repository_name stringlengths 5 67 | func_path_in_repository stringlengths 4 234 | func_name stringlengths 0 314 | whole_func_string stringlengths 52 3.87M | language stringclasses 6
values | func_code_string stringlengths 52 3.87M | func_documentation_string stringlengths 1 47.2k | func_code_url stringlengths 85 339 |
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bxlab/bx-python | lib/bx_extras/pstat.py | colex | def colex (listoflists,cnums):
"""
Extracts from listoflists the columns specified in the list 'cnums'
(cnums can be an integer, a sequence of integers, or a string-expression that
corresponds to a slice operation on the variable x ... e.g., 'x[3:]' will colex
columns 3 onward from the listoflists).
Usage: colex... | python | def colex (listoflists,cnums):
"""
Extracts from listoflists the columns specified in the list 'cnums'
(cnums can be an integer, a sequence of integers, or a string-expression that
corresponds to a slice operation on the variable x ... e.g., 'x[3:]' will colex
columns 3 onward from the listoflists).
Usage: colex... | Extracts from listoflists the columns specified in the list 'cnums'
(cnums can be an integer, a sequence of integers, or a string-expression that
corresponds to a slice operation on the variable x ... e.g., 'x[3:]' will colex
columns 3 onward from the listoflists).
Usage: colex (listoflists,cnums)
Returns: a list-of... | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx_extras/pstat.py#L205-L230 |
bxlab/bx-python | lib/bx_extras/pstat.py | collapse | def collapse (listoflists,keepcols,collapsecols,fcn1=None,fcn2=None,cfcn=None):
"""
Averages data in collapsecol, keeping all unique items in keepcols
(using unique, which keeps unique LISTS of column numbers), retaining the
unique sets of values in keepcols, the mean for each. Setting fcn1
and/or fcn2 to point t... | python | def collapse (listoflists,keepcols,collapsecols,fcn1=None,fcn2=None,cfcn=None):
"""
Averages data in collapsecol, keeping all unique items in keepcols
(using unique, which keeps unique LISTS of column numbers), retaining the
unique sets of values in keepcols, the mean for each. Setting fcn1
and/or fcn2 to point t... | Averages data in collapsecol, keeping all unique items in keepcols
(using unique, which keeps unique LISTS of column numbers), retaining the
unique sets of values in keepcols, the mean for each. Setting fcn1
and/or fcn2 to point to a function rather than None (e.g., stats.sterr, len)
will append those results (e.g., t... | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx_extras/pstat.py#L233-L308 |
bxlab/bx-python | lib/bx_extras/pstat.py | flat | def flat(l):
"""
Returns the flattened version of a '2D' list. List-correlate to the a.flat()
method of NumPy arrays.
Usage: flat(l)
"""
newl = []
for i in range(len(l)):
for j in range(len(l[i])):
newl.append(l[i][j])
return newl | python | def flat(l):
"""
Returns the flattened version of a '2D' list. List-correlate to the a.flat()
method of NumPy arrays.
Usage: flat(l)
"""
newl = []
for i in range(len(l)):
for j in range(len(l[i])):
newl.append(l[i][j])
return newl | Returns the flattened version of a '2D' list. List-correlate to the a.flat()
method of NumPy arrays.
Usage: flat(l) | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx_extras/pstat.py#L326-L337 |
bxlab/bx-python | lib/bx_extras/pstat.py | linexand | def linexand (listoflists,columnlist,valuelist):
"""
Returns the rows of a list of lists where col (from columnlist) = val
(from valuelist) for EVERY pair of values (columnlist[i],valuelists[i]).
len(columnlist) must equal len(valuelist).
Usage: linexand (listoflists,columnlist,valuelist)
Returns: the rows of li... | python | def linexand (listoflists,columnlist,valuelist):
"""
Returns the rows of a list of lists where col (from columnlist) = val
(from valuelist) for EVERY pair of values (columnlist[i],valuelists[i]).
len(columnlist) must equal len(valuelist).
Usage: linexand (listoflists,columnlist,valuelist)
Returns: the rows of li... | Returns the rows of a list of lists where col (from columnlist) = val
(from valuelist) for EVERY pair of values (columnlist[i],valuelists[i]).
len(columnlist) must equal len(valuelist).
Usage: linexand (listoflists,columnlist,valuelist)
Returns: the rows of listoflists where columnlist[i]=valuelist[i] for ALL i | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx_extras/pstat.py#L340-L363 |
bxlab/bx-python | lib/bx_extras/pstat.py | linedelimited | def linedelimited (inlist,delimiter):
"""
Returns a string composed of elements in inlist, with each element
separated by 'delimiter.' Used by function writedelimited. Use '\t'
for tab-delimiting.
Usage: linedelimited (inlist,delimiter)
"""
outstr = ''
for item in inlist:
if type(item) != Strin... | python | def linedelimited (inlist,delimiter):
"""
Returns a string composed of elements in inlist, with each element
separated by 'delimiter.' Used by function writedelimited. Use '\t'
for tab-delimiting.
Usage: linedelimited (inlist,delimiter)
"""
outstr = ''
for item in inlist:
if type(item) != Strin... | Returns a string composed of elements in inlist, with each element
separated by 'delimiter.' Used by function writedelimited. Use '\t'
for tab-delimiting.
Usage: linedelimited (inlist,delimiter) | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx_extras/pstat.py#L396-L410 |
bxlab/bx-python | lib/bx_extras/pstat.py | lineincols | def lineincols (inlist,colsize):
"""
Returns a string composed of elements in inlist, with each element
right-aligned in columns of (fixed) colsize.
Usage: lineincols (inlist,colsize) where colsize is an integer
"""
outstr = ''
for item in inlist:
if type(item) != StringType:
item =... | python | def lineincols (inlist,colsize):
"""
Returns a string composed of elements in inlist, with each element
right-aligned in columns of (fixed) colsize.
Usage: lineincols (inlist,colsize) where colsize is an integer
"""
outstr = ''
for item in inlist:
if type(item) != StringType:
item =... | Returns a string composed of elements in inlist, with each element
right-aligned in columns of (fixed) colsize.
Usage: lineincols (inlist,colsize) where colsize is an integer | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx_extras/pstat.py#L413-L431 |
bxlab/bx-python | lib/bx_extras/pstat.py | lineincustcols | def lineincustcols (inlist,colsizes):
"""
Returns a string composed of elements in inlist, with each element
right-aligned in a column of width specified by a sequence colsizes. The
length of colsizes must be greater than or equal to the number of columns
in inlist.
Usage: lineincustcols (inlist,colsizes)
Retur... | python | def lineincustcols (inlist,colsizes):
"""
Returns a string composed of elements in inlist, with each element
right-aligned in a column of width specified by a sequence colsizes. The
length of colsizes must be greater than or equal to the number of columns
in inlist.
Usage: lineincustcols (inlist,colsizes)
Retur... | Returns a string composed of elements in inlist, with each element
right-aligned in a column of width specified by a sequence colsizes. The
length of colsizes must be greater than or equal to the number of columns
in inlist.
