
else
:
else
:
return
htmlstr
return
htmlstr
...
@@ -985,12 +985,12 @@ def readClustal(string, alphabet):
...
@@ -985,12 +985,12 @@ def readClustal(string, alphabet):
index
=
name
.
find
(
'/'
)
index
=
name
.
find
(
'/'
)
if
index
>=
0
:
if
index
>=
0
:
name
=
name
[
0
:
index
]
name
=
name
[
0
:
index
]
if
seqs
.
has_key
(
name
)
:
if
name
in
seqs
:
seqs
[
name
]
+=
seqstr
seqs
[
name
]
+=
seqstr
else
:
else
:
seqs
[
name
]
=
seqstr
seqs
[
name
]
=
seqstr
sequences
=
[]
sequences
=
[]
for
name
,
seqstr
in
seqs
.
items
(
):
for
name
,
seqstr
in
list
(
seqs
.
items
()
):
sequences
.
append
(
Sequence
(
seqstr
,
alphabet
,
name
,
gappy
=
True
))
sequences
.
append
(
Sequence
(
seqstr
,
alphabet
,
name
,
gappy
=
True
))
return
Alignment
(
sequences
)
return
Alignment
(
sequences
)
...
@@ -1180,12 +1180,12 @@ class PWM(object):
...
@@ -1180,12 +1180,12 @@ class PWM(object):
def
display
(
self
,
format
=
'COLUMN'
):
def
display
(
self
,
format
=
'COLUMN'
):
if
format
==
'COLUMN'
:
if
format
==
'COLUMN'
:
print
"
\t
%
s"
%
(
' '
.
join
(
"
%5
d"
%
(
i
+
1
)
for
i
in
range
(
self
.
length
)))
print
((
"
\t
%
s"
%
(
' '
.
join
(
"
%5
d"
%
(
i
+
1
)
for
i
in
range
(
self
.
length
))
)))
for
j
in
range
(
len
(
self
.
alphabet
)):
for
j
in
range
(
len
(
self
.
alphabet
)):
print
"
%
s
\t
%
s"
%
(
self
.
alphabet
[
j
],
' '
.
join
(
"
%+6.2
f"
%
(
y
)
for
y
in
self
.
m
[
j
]
))
print
((
"
%
s
\t
%
s"
%
(
self
.
alphabet
[
j
],
' '
.
join
(
"
%+6.2
f"
%
(
y
)
for
y
in
self
.
m
[
j
]))
))
elif
format
==
'JASPAR'
:
elif
format
==
'JASPAR'
:
for
j
in
range
(
len
(
self
.
alphabet
)):
for
j
in
range
(
len
(
self
.
alphabet
)):
print
"
%
s
\t
[
%
s]"
%
(
self
.
alphabet
[
j
],
' '
.
join
(
"
%+6.2
f"
%
(
y
)
for
y
in
self
.
m
[
j
]
))
print
((
"
%
s
\t
[
%
s]"
%
(
self
.
alphabet
[
j
],
' '
.
join
(
"
%+6.2
f"
%
(
y
)
for
y
in
self
.
m
[
j
]))
))
def
search
(
self
,
sequence
,
lowerBound
=
0
):
def
search
(
self
,
sequence
,
lowerBound
=
0
):
""" Find matches to the motif in a specified sequence. Returns a list
""" Find matches to the motif in a specified sequence. Returns a list
...
@@ -1229,7 +1229,7 @@ def getSequence(id, database = 'uniprotkb', start=None, end=None):
...
@@ -1229,7 +1229,7 @@ def getSequence(id, database = 'uniprotkb', start=None, end=None):
""" Get the sequence identified by the given ID from the given database
""" Get the sequence identified by the given ID from the given database
(e.g. 'uniprotkb', 'refseqn' or 'refseqp'), and return it as a Sequence
(e.g. 'uniprotkb', 'refseqn' or 'refseqp'), and return it as a Sequence
object. An error is caused if the sequence ID is not found. If start and
object. An error is caused if the sequence ID is not found. If start and
end are given, then only that section of the sequence is returned.
end are given, then only that section of the sequence is returned.
Note: more flexible search options are supported by using webservice.fetch
Note: more flexible search options are supported by using webservice.fetch
directly."""
directly."""
...
@@ -1237,12 +1237,12 @@ def getSequence(id, database = 'uniprotkb', start=None, end=None):
...