Usage: lineincustcols (inlist,colsizes)
Returns: formatted string created from inlist | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx_extras/pstat.py#L434-L457 |
bxlab/bx-python | lib/bx_extras/pstat.py | list2string | def list2string (inlist,delimit=' '):
"""
Converts a 1D list to a single long string for file output, using
the string.join function.
Usage: list2string (inlist,delimit=' ')
Returns: the string created from inlist
"""
stringlist = [makestr(_) for _ in inlist]
return string.join(stringlist,delimit) | python | def list2string (inlist,delimit=' '):
"""
Converts a 1D list to a single long string for file output, using
the string.join function.
Usage: list2string (inlist,delimit=' ')
Returns: the string created from inlist
"""
stringlist = [makestr(_) for _ in inlist]
return string.join(stringlist,delimit) | Converts a 1D list to a single long string for file output, using
the string.join function.
Usage: list2string (inlist,delimit=' ')
Returns: the string created from inlist | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx_extras/pstat.py#L460-L469 |
bxlab/bx-python | lib/bx_extras/pstat.py | printcc | def printcc (lst,extra=2):
"""
Prints a list of lists in columns, customized by the max size of items
within the columns (max size of items in col, plus 'extra' number of spaces).
Use 'dashes' or '\\n' in the list-of-lists to print dashes or blank lines,
respectively.
Usage: printcc (lst,extra=2)
Returns: None
"... | python | def printcc (lst,extra=2):
"""
Prints a list of lists in columns, customized by the max size of items
within the columns (max size of items in col, plus 'extra' number of spaces).
Use 'dashes' or '\\n' in the list-of-lists to print dashes or blank lines,
respectively.
Usage: printcc (lst,extra=2)
Returns: None
"... | Prints a list of lists in columns, customized by the max size of items
within the columns (max size of items in col, plus 'extra' number of spaces).
Use 'dashes' or '\\n' in the list-of-lists to print dashes or blank lines,
respectively.
Usage: printcc (lst,extra=2)
Returns: None | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx_extras/pstat.py#L492-L527 |
bxlab/bx-python | lib/bx_extras/pstat.py | pl | def pl (listoflists):
"""
Prints a list of lists, 1 list (row) at a time.
Usage: pl(listoflists)
Returns: None
"""
for row in listoflists:
if row[-1] == '\n':
print(row, end=' ')
else:
print(row)
return None | python | def pl (listoflists):
"""
Prints a list of lists, 1 list (row) at a time.
Usage: pl(listoflists)
Returns: None
"""
for row in listoflists:
if row[-1] == '\n':
print(row, end=' ')
else:
print(row)
return None | Prints a list of lists, 1 list (row) at a time.
Usage: pl(listoflists)
Returns: None | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx_extras/pstat.py#L543-L555 |
bxlab/bx-python | lib/bx_extras/pstat.py | replace | def replace (inlst,oldval,newval):
"""
Replaces all occurrences of 'oldval' with 'newval', recursively.
Usage: replace (inlst,oldval,newval)
"""
lst = inlst*1
for i in range(len(lst)):
if type(lst[i]) not in [ListType,TupleType]:
if lst[i]==oldval: lst[i]=newval
else:
... | python | def replace (inlst,oldval,newval):
"""
Replaces all occurrences of 'oldval' with 'newval', recursively.
Usage: replace (inlst,oldval,newval)
"""
lst = inlst*1
for i in range(len(lst)):
if type(lst[i]) not in [ListType,TupleType]:
if lst[i]==oldval: lst[i]=newval
else:
... | Replaces all occurrences of 'oldval' with 'newval', recursively.
Usage: replace (inlst,oldval,newval) | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx_extras/pstat.py#L564-L576 |
bxlab/bx-python | lib/bx_extras/pstat.py | recode | def recode (inlist,listmap,cols=None):
"""
Changes the values in a list to a new set of values (useful when
you need to recode data from (e.g.) strings to numbers. cols defaults
to None (meaning all columns are recoded).
Usage: recode (inlist,listmap,cols=None) cols=recode cols, listmap=2D list
Returns: inlist... | python | def recode (inlist,listmap,cols=None):
"""
Changes the values in a list to a new set of values (useful when
you need to recode data from (e.g.) strings to numbers. cols defaults
to None (meaning all columns are recoded).
Usage: recode (inlist,listmap,cols=None) cols=recode cols, listmap=2D list
Returns: inlist... | Changes the values in a list to a new set of values (useful when
you need to recode data from (e.g.) strings to numbers. cols defaults
to None (meaning all columns are recoded).
Usage: recode (inlist,listmap,cols=None) cols=recode cols, listmap=2D list
Returns: inlist with the appropriate values replaced with new ... | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx_extras/pstat.py#L579-L607 |
bxlab/bx-python | lib/bx_extras/pstat.py | roundlist | def roundlist (inlist,digits):
"""
Goes through each element in a 1D or 2D inlist, and applies the following
function to all elements of FloatType ... round(element,digits).
Usage: roundlist(inlist,digits)
Returns: list with rounded floats
"""
if type(inlist[0]) in [IntType, FloatType]:
inlist = [inl... | python | def roundlist (inlist,digits):
"""
Goes through each element in a 1D or 2D inlist, and applies the following
function to all elements of FloatType ... round(element,digits).
Usage: roundlist(inlist,digits)
Returns: list with rounded floats
"""
if type(inlist[0]) in [IntType, FloatType]:
inlist = [inl... | Goes through each element in a 1D or 2D inlist, and applies the following
function to all elements of FloatType ... round(element,digits).
Usage: roundlist(inlist,digits)
Returns: list with rounded floats | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx_extras/pstat.py#L624-L639 |
bxlab/bx-python | lib/bx_extras/pstat.py | sortby | def sortby(listoflists,sortcols):
"""
Sorts a list of lists on the column(s) specified in the sequence
sortcols.
Usage: sortby(listoflists,sortcols)
Returns: sorted list, unchanged column ordering
"""
newlist = abut(colex(listoflists,sortcols),listoflists)
newlist.sort()
try:
numcols = len(so... | python | def sortby(listoflists,sortcols):
"""
Sorts a list of lists on the column(s) specified in the sequence
sortcols.
Usage: sortby(listoflists,sortcols)
Returns: sorted list, unchanged column ordering
"""
newlist = abut(colex(listoflists,sortcols),listoflists)
newlist.sort()
try:
numcols = len(so... | Sorts a list of lists on the column(s) specified in the sequence
sortcols.
Usage: sortby(listoflists,sortcols)
Returns: sorted list, unchanged column ordering | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx_extras/pstat.py#L642-L658 |
bxlab/bx-python | lib/bx_extras/pstat.py | unique | def unique (inlist):
"""
Returns all unique items in the passed list. If the a list-of-lists
is passed, unique LISTS are found (i.e., items in the first dimension are
compared).
Usage: unique (inlist)
Returns: the unique elements (or rows) in inlist
"""
uniques = []
for item in inlist:
if item n... | python | def unique (inlist):
"""
Returns all unique items in the passed list. If the a list-of-lists
is passed, unique LISTS are found (i.e., items in the first dimension are
compared).
Usage: unique (inlist)
Returns: the unique elements (or rows) in inlist
"""
uniques = []
for item in inlist:
if item n... | Returns all unique items in the passed list. If the a list-of-lists
is passed, unique LISTS are found (i.e., items in the first dimension are
compared).
Usage: unique (inlist)
Returns: the unique elements (or rows) in inlist | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx_extras/pstat.py#L661-L674 |
bxlab/bx-python | lib/bx_extras/pstat.py | duplicates | def duplicates(inlist):
"""
Returns duplicate items in the FIRST dimension of the passed list.
Usage: duplicates (inlist)
"""
dups = []
for i in range(len(inlist)):
if inlist[i] in inlist[i+1:]:
dups.append(inlist[i])
return dups | python | def duplicates(inlist):
"""
Returns duplicate items in the FIRST dimension of the passed list.
Usage: duplicates (inlist)
"""
dups = []
for i in range(len(inlist)):
if inlist[i] in inlist[i+1:]:
dups.append(inlist[i])
return dups | Returns duplicate items in the FIRST dimension of the passed list.
Usage: duplicates (inlist) | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx_extras/pstat.py#L676-L686 |
bxlab/bx-python | lib/bx_extras/pstat.py | nonrepeats | def nonrepeats(inlist):
"""
Returns items that are NOT duplicated in the first dim of the passed list.
Usage: nonrepeats (inlist)
"""
nonrepeats = []
for i in range(len(inlist)):
if inlist.count(inlist[i]) == 1:
nonrepeats.append(inlist[i])
return nonrepeats | python | def nonrepeats(inlist):
"""
Returns items that are NOT duplicated in the first dim of the passed list.
Usage: nonrepeats (inlist)
"""
nonrepeats = []
for i in range(len(inlist)):
if inlist.count(inlist[i]) == 1:
nonrepeats.append(inlist[i])
return nonrepeats | Returns items that are NOT duplicated in the first dim of the passed list.
Usage: nonrepeats (inlist) | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx_extras/pstat.py#L689-L699 |
bxlab/bx-python | lib/bx_extras/stats.py | lgeometricmean | def lgeometricmean (inlist):
"""
Calculates the geometric mean of the values in the passed list.
That is: n-th root of (x1 * x2 * ... * xn). Assumes a '1D' list.
Usage: lgeometricmean(inlist)
"""
mult = 1.0
one_over_n = 1.0/len(inlist)
for item in inlist:
mult = mult * pow(item,one_over_n)
... | python | def lgeometricmean (inlist):
"""
Calculates the geometric mean of the values in the passed list.
That is: n-th root of (x1 * x2 * ... * xn). Assumes a '1D' list.
Usage: lgeometricmean(inlist)
"""
mult = 1.0
one_over_n = 1.0/len(inlist)
for item in inlist:
mult = mult * pow(item,one_over_n)
... | Calculates the geometric mean of the values in the passed list.
That is: n-th root of (x1 * x2 * ... * xn). Assumes a '1D' list.
Usage: lgeometricmean(inlist) | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx_extras/stats.py#L271-L282 |
bxlab/bx-python | lib/bx_extras/stats.py | lharmonicmean | def lharmonicmean (inlist):
"""
Calculates the harmonic mean of the values in the passed list.
That is: n / (1/x1 + 1/x2 + ... + 1/xn). Assumes a '1D' list.
Usage: lharmonicmean(inlist)
"""
sum = 0
for item in inlist:
sum = sum + 1.0/item
return len(inlist) / sum | python | def lharmonicmean (inlist):
"""
Calculates the harmonic mean of the values in the passed list.
That is: n / (1/x1 + 1/x2 + ... + 1/xn). Assumes a '1D' list.
Usage: lharmonicmean(inlist)
"""
sum = 0
for item in inlist:
sum = sum + 1.0/item
return len(inlist) / sum | Calculates the harmonic mean of the values in the passed list.
That is: n / (1/x1 + 1/x2 + ... + 1/xn). Assumes a '1D' list.
Usage: lharmonicmean(inlist) | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx_extras/stats.py#L285-L295 |
bxlab/bx-python | lib/bx_extras/stats.py | lmean | def lmean (inlist):
"""
Returns the arithematic mean of the values in the passed list.
Assumes a '1D' list, but will function on the 1st dim of an array(!).
Usage: lmean(inlist)
"""
sum = 0
for item in inlist:
sum = sum + item
return sum/float(len(inlist)) | python | def lmean (inlist):
"""
Returns the arithematic mean of the values in the passed list.
Assumes a '1D' list, but will function on the 1st dim of an array(!).
Usage: lmean(inlist)
"""
sum = 0
for item in inlist:
sum = sum + item
return sum/float(len(inlist)) | Returns the arithematic mean of the values in the passed list.
Assumes a '1D' list, but will function on the 1st dim of an array(!).
Usage: lmean(inlist) | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx_extras/stats.py#L298-L308 |
bxlab/bx-python | lib/bx_extras/stats.py | lmedian | def lmedian (inlist,numbins=1000):
"""
Returns the computed median value of a list of numbers, given the
number of bins to use for the histogram (more bins brings the computed value
closer to the median score, default number of bins = 1000). See G.W.
Heiman's Basic Stats (1st Edition), or CRC Probability & Statist... | python | def lmedian (inlist,numbins=1000):
"""
Returns the computed median value of a list of numbers, given the
number of bins to use for the histogram (more bins brings the computed value
closer to the median score, default number of bins = 1000). See G.W.
Heiman's Basic Stats (1st Edition), or CRC Probability & Statist... | Returns the computed median value of a list of numbers, given the
number of bins to use for the histogram (more bins brings the computed value
closer to the median score, default number of bins = 1000). See G.W.
Heiman's Basic Stats (1st Edition), or CRC Probability & Statistics.
Usage: lmedian (inlist, numbins=100... | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx_extras/stats.py#L311-L330 |
bxlab/bx-python | lib/bx_extras/stats.py | litemfreq | def litemfreq(inlist):
"""
Returns a list of pairs. Each pair consists of one of the scores in inlist
and it's frequency count. Assumes a 1D list is passed.
Usage: litemfreq(inlist)
Returns: a 2D frequency table (col [0:n-1]=scores, col n=frequencies)
"""
scores = pstat.unique(inlist)
scores.sort()
... | python | def litemfreq(inlist):
"""
Returns a list of pairs. Each pair consists of one of the scores in inlist
and it's frequency count. Assumes a 1D list is passed.
Usage: litemfreq(inlist)
Returns: a 2D frequency table (col [0:n-1]=scores, col n=frequencies)
"""
scores = pstat.unique(inlist)
scores.sort()
... | Returns a list of pairs. Each pair consists of one of the scores in inlist
and it's frequency count. Assumes a 1D list is passed.