@@ -1237,12 +1237,12 @@ def getSequence(id, database = 'uniprotkb', start=None, end=None):
for
i
in
range
(
MAX_TRY
):
for
i
in
range
(
MAX_TRY
):
try
:
try
:
fastaData
=
fetch
(
id
,
database
)
fastaData
=
fetch
(
id
,
database
)
.
decode
(
"utf-8"
)
seq
=
readFasta
(
fastaData
)[
0
]
seq
=
readFasta
(
fastaData
)[
0
]
break
break
except
:
except
:
from
time
import
sleep
from
time
import
sleep
print
'Failed on {i}th try for id {id}'
.
format
(
i
=
i
,
id
=
id
)
print
((
'Failed on {i}th try for id {id}'
.
format
(
i
=
i
,
id
=
id
))
)
sleep
(
0.1
)
sleep
(
0.1
)
try
:
try
:
return
Sequence
(
seq
[
start
:
end
],
seq
.
alphabet
,
seq
.
name
,
seq
.
info
)
return
Sequence
(
seq
[
start
:
end
],
seq
.
alphabet
,
seq
.
name
,
seq
.
info
)
...
@@ -1319,5 +1319,4 @@ def runBLAST(sequence, program='blastp', database='uniprotkb', exp='1e-1'):
...
@@ -1319,5 +1319,4 @@ def runBLAST(sequence, program='blastp', database='uniprotkb', exp='1e-1'):
if
__name__
==
'__main__'
:
if
__name__
==
'__main__'
:
seqs
=
readFastaFile
(
'/Users/mikael/ASR/CYP11/CYP11_aln_full.fa'
,
Protein_wX
,
gappy
=
True
)
seqs
=
readFastaFile
(
'/Users/mikael/ASR/CYP11/CYP11_aln_full.fa'
,
Protein_wX
,
gappy
=
True
)
print
'Read'
,
len
(
seqs
),
'sequences'
print
((
'Read'
,
len
(
seqs
),
'sequences'
))
spred.py
View file @
ac6c5d6b
...
@@ -71,7 +71,7 @@ class SeqNN():
...
@@ -71,7 +71,7 @@ class SeqNN():
im
[
row
,
_onehotIndex
(
alpha
,
subseqs
[
k
])]
=
1
im
[
row
,
_onehotIndex
(
alpha
,
subseqs
[
k
])]
=
1
if
targets
:
om
[
row
,
self
.
outp_alpha
.
index
(
subtarg
[
k
])]
=
1
if
targets
:
om
[
row
,
self
.
outp_alpha
.
index
(
subtarg
[
k
])]
=
1
row
+=
1
row
+=
1
print
"There are"
,
row
,
"entries in data set"
print
(
"There are"
,
row
,
"entries in data set"
)
if
targets
:
if
targets
:
return
im
,
om
return
im
,
om
else
:
else
:
...
@@ -85,7 +85,7 @@ class SeqNN():
...
@@ -85,7 +85,7 @@ class SeqNN():
im
,
om
=
self
.
_encodeseq
(
seqs
,
targets
)
im
,
om
=
self
.
_encodeseq
(
seqs
,
targets
)
for
i
in
range
(
niter
):
# train first NN
for
i
in
range
(
niter
):
# train first NN
rmse
=
self
.
nn1
.
train
(
im
,
om
,
eta
=
eta
,
niter
=
1
)
rmse
=
self
.
nn1
.
train
(
im
,
om
,
eta
=
eta
,
niter
=
1
)
print
i
,
":"
,
rmse
print
(
i
,
":"
,
rmse
)
if
not
self
.
cascade
:
# if there's no cascaded NN, finish here
if
not
self
.
cascade
:
# if there's no cascaded NN, finish here
return
rmse
return
rmse
nn1seqs
=
[]
# a list of new SS sequences ...
nn1seqs
=
[]
# a list of new SS sequences ...
...
@@ -95,7 +95,7 @@ class SeqNN():
...
@@ -95,7 +95,7 @@ class SeqNN():
im
,
om
=
self
.
_encodeseq
(
nn1seqs
,
targets
)
# construct input/output patterns from SS sequences
im
,
om
=
self
.