Usage: litemfreq(inlist)
Returns: a 2D frequency table (col [0:n-1]=scores, col n=frequencies) | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx_extras/stats.py#L454-L467 |
bxlab/bx-python | lib/bx_extras/stats.py | lhistogram | def lhistogram (inlist,numbins=10,defaultreallimits=None,printextras=0):
"""
Returns (i) a list of histogram bin counts, (ii) the smallest value
of the histogram binning, and (iii) the bin width (the last 2 are not
necessarily integers). Default number of bins is 10. If no sequence object
is given for defaultreal... | python | def lhistogram (inlist,numbins=10,defaultreallimits=None,printextras=0):
"""
Returns (i) a list of histogram bin counts, (ii) the smallest value
of the histogram binning, and (iii) the bin width (the last 2 are not
necessarily integers). Default number of bins is 10. If no sequence object
is given for defaultreal... | Returns (i) a list of histogram bin counts, (ii) the smallest value
of the histogram binning, and (iii) the bin width (the last 2 are not
necessarily integers). Default number of bins is 10. If no sequence object
is given for defaultreallimits, the routine picks (usually non-pretty) bins
spanning all the numbers in t... | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx_extras/stats.py#L505-L541 |
bxlab/bx-python | lib/bx_extras/stats.py | lsem | def lsem (inlist):
"""
Returns the estimated standard error of the mean (sx-bar) of the
values in the passed list. sem = stdev / sqrt(n)
Usage: lsem(inlist)
"""
sd = stdev(inlist)
n = len(inlist)
return sd/math.sqrt(n) | python | def lsem (inlist):
"""
Returns the estimated standard error of the mean (sx-bar) of the
values in the passed list. sem = stdev / sqrt(n)
Usage: lsem(inlist)
"""
sd = stdev(inlist)
n = len(inlist)
return sd/math.sqrt(n) | Returns the estimated standard error of the mean (sx-bar) of the
values in the passed list. sem = stdev / sqrt(n)
Usage: lsem(inlist) | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx_extras/stats.py#L669-L678 |
bxlab/bx-python | lib/bx_extras/stats.py | lz | def lz (inlist, score):
"""
Returns the z-score for a given input score, given that score and the
list from which that score came. Not appropriate for population calculations.
Usage: lz(inlist, score)
"""
z = (score-mean(inlist))/samplestdev(inlist)
return z | python | def lz (inlist, score):
"""
Returns the z-score for a given input score, given that score and the
list from which that score came. Not appropriate for population calculations.
Usage: lz(inlist, score)
"""
z = (score-mean(inlist))/samplestdev(inlist)
return z | Returns the z-score for a given input score, given that score and the
list from which that score came. Not appropriate for population calculations.
Usage: lz(inlist, score) | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx_extras/stats.py#L681-L689 |
bxlab/bx-python | lib/bx_extras/stats.py | lzs | def lzs (inlist):
"""
Returns a list of z-scores, one for each score in the passed list.
Usage: lzs(inlist)
"""
zscores = []
for item in inlist:
zscores.append(z(inlist,item))
return zscores | python | def lzs (inlist):
"""
Returns a list of z-scores, one for each score in the passed list.
Usage: lzs(inlist)
"""
zscores = []
for item in inlist:
zscores.append(z(inlist,item))
return zscores | Returns a list of z-scores, one for each score in the passed list.
Usage: lzs(inlist) | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx_extras/stats.py#L692-L701 |
bxlab/bx-python | lib/bx_extras/stats.py | ltrimboth | def ltrimboth (l,proportiontocut):
"""
Slices off the passed proportion of items from BOTH ends of the passed
list (i.e., with proportiontocut=0.1, slices 'leftmost' 10% AND 'rightmost'
10% of scores. Assumes list is sorted by magnitude. Slices off LESS if
proportion results in a non-integer slice index (i.e., co... | python | def ltrimboth (l,proportiontocut):
"""
Slices off the passed proportion of items from BOTH ends of the passed
list (i.e., with proportiontocut=0.1, slices 'leftmost' 10% AND 'rightmost'
10% of scores. Assumes list is sorted by magnitude. Slices off LESS if
proportion results in a non-integer slice index (i.e., co... | Slices off the passed proportion of items from BOTH ends of the passed
list (i.e., with proportiontocut=0.1, slices 'leftmost' 10% AND 'rightmost'
10% of scores. Assumes list is sorted by magnitude. Slices off LESS if
proportion results in a non-integer slice index (i.e., conservatively
slices off proportiontocut).
... | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx_extras/stats.py#L708-L721 |
bxlab/bx-python | lib/bx_extras/stats.py | ltrim1 | def ltrim1 (l,proportiontocut,tail='right'):
"""
Slices off the passed proportion of items from ONE end of the passed
list (i.e., if proportiontocut=0.1, slices off 'leftmost' or 'rightmost'
10% of scores). Slices off LESS if proportion results in a non-integer
slice index (i.e., conservatively slices off proporti... | python | def ltrim1 (l,proportiontocut,tail='right'):
"""
Slices off the passed proportion of items from ONE end of the passed
list (i.e., if proportiontocut=0.1, slices off 'leftmost' or 'rightmost'
10% of scores). Slices off LESS if proportion results in a non-integer
slice index (i.e., conservatively slices off proporti... | Slices off the passed proportion of items from ONE end of the passed
list (i.e., if proportiontocut=0.1, slices off 'leftmost' or 'rightmost'
10% of scores). Slices off LESS if proportion results in a non-integer
slice index (i.e., conservatively slices off proportiontocut).
Usage: ltrim1 (l,proportiontocut,tail='r... | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx_extras/stats.py#L724-L740 |
bxlab/bx-python | lib/bx_extras/stats.py | lpearsonr | def lpearsonr(x,y):
"""
Calculates a Pearson correlation coefficient and the associated
probability value. Taken from Heiman's Basic Statistics for the Behav.
Sci (2nd), p.195.
Usage: lpearsonr(x,y) where x and y are equal-length lists
Returns: Pearson's r value, two-tailed p-value
"""
TINY = 1.0e-30
... | python | def lpearsonr(x,y):
"""
Calculates a Pearson correlation coefficient and the associated
probability value. Taken from Heiman's Basic Statistics for the Behav.
Sci (2nd), p.195.
Usage: lpearsonr(x,y) where x and y are equal-length lists
Returns: Pearson's r value, two-tailed p-value
"""
TINY = 1.0e-30
... | Calculates a Pearson correlation coefficient and the associated
probability value. Taken from Heiman's Basic Statistics for the Behav.
Sci (2nd), p.195.
Usage: lpearsonr(x,y) where x and y are equal-length lists
Returns: Pearson's r value, two-tailed p-value | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx_extras/stats.py#L811-L834 |
bxlab/bx-python | lib/bx_extras/stats.py | lspearmanr | def lspearmanr(x,y):
"""
Calculates a Spearman rank-order correlation coefficient. Taken
from Heiman's Basic Statistics for the Behav. Sci (1st), p.192.
Usage: lspearmanr(x,y) where x and y are equal-length lists
Returns: Spearman's r, two-tailed p-value
"""
TINY = 1e-30
if len(x) != len(y):
... | python | def lspearmanr(x,y):
"""
Calculates a Spearman rank-order correlation coefficient. Taken
from Heiman's Basic Statistics for the Behav. Sci (1st), p.192.
Usage: lspearmanr(x,y) where x and y are equal-length lists
Returns: Spearman's r, two-tailed p-value
"""
TINY = 1e-30
if len(x) != len(y):
... | Calculates a Spearman rank-order correlation coefficient. Taken
from Heiman's Basic Statistics for the Behav. Sci (1st), p.192.
Usage: lspearmanr(x,y) where x and y are equal-length lists
Returns: Spearman's r, two-tailed p-value | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx_extras/stats.py#L837-L858 |
bxlab/bx-python | lib/bx_extras/stats.py | lpointbiserialr | def lpointbiserialr(x,y):
"""
Calculates a point-biserial correlation coefficient and the associated
probability value. Taken from Heiman's Basic Statistics for the Behav.
Sci (1st), p.194.
Usage: lpointbiserialr(x,y) where x,y are equal-length lists
Returns: Point-biserial r, two-tailed p-value
"""
TI... | python | def lpointbiserialr(x,y):
"""
Calculates a point-biserial correlation coefficient and the associated
probability value. Taken from Heiman's Basic Statistics for the Behav.
Sci (1st), p.194.
Usage: lpointbiserialr(x,y) where x,y are equal-length lists
Returns: Point-biserial r, two-tailed p-value
"""
TI... | Calculates a point-biserial correlation coefficient and the associated
probability value. Taken from Heiman's Basic Statistics for the Behav.
Sci (1st), p.194.
Usage: lpointbiserialr(x,y) where x,y are equal-length lists
Returns: Point-biserial r, two-tailed p-value | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx_extras/stats.py#L861-L890 |
bxlab/bx-python | lib/bx_extras/stats.py | lkendalltau | def lkendalltau(x,y):
"""
Calculates Kendall's tau ... correlation of ordinal data. Adapted
from function kendl1 in Numerical Recipies. Needs good test-routine.@@@
Usage: lkendalltau(x,y)
Returns: Kendall's tau, two-tailed p-value
"""
n1 = 0
n2 = 0
iss = 0
for j in range(len(x)-1):
for ... | python | def lkendalltau(x,y):
"""
Calculates Kendall's tau ... correlation of ordinal data. Adapted
from function kendl1 in Numerical Recipies. Needs good test-routine.@@@
Usage: lkendalltau(x,y)
Returns: Kendall's tau, two-tailed p-value
"""
n1 = 0
n2 = 0
iss = 0
for j in range(len(x)-1):
for ... | Calculates Kendall's tau ... correlation of ordinal data. Adapted
from function kendl1 in Numerical Recipies. Needs good test-routine.@@@
Usage: lkendalltau(x,y)
Returns: Kendall's tau, two-tailed p-value | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx_extras/stats.py#L893-L925 |
bxlab/bx-python | lib/bx_extras/stats.py | llinregress | def llinregress(x,y):
"""
Calculates a regression line on x,y pairs.
Usage: llinregress(x,y) x,y are equal-length lists of x-y coordinates
Returns: slope, intercept, r, two-tailed prob, sterr-of-estimate
"""
TINY = 1.0e-20
if len(x) != len(y):
raise ValueError('Input values not paired in l... | python | def llinregress(x,y):
"""
Calculates a regression line on x,y pairs.
Usage: llinregress(x,y) x,y are equal-length lists of x-y coordinates
Returns: slope, intercept, r, two-tailed prob, sterr-of-estimate
"""
TINY = 1.0e-20
if len(x) != len(y):
raise ValueError('Input values not paired in l... | Calculates a regression line on x,y pairs.
Usage: llinregress(x,y) x,y are equal-length lists of x-y coordinates
Returns: slope, intercept, r, two-tailed prob, sterr-of-estimate | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx_extras/stats.py#L928-L953 |
bxlab/bx-python | lib/bx_extras/stats.py | lchisquare | def lchisquare(f_obs,f_exp=None):
"""
Calculates a one-way chi square for list of observed frequencies and returns
the result. If no expected frequencies are given, the total N is assumed to
be equally distributed across all groups.
Usage: lchisquare(f_obs, f_exp=None) f_obs = list of observed cell freq.
Retu... | python | def lchisquare(f_obs,f_exp=None):
"""
Calculates a one-way chi square for list of observed frequencies and returns
the result. If no expected frequencies are given, the total N is assumed to
be equally distributed across all groups.
Usage: lchisquare(f_obs, f_exp=None) f_obs = list of observed cell freq.
Retu... | Calculates a one-way chi square for list of observed frequencies and returns
the result. If no expected frequencies are given, the total N is assumed to
be equally distributed across all groups.
Usage: lchisquare(f_obs, f_exp=None) f_obs = list of observed cell freq.
Returns: chisquare-statistic, associated p-val... | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx_extras/stats.py#L1054-L1069 |
bxlab/bx-python | lib/bx_extras/stats.py | lks_2samp | def lks_2samp (data1,data2):
"""
Computes the Kolmogorov-Smirnof statistic on 2 samples. From
Numerical Recipies in C, page 493.
Usage: lks_2samp(data1,data2) data1&2 are lists of values for 2 conditions
Returns: KS D-value, associated p-value
"""
j1 = 0
j2 = 0
fn1 = 0.0
fn2 = 0.0
n1 = len... | python | def lks_2samp (data1,data2):
"""
Computes the Kolmogorov-Smirnof statistic on 2 samples. From
Numerical Recipies in C, page 493.
Usage: lks_2samp(data1,data2) data1&2 are lists of values for 2 conditions
Returns: KS D-value, associated p-value
"""
j1 = 0
j2 = 0
fn1 = 0.0
fn2 = 0.0
n1 = len... | Computes the Kolmogorov-Smirnof statistic on 2 samples. From
Numerical Recipies in C, page 493.