_encodeseq
(
nn1seqs
,
targets
)
# construct input/output patterns from SS sequences
for
i
in
range
(
niter
):
# train cascaded NN
for
i
in
range
(
niter
):
# train cascaded NN
rmse
=
self
.
nn2
.
train
(
im
,
om
,
eta
=
eta
,
niter
=
1
)
rmse
=
self
.
nn2
.
train
(
im
,
om
,
eta
=
eta
,
niter
=
1
)
print
i
,
":"
,
rmse
print
(
i
,
":"
,
rmse
)
return
rmse
return
rmse
def
testAll
(
self
,
seqs
,
targets
):
def
testAll
(
self
,
seqs
,
targets
):
...
...
sstruct.py
View file @
ac6c5d6b
...
@@ -85,7 +85,7 @@ def extendDownstream(scores, calls, width = 4):
...
@@ -85,7 +85,7 @@ def extendDownstream(scores, calls, width = 4):
specified width average of 100.
specified width average of 100.
"""
"""
sum
=
0.0
sum
=
0.0
order
=
range
(
0
,
len
(
calls
)
-
1
,
+
1
)
# we are extending calls downstream
order
=
list
(
range
(
0
,
len
(
calls
)
-
1
,
+
1
)
)
# we are extending calls downstream
cnt
=
0
cnt
=
0
for
i
in
order
:
# extend to the right
for
i
in
order
:
# extend to the right
if
calls
[
i
]:
# to extend a call is required in the first place
if
calls
[
i
]:
# to extend a call is required in the first place
...
@@ -105,7 +105,7 @@ def extendUpstream(scores, calls, width = 4):
...
@@ -105,7 +105,7 @@ def extendUpstream(scores, calls, width = 4):
AND extend this list upstream containing a specified width average of 100.
AND extend this list upstream containing a specified width average of 100.
"""
"""
sum
=
0.0
sum
=
0.0
order
=
range
(
len
(
calls
)
-
1
,
0
,
-
1
)
# we are extending calls upstream/to-the-left
order
=
list
(
range
(
len
(
calls
)
-
1
,
0
,
-
1
)
)
# we are extending calls upstream/to-the-left
cnt
=
0
cnt
=
0
for
i
in
order
:
# extend to the right
for
i
in
order
:
# extend to the right
if
calls
[
i
]:
# a requirement to extend is to have a call in the first place
if
calls
[
i
]:
# a requirement to extend is to have a call in the first place
...
...
sym.py
View file @
ac6c5d6b
...
@@ -291,7 +291,7 @@ class TupleEntries(object):
...
@@ -291,7 +291,7 @@ class TupleEntries(object):
def
__iter__
(
self
):
def
__iter__
(
self
):
return
self
return
self
def
next
(
self
):
def
__next__
(
self
):
""" Step through sequence of entries, either
""" Step through sequence of entries, either
(if not sparse) with a step-size based on alphabet-sizes and what symbols are specified or
(if not sparse) with a step-size based on alphabet-sizes and what symbols are specified or
(if sparse) with calls to tuple store based on all possible symbol combinations."""
(if sparse) with calls to tuple store based on all possible symbol combinations."""
...
...
webservice.py
View file @
ac6c5d6b
This diff is collapsed.
Click to expand it.
wordcount.py
View file @
ac6c5d6b
...
@@ -45,7 +45,7 @@ def countWordsReport(seqs, WordWidth = 8, PeakWidth = 100, PeakMargin = 100):
...
@@ -45,7 +45,7 @@ def countWordsReport(seqs, WordWidth = 8, PeakWidth = 100, PeakMargin = 100):
neg
[
word
]
=
1
neg
[
word
]
=
1
logratio
=
RCDict
()
# DNA dictionary for storing the log-ration between pos and neg
logratio
=
RCDict
()
# DNA dictionary for storing the log-ration between pos and neg
for
(
word
,
cnt_pos
)
in
pos
.
items
(
):
for
(
word
,
cnt_pos
)
in
list
(
pos
.
items
()
):
cnt_neg
=
0.0001
cnt_neg
=
0.0001
try
:
try
:
cnt_neg
=
neg
[
word
]
cnt_neg
=
neg
[
word
]
...
@@ -53,10 +53,10 @@ def countWordsReport(seqs, WordWidth = 8, PeakWidth = 100, PeakMargin = 100):
...