Usage: lks_2samp(data1,data2) data1&2 are lists of values for 2 conditions
Returns: KS D-value, associated p-value | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx_extras/stats.py#L1072-L1108 |
bxlab/bx-python | lib/bx_extras/stats.py | lmannwhitneyu | def lmannwhitneyu(x,y):
"""
Calculates a Mann-Whitney U statistic on the provided scores and
returns the result. Use only when the n in each condition is < 20 and
you have 2 independent samples of ranks. NOTE: Mann-Whitney U is
significant if the u-obtained is LESS THAN or equal to the critical
value of U found i... | python | def lmannwhitneyu(x,y):
"""
Calculates a Mann-Whitney U statistic on the provided scores and
returns the result. Use only when the n in each condition is < 20 and
you have 2 independent samples of ranks. NOTE: Mann-Whitney U is
significant if the u-obtained is LESS THAN or equal to the critical
value of U found i... | Calculates a Mann-Whitney U statistic on the provided scores and
returns the result. Use only when the n in each condition is < 20 and
you have 2 independent samples of ranks. NOTE: Mann-Whitney U is
significant if the u-obtained is LESS THAN or equal to the critical
value of U found in the tables. Equivalent to Kru... | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx_extras/stats.py#L1111-L1137 |
bxlab/bx-python | lib/bx_extras/stats.py | ltiecorrect | def ltiecorrect(rankvals):
"""
Corrects for ties in Mann Whitney U and Kruskal Wallis H tests. See
Siegel, S. (1956) Nonparametric Statistics for the Behavioral Sciences.
New York: McGraw-Hill. Code adapted from |Stat rankind.c code.
Usage: ltiecorrect(rankvals)
Returns: T correction factor for U or H
"""
... | python | def ltiecorrect(rankvals):
"""
Corrects for ties in Mann Whitney U and Kruskal Wallis H tests. See
Siegel, S. (1956) Nonparametric Statistics for the Behavioral Sciences.
New York: McGraw-Hill. Code adapted from |Stat rankind.c code.
Usage: ltiecorrect(rankvals)
Returns: T correction factor for U or H
"""
... | Corrects for ties in Mann Whitney U and Kruskal Wallis H tests. See
Siegel, S. (1956) Nonparametric Statistics for the Behavioral Sciences.
New York: McGraw-Hill. Code adapted from |Stat rankind.c code.
Usage: ltiecorrect(rankvals)
Returns: T correction factor for U or H | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx_extras/stats.py#L1140-L1162 |
bxlab/bx-python | lib/bx_extras/stats.py | lranksums | def lranksums(x,y):
"""
Calculates the rank sums statistic on the provided scores and
returns the result. Use only when the n in each condition is > 20 and you
have 2 independent samples of ranks.
Usage: lranksums(x,y)
Returns: a z-statistic, two-tailed p-value
"""
n1 = len(x)
n2 = len(y)
alldata = ... | python | def lranksums(x,y):
"""
Calculates the rank sums statistic on the provided scores and
returns the result. Use only when the n in each condition is > 20 and you
have 2 independent samples of ranks.
Usage: lranksums(x,y)
Returns: a z-statistic, two-tailed p-value
"""
n1 = len(x)
n2 = len(y)
alldata = ... | Calculates the rank sums statistic on the provided scores and
returns the result. Use only when the n in each condition is > 20 and you
have 2 independent samples of ranks.
Usage: lranksums(x,y)
Returns: a z-statistic, two-tailed p-value | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx_extras/stats.py#L1165-L1184 |
bxlab/bx-python | lib/bx_extras/stats.py | lkruskalwallish | def lkruskalwallish(*args):
"""
The Kruskal-Wallis H-test is a non-parametric ANOVA for 3 or more
groups, requiring at least 5 subjects in each group. This function
calculates the Kruskal-Wallis H-test for 3 or more independent samples
and returns the result.
Usage: lkruskalwallish(*args)
Returns: H-statistic... | python | def lkruskalwallish(*args):
"""
The Kruskal-Wallis H-test is a non-parametric ANOVA for 3 or more
groups, requiring at least 5 subjects in each group. This function
calculates the Kruskal-Wallis H-test for 3 or more independent samples
and returns the result.
Usage: lkruskalwallish(*args)
Returns: H-statistic... | The Kruskal-Wallis H-test is a non-parametric ANOVA for 3 or more
groups, requiring at least 5 subjects in each group. This function
calculates the Kruskal-Wallis H-test for 3 or more independent samples
and returns the result.
Usage: lkruskalwallish(*args)
Returns: H-statistic (corrected for ties), associated p-... | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx_extras/stats.py#L1220-L1252 |
bxlab/bx-python | lib/bx_extras/stats.py | lfriedmanchisquare | def lfriedmanchisquare(*args):
"""
Friedman Chi-Square is a non-parametric, one-way within-subjects
ANOVA. This function calculates the Friedman Chi-square test for repeated
measures and returns the result, along with the associated probability
value. It assumes 3 or more repeated measures. Only 3 levels require... | python | def lfriedmanchisquare(*args):
"""
Friedman Chi-Square is a non-parametric, one-way within-subjects
ANOVA. This function calculates the Friedman Chi-square test for repeated
measures and returns the result, along with the associated probability
value. It assumes 3 or more repeated measures. Only 3 levels require... | Friedman Chi-Square is a non-parametric, one-way within-subjects
ANOVA. This function calculates the Friedman Chi-square test for repeated
measures and returns the result, along with the associated probability
value. It assumes 3 or more repeated measures. Only 3 levels requires a
minimum of 10 subjects in the study... | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx_extras/stats.py#L1255-L1278 |
bxlab/bx-python | lib/bx_extras/stats.py | lchisqprob | def lchisqprob(chisq,df):
"""
Returns the (1-tailed) probability value associated with the provided
chi-square value and df. Adapted from chisq.c in Gary Perlman's |Stat.
Usage: lchisqprob(chisq,df)
"""
BIG = 20.0
def ex(x):
BIG = 20.0
if x < -BIG:
return 0.0
else:
... | python | def lchisqprob(chisq,df):
"""
Returns the (1-tailed) probability value associated with the provided
chi-square value and df. Adapted from chisq.c in Gary Perlman's |Stat.
Usage: lchisqprob(chisq,df)
"""
BIG = 20.0
def ex(x):
BIG = 20.0
if x < -BIG:
return 0.0
else:
... | Returns the (1-tailed) probability value associated with the provided
chi-square value and df. Adapted from chisq.c in Gary Perlman's |Stat.
Usage: lchisqprob(chisq,df) | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx_extras/stats.py#L1285-L1342 |
bxlab/bx-python | lib/bx_extras/stats.py | lerfcc | def lerfcc(x):
"""
Returns the complementary error function erfc(x) with fractional
error everywhere less than 1.2e-7. Adapted from Numerical Recipies.
Usage: lerfcc(x)
"""
z = abs(x)
t = 1.0 / (1.0+0.5*z)
ans = t * math.exp(-z*z-1.26551223 + t*(1.00002368+t*(0.37409196+t*(0.09678418+t*(-0.18628806+... | python | def lerfcc(x):
"""
Returns the complementary error function erfc(x) with fractional
error everywhere less than 1.2e-7. Adapted from Numerical Recipies.
Usage: lerfcc(x)
"""
z = abs(x)
t = 1.0 / (1.0+0.5*z)
ans = t * math.exp(-z*z-1.26551223 + t*(1.00002368+t*(0.37409196+t*(0.09678418+t*(-0.18628806+... | Returns the complementary error function erfc(x) with fractional
error everywhere less than 1.2e-7. Adapted from Numerical Recipies.
Usage: lerfcc(x) | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx_extras/stats.py#L1345-L1358 |
bxlab/bx-python | lib/bx_extras/stats.py | lzprob | def lzprob(z):
"""
Returns the area under the normal curve 'to the left of' the given z value.
Thus,
for z<0, zprob(z) = 1-tail probability
for z>0, 1.0-zprob(z) = 1-tail probability
for any z, 2.0*(1.0-zprob(abs(z))) = 2-tail probability
Adapted from z.c in Gary Perlman's |Stat.
Usage: lzprob(z)
""... | python | def lzprob(z):
"""
Returns the area under the normal curve 'to the left of' the given z value.
Thus,
for z<0, zprob(z) = 1-tail probability
for z>0, 1.0-zprob(z) = 1-tail probability
for any z, 2.0*(1.0-zprob(abs(z))) = 2-tail probability
Adapted from z.c in Gary Perlman's |Stat.
Usage: lzprob(z)
""... | Returns the area under the normal curve 'to the left of' the given z value.
Thus,
for z<0, zprob(z) = 1-tail probability
for z>0, 1.0-zprob(z) = 1-tail probability
for any z, 2.0*(1.0-zprob(abs(z))) = 2-tail probability
Adapted from z.c in Gary Perlman's |Stat.
Usage: lzprob(z) | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx_extras/stats.py#L1361-L1400 |
bxlab/bx-python | lib/bx_extras/stats.py | lksprob | def lksprob(alam):
"""
Computes a Kolmolgorov-Smirnov t-test significance level. Adapted from
Numerical Recipies.
Usage: lksprob(alam)
"""
fac = 2.0
sum = 0.0
termbf = 0.0
a2 = -2.0*alam*alam
for j in range(1,201):
term = fac*math.exp(a2*j*j)
sum = sum + term
if math.... | python | def lksprob(alam):
"""
Computes a Kolmolgorov-Smirnov t-test significance level. Adapted from
Numerical Recipies.
Usage: lksprob(alam)
"""
fac = 2.0
sum = 0.0
termbf = 0.0
a2 = -2.0*alam*alam
for j in range(1,201):
term = fac*math.exp(a2*j*j)
sum = sum + term
if math.... | Computes a Kolmolgorov-Smirnov t-test significance level. Adapted from
Numerical Recipies.
Usage: lksprob(alam) | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx_extras/stats.py#L1403-L1421 |
bxlab/bx-python | lib/bx_extras/stats.py | lfprob | def lfprob (dfnum, dfden, F):
"""
Returns the (1-tailed) significance level (p-value) of an F
statistic given the degrees of freedom for the numerator (dfR-dfF) and
the degrees of freedom for the denominator (dfF).
Usage: lfprob(dfnum, dfden, F) where usually dfnum=dfbn, dfden=dfwn
"""
p = betai(0.5*dfden,... | python | def lfprob (dfnum, dfden, F):
"""
Returns the (1-tailed) significance level (p-value) of an F
statistic given the degrees of freedom for the numerator (dfR-dfF) and
the degrees of freedom for the denominator (dfF).
Usage: lfprob(dfnum, dfden, F) where usually dfnum=dfbn, dfden=dfwn
"""
p = betai(0.5*dfden,... | Returns the (1-tailed) significance level (p-value) of an F
statistic given the degrees of freedom for the numerator (dfR-dfF) and
the degrees of freedom for the denominator (dfF).
Usage: lfprob(dfnum, dfden, F) where usually dfnum=dfbn, dfden=dfwn | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx_extras/stats.py#L1424-L1433 |
bxlab/bx-python | lib/bx_extras/stats.py | lgammln | def lgammln(xx):
"""
Returns the gamma function of xx.
Gamma(z) = Integral(0,infinity) of t^(z-1)exp(-t) dt.
(Adapted from: Numerical Recipies in C.)
Usage: lgammln(xx)
"""
coeff = [76.18009173, -86.50532033, 24.01409822, -1.231739516,
0.120858003e-2, -0.536382e-5]
x = xx - 1.0
tmp ... | python | def lgammln(xx):
"""
Returns the gamma function of xx.
Gamma(z) = Integral(0,infinity) of t^(z-1)exp(-t) dt.
(Adapted from: Numerical Recipies in C.)
Usage: lgammln(xx)
"""
coeff = [76.18009173, -86.50532033, 24.01409822, -1.231739516,
0.120858003e-2, -0.536382e-5]
x = xx - 1.0
tmp ... | Returns the gamma function of xx.
Gamma(z) = Integral(0,infinity) of t^(z-1)exp(-t) dt.
(Adapted from: Numerical Recipies in C.)
Usage: lgammln(xx) | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx_extras/stats.py#L1470-L1488 |
bxlab/bx-python | lib/bx_extras/stats.py | lbetai | def lbetai(a,b,x):
"""
Returns the incomplete beta function:
I-sub-x(a,b) = 1/B(a,b)*(Integral(0,x) of t^(a-1)(1-t)^(b-1) dt)
where a,b>0 and B(a,b) = G(a)*G(b)/(G(a+b)) where G(a) is the gamma
function of a. The continued fraction formulation is implemented here,
using the betacf function. (Adapted from: N... | python | def lbetai(a,b,x):
"""
Returns the incomplete beta function:
I-sub-x(a,b) = 1/B(a,b)*(Integral(0,x) of t^(a-1)(1-t)^(b-1) dt)
where a,b>0 and B(a,b) = G(a)*G(b)/(G(a+b)) where G(a) is the gamma
function of a. The continued fraction formulation is implemented here,
using the betacf function. (Adapted from: N... | Returns the incomplete beta function:
I-sub-x(a,b) = 1/B(a,b)*(Integral(0,x) of t^(a-1)(1-t)^(b-1) dt)
where a,b>0 and B(a,b) = G(a)*G(b)/(G(a+b)) where G(a) is the gamma
function of a. The continued fraction formulation is implemented here,
using the betacf function. (Adapted from: Numerical Recipies in C.)
U... | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx_extras/stats.py#L1491-L1513 |
bxlab/bx-python | lib/bx_extras/stats.py | lF_oneway | def lF_oneway(*lists):
"""
Performs a 1-way ANOVA, returning an F-value and probability given
any number of groups. From Heiman, pp.394-7.
Usage: F_oneway(*lists) where *lists is any number of lists, one per
treatment group
Returns: F value, one-tailed p-value
"""
a = le... | python | def lF_oneway(*lists):
"""
Performs a 1-way ANOVA, returning an F-value and probability given
any number of groups. From Heiman, pp.394-7.
Usage: F_oneway(*lists) where *lists is any number of lists, one per
treatment group
Returns: F value, one-tailed p-value
"""
a = le... | Performs a 1-way ANOVA, returning an F-value and probability given
any number of groups. From Heiman, pp.394-7.