@@ -53,10 +53,10 @@ def countWordsReport(seqs, WordWidth = 8, PeakWidth = 100, PeakMargin = 100):
pass
pass
logratio
[
word
]
=
math
.
log
(
float
(
cnt_pos
)
/
float
(
cnt_neg
))
logratio
[
word
]
=
math
.
log
(
float
(
cnt_pos
)
/
float
(
cnt_neg
))
allpos
=
l
ogratio
.
items
(
)
# extract all pairs of words:log-ratio
allpos
=
l
ist
(
logratio
.
items
()
)
# extract all pairs of words:log-ratio
sortpos
=
sorted
(
allpos
,
key
=
lambda
v
:
v
[
1
],
reverse
=
True
)
# sort them
sortpos
=
sorted
(
allpos
,
key
=
lambda
v
:
v
[
1
],
reverse
=
True
)
# sort them
print
"Enriched words (sorted by ln pos/neg)"
print
(
"Enriched words (sorted by ln pos/neg)"
)
print
"Word
\t
ln pos/neg
\t
E-value"
print
(
"Word
\t
ln pos/neg
\t
E-value"
)
for
(
word
,
lgr
)
in
sortpos
[
0
:
100
]:
# Look at the top-entries according to log-ratio, compute e-values
for
(
word
,
lgr
)
in
sortpos
[
0
:
100
]:
# Look at the top-entries according to log-ratio, compute e-values
cnt_pos
=
int
(
pos
[
word
])
cnt_pos
=
int
(
pos
[
word
])
try
:
cnt_neg
=
int
(
neg
[
word
])
try
:
cnt_neg
=
int
(
neg
[
word
])
...
@@ -65,7 +65,7 @@ def countWordsReport(seqs, WordWidth = 8, PeakWidth = 100, PeakMargin = 100):
...
@@ -65,7 +65,7 @@ def countWordsReport(seqs, WordWidth = 8, PeakWidth = 100, PeakMargin = 100):
pval
=
stats
.
getFETpval
(
cnt_pos
,
cnt_neg
,
len
(
seqs
)
*
(
PeakWidth
-
WordWidth
+
1
)
-
cnt_pos
,
len
(
seqs
)
*
(
len
(
seq
)
-
(
PeakMargin
*
2
+
PeakWidth
)
-
(
WordWidth
-
1
)
*
2
)
-
cnt_neg
,
False
)
pval
=
stats
.
getFETpval
(
cnt_pos
,
cnt_neg
,
len
(
seqs
)
*
(
PeakWidth
-
WordWidth
+
1
)
-
cnt_pos
,
len
(
seqs
)
*
(
len
(
seq
)
-
(
PeakMargin
*
2
+
PeakWidth
)
-
(
WordWidth
-
1
)
*
2
)
-
cnt_neg
,
False
)
# Correct for multiple testing (very conservatively)
# Correct for multiple testing (very conservatively)
eval
=
pval
*
len
(
allpos
)
eval
=
pval
*
len
(
allpos
)
print
"
%
s
\t
%6.3
f
\t
%
e"
%
(
word
,
lgr
,
eval
)
print
(
"
%
s
\t
%6.3
f
\t
%
e"
%
(
word
,
lgr
,
eval
)
)
def
getReverse
(
distribs
):
def
getReverse
(
distribs
):
""" Construct a new list of probability distributions of DNA, by
""" Construct a new list of probability distributions of DNA, by
...
@@ -94,10 +94,10 @@ def scanMotifReport(seqs, motif, threshold=0, jaspar = 'JASPAR_matrices.txt'):
...
@@ -94,10 +94,10 @@ def scanMotifReport(seqs, motif, threshold=0, jaspar = 'JASPAR_matrices.txt'):
except
KeyError
:
except
KeyError
:
usage
(
sys
.
argv
[
0
],
"Unknown motif
%
s"
%
motif
)
usage
(
sys
.
argv
[
0
],
"Unknown motif
%
s"
%
motif
)
return
return
print
"Motif
%
s:"
%
motif
print
(
"Motif
%
s:"
%
motif
)
pwm1
=
sequence
.
PWM
(
fg1
,
bg
)
pwm1
=
sequence
.
PWM
(
fg1
,
bg
)
pwm1
.
display
(
format
=
'JASPAR'
)
pwm1
.
display
(
format
=
'JASPAR'
)
print
"Motif
%
s (reverse complement):"
%
motif
print
(
"Motif
%
s (reverse complement):"
%
motif
)
pwm2
=
sequence
.
PWM
(
fg2
,
bg
)
pwm2
=
sequence
.
PWM
(
fg2
,
bg
)
pwm2
.
display
(
format
=
'JASPAR'
)
pwm2
.
display
(
format
=
'JASPAR'
)
...
@@ -141,7 +141,7 @@ def scanMotifReport(seqs, motif, threshold=0, jaspar = 'JASPAR_matrices.txt'):
...
@@ -141,7 +141,7 @@ def scanMotifReport(seqs, motif, threshold=0, jaspar = 'JASPAR_matrices.txt'):
# plot the average score curve
# plot the average score curve
# print >> sys.stderr, ""
# print >> sys.stderr, ""
x
=
range
(
-
(
seq_len
/
2
),
(
seq_len
/
2
))
# call center of sequence X=0
x
=
list
(
range
(
-
(
seq_len
/
2
),
(
seq_len
/
2
)
))
# call center of sequence X=0
lbl
=
"
%
s"
%
(
motif
)
lbl
=
"
%
s"
%
(
motif
)
plt
.
plot
(
x
,
avg_motif_score
,
label
=
lbl
)
plt
.
plot
(
x
,
avg_motif_score
,
label
=
lbl
)
#plt.plot(x, smoothed_avg_motif_score, label=lbl)
#plt.plot(x, smoothed_avg_motif_score, label=lbl)
...
@@ -187,10 +187,10 @@ def scanMotifReport_new(seqs, motif, threshold=3.4567, jaspar = 'JASPAR_matrices
...
@@ -187,10 +187,10 @@ def scanMotifReport_new(seqs, motif, threshold=3.4567, jaspar = 'JASPAR_matrices
except
KeyError
:
except
KeyError
:
usage
(
sys
.
argv
[
0
],
"Unknown motif
%
s"
%
motif
)
usage
(
sys
.
argv
[
0
],
"Unknown motif
%
s"
%
motif
)
return
return
print
"Motif
%
s:"
%
motif
print
(
"Motif
%
s:"
%
motif
)
pwm1
=
sequence
.
PWM
(
fg1
,
bg
)
pwm1
=
sequence
.
PWM
(
fg1
,
bg
)
pwm1
.
display
(
format
=
'JASPAR'
)
pwm1
.
display
(
format
=
'JASPAR'
)
print
"Motif
%
s (reverse complement):"
%
motif
print
(
"Motif
%
s (reverse complement):"
%
motif
)
pwm2
=
sequence
.
PWM
(
fg2
,
bg
)
pwm2
=
sequence
.
PWM
(
fg2
,
bg
)
pwm2
.
display
(
format
=
'JASPAR'
)
pwm2
.
display
(
format
=
'JASPAR'
)
...
@@ -222,7 +222,7 @@ def scanMotifReport_new(seqs, motif, threshold=3.4567, jaspar = 'JASPAR_matrices
...
@@ -222,7 +222,7 @@ def scanMotifReport_new(seqs, motif, threshold=3.4567, jaspar = 'JASPAR_matrices
# divide number of sequences with hit by total number of hits
# divide number of sequences with hit by total number of hits
site_probability
=
[
(
cnt
/
n_seqs_with_hits
)
for
cnt
in
hit_count
]
site_probability
=
[
(
cnt
/
n_seqs_with_hits
)
for
cnt
in
hit_count
]
print
>>
sys
.
stderr
,
"Number of sequences with hit (score >=
%
f):
%
d"
%
(
threshold
,
n_seqs_with_hits
)
print
(
"Number of sequences with hit (score >=
%
f):
%
d"
%
(
threshold
,
n_seqs_with_hits
),
file
=
sys
.
stderr
)
# STATISTICS
# STATISTICS
# Get the cumulative hit counts in concentric windows
# Get the cumulative hit counts in concentric windows
...
@@ -250,7 +250,7 @@ def scanMotifReport_new(seqs, motif, threshold=3.4567, jaspar = 'JASPAR_matrices
...
@@ -250,7 +250,7 @@ def scanMotifReport_new(seqs, motif, threshold=3.4567, jaspar = 'JASPAR_matrices
for
i
in
range
(
hw
,
seq_len
-
motif_width
+
1
-
hw
):
for
i
in
range
(
hw
,
seq_len
-
motif_width
+
1
-
hw
):
smoothed_site_probability
[
i
]
=
sum
(
site_probability
[
i
-
hw
:
i
+
hw
+
1
])
/
(
2
*
hw
+
1
)
smoothed_site_probability
[
i
]
=
sum
(
site_probability
[
i
-
hw
:
i
+
hw
+
1
])
/
(
2
*
hw
+
1
)
x
=
range
(
-
(
seq_len
/
2
),
(
seq_len
/
2
))
# call center of sequence X=0
x
=
list
(
range
(
-
(
seq_len
/
2
),
(
seq_len
/
2
)
))
# call center of sequence X=0
lbl
=
"
%
s, t=
%.2
f"
%
(
motif
,
threshold
)
lbl
=
"
%
s, t=
%.2
f"
%
(
motif
,
threshold
)
#lbl = "%s, t=%.2f, w=%d, p=%.2e" % (motif, threshold, best_r, math.exp(best_log_pvalue))
#lbl = "%s, t=%.2f, w=%d, p=%.2e" % (motif, threshold, best_r, math.exp(best_log_pvalue))
plt
.
plot
(
x
,
smoothed_site_probability
,
label
=
lbl
)
plt
.
plot
(
x
,
smoothed_site_probability
,
label
=
lbl
)
...
@@ -263,20 +263,20 @@ def scanMotifReport_new(seqs, motif, threshold=3.4567, jaspar = 'JASPAR_matrices
...
@@ -263,20 +263,20 @@ def scanMotifReport_new(seqs, motif, threshold=3.4567, jaspar = 'JASPAR_matrices
def
usage
(
name
,
errmsg
=
None
):
def
usage
(
name
,
errmsg
=
None
):
if
errmsg
!=
None
:
if
errmsg
!=
None
:
print
"Error:
%
s"
%
errmsg
print
(
"Error:
%
s"
%
errmsg
)
print
"""Usage:
%
s [options]
print
(
"""Usage:
%
s [options]
-f <fasta-filename> (required)
-f <fasta-filename> (required)
-d discover enriched words
-d discover enriched words
-w <word width, default 8>
-w <word width, default 8>
-p <peak width, default 100>
-p <peak width, default 100>
-m <peak margin, default 100>
-m <peak margin, default 100>
-s <JASPAR-ID> scan for JASPAR motif
-s <JASPAR-ID> scan for JASPAR motif
-h print this help"""
%
name
-h print this help"""
%
name
)
if
__name__
==
'__main__'
:
if
__name__
==
'__main__'
:
try
:
try
:
optlst
,
args
=
getopt
.
getopt
(
sys
.
argv
[
1
:],
'f:hds:j:w:p:m:'
)
optlst
,
args
=
getopt
.
getopt
(
sys
.
argv
[
1
:],
'f:hds:j:w:p:m:'
)
except
getopt
.
GetoptError
,
err
:
except
getopt
.
GetoptError
as
err
:
usage
(
sys
.
argv
[
0
],
str
(
err
))
usage
(
sys
.
argv
[
0
],
str
(
err
))
sys
.
exit
(
2
)
sys
.
exit
(
2
)
FILENAME
=
None
FILENAME
=
None
...
@@ -301,7 +301,7 @@ if __name__ == '__main__':
...
@@ -301,7 +301,7 @@ if __name__ == '__main__':
sys
.
exit
(
3
)
sys
.
exit
(
3
)
seqs
=
sequence
.
readFastaFile
(
FILENAME
,
sym
.
DNA_Alphabet_wN
)
seqs
=
sequence
.
readFastaFile
(
FILENAME
,
sym
.
DNA_Alphabet_wN
)
if
DISCOVER_MODE
:
if
DISCOVER_MODE
:
print
"Discover (f=
%
s; w=
%
d; p=
%
d; m=
%
d)"
%
(
FILENAME
,
WORD_WIDTH
,
PEAK_WIDTH
,
PEAK_MARGIN
)
print
(
"Discover (f=
%
s; w=
%
d; p=
%
d; m=
%
d)"
%
(
FILENAME
,
WORD_WIDTH
,
PEAK_WIDTH
,
PEAK_MARGIN
)
)
countWordsReport
(
seqs
,
WORD_WIDTH
,
PEAK_WIDTH
,
PEAK_MARGIN
)
countWordsReport
(
seqs
,
WORD_WIDTH
,
PEAK_WIDTH
,
PEAK_MARGIN
)
elif
SCAN_MODE
:
elif
SCAN_MODE
:
scanMotifReport
(
seqs
,
MOTIF_ID
)
scanMotifReport
(
seqs
,
MOTIF_ID
)
...
...
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