Usage: F_oneway(*lists) where *lists is any number of lists, one per
treatment group
Returns: F value, one-tailed p-value | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx_extras/stats.py#L1520-L1554 |
bxlab/bx-python | lib/bx_extras/stats.py | lF_value | def lF_value (ER,EF,dfnum,dfden):
"""
Returns an F-statistic given the following:
ER = error associated with the null hypothesis (the Restricted model)
EF = error associated with the alternate hypothesis (the Full model)
dfR-dfF = degrees of freedom of the numerator
dfF = degrees o... | python | def lF_value (ER,EF,dfnum,dfden):
"""
Returns an F-statistic given the following:
ER = error associated with the null hypothesis (the Restricted model)
EF = error associated with the alternate hypothesis (the Full model)
dfR-dfF = degrees of freedom of the numerator
dfF = degrees o... | Returns an F-statistic given the following:
ER = error associated with the null hypothesis (the Restricted model)
EF = error associated with the alternate hypothesis (the Full model)
dfR-dfF = degrees of freedom of the numerator
dfF = degrees of freedom associated with the denominator/... | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx_extras/stats.py#L1557-L1567 |
bxlab/bx-python | lib/bx_extras/stats.py | writecc | def writecc (listoflists,file,writetype='w',extra=2):
"""
Writes a list of lists to a file in columns, customized by the max
size of items within the columns (max size of items in col, +2 characters)
to specified file. File-overwrite is the default.
Usage: writecc (listoflists,file,writetype='w',extra=2)
Return... | python | def writecc (listoflists,file,writetype='w',extra=2):
"""
Writes a list of lists to a file in columns, customized by the max
size of items within the columns (max size of items in col, +2 characters)
to specified file. File-overwrite is the default.
Usage: writecc (listoflists,file,writetype='w',extra=2)
Return... | Writes a list of lists to a file in columns, customized by the max
size of items within the columns (max size of items in col, +2 characters)
to specified file. File-overwrite is the default.
Usage: writecc (listoflists,file,writetype='w',extra=2)
Returns: None | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx_extras/stats.py#L1574-L1611 |
bxlab/bx-python | lib/bx_extras/stats.py | lincr | def lincr(l,cap): # to increment a list up to a max-list of 'cap'
"""
Simulate a counting system from an n-dimensional list.
Usage: lincr(l,cap) l=list to increment, cap=max values for each list pos'n
Returns: next set of values for list l, OR -1 (if overflow)
"""
l[0] = l[0] + 1 # e.g., [0,0,0]... | python | def lincr(l,cap): # to increment a list up to a max-list of 'cap'
"""
Simulate a counting system from an n-dimensional list.
Usage: lincr(l,cap) l=list to increment, cap=max values for each list pos'n
Returns: next set of values for list l, OR -1 (if overflow)
"""
l[0] = l[0] + 1 # e.g., [0,0,0]... | Simulate a counting system from an n-dimensional list.
Usage: lincr(l,cap) l=list to increment, cap=max values for each list pos'n
Returns: next set of values for list l, OR -1 (if overflow) | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx_extras/stats.py#L1614-L1628 |
bxlab/bx-python | lib/bx_extras/stats.py | lcumsum | def lcumsum (inlist):
"""
Returns a list consisting of the cumulative sum of the items in the
passed list.
Usage: lcumsum(inlist)
"""
newlist = copy.deepcopy(inlist)
for i in range(1,len(newlist)):
newlist[i] = newlist[i] + newlist[i-1]
return newlist | python | def lcumsum (inlist):
"""
Returns a list consisting of the cumulative sum of the items in the
passed list.
Usage: lcumsum(inlist)
"""
newlist = copy.deepcopy(inlist)
for i in range(1,len(newlist)):
newlist[i] = newlist[i] + newlist[i-1]
return newlist | Returns a list consisting of the cumulative sum of the items in the
passed list.
Usage: lcumsum(inlist) | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx_extras/stats.py#L1643-L1653 |
bxlab/bx-python | lib/bx_extras/stats.py | lss | def lss(inlist):
"""
Squares each value in the passed list, adds up these squares and
returns the result.
Usage: lss(inlist)
"""
ss = 0
for item in inlist:
ss = ss + item*item
return ss | python | def lss(inlist):
"""
Squares each value in the passed list, adds up these squares and
returns the result.
Usage: lss(inlist)
"""
ss = 0
for item in inlist:
ss = ss + item*item
return ss | Squares each value in the passed list, adds up these squares and
returns the result.
Usage: lss(inlist) | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx_extras/stats.py#L1656-L1666 |
bxlab/bx-python | lib/bx_extras/stats.py | lsummult | def lsummult (list1,list2):
"""
Multiplies elements in list1 and list2, element by element, and
returns the sum of all resulting multiplications. Must provide equal
length lists.
Usage: lsummult(list1,list2)
"""
if len(list1) != len(list2):
raise ValueError("Lists not equal length in summult.")
... | python | def lsummult (list1,list2):
"""
Multiplies elements in list1 and list2, element by element, and
returns the sum of all resulting multiplications. Must provide equal
length lists.
Usage: lsummult(list1,list2)
"""
if len(list1) != len(list2):
raise ValueError("Lists not equal length in summult.")
... | Multiplies elements in list1 and list2, element by element, and
returns the sum of all resulting multiplications. Must provide equal
length lists.
Usage: lsummult(list1,list2) | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx_extras/stats.py#L1669-L1682 |
bxlab/bx-python | lib/bx_extras/stats.py | lsumdiffsquared | def lsumdiffsquared(x,y):
"""
Takes pairwise differences of the values in lists x and y, squares
these differences, and returns the sum of these squares.
Usage: lsumdiffsquared(x,y)
Returns: sum[(x[i]-y[i])**2]
"""
sds = 0
for i in range(len(x)):
sds = sds + (x[i]-y[i])**2
return sds | python | def lsumdiffsquared(x,y):
"""
Takes pairwise differences of the values in lists x and y, squares
these differences, and returns the sum of these squares.
Usage: lsumdiffsquared(x,y)
Returns: sum[(x[i]-y[i])**2]
"""
sds = 0
for i in range(len(x)):
sds = sds + (x[i]-y[i])**2
return sds | Takes pairwise differences of the values in lists x and y, squares
these differences, and returns the sum of these squares.
Usage: lsumdiffsquared(x,y)
Returns: sum[(x[i]-y[i])**2] | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx_extras/stats.py#L1685-L1696 |
bxlab/bx-python | lib/bx_extras/stats.py | outputpairedstats | def outputpairedstats(fname,writemode,name1,n1,m1,se1,min1,max1,name2,n2,m2,se2,min2,max2,statname,stat,prob):
"""
Prints or write to a file stats for two groups, using the name, n,
mean, sterr, min and max for each group, as well as the statistic name,
its value, and the associated p-value.
Usage: outputpaireds... | python | def outputpairedstats(fname,writemode,name1,n1,m1,se1,min1,max1,name2,n2,m2,se2,min2,max2,statname,stat,prob):
"""
Prints or write to a file stats for two groups, using the name, n,
mean, sterr, min and max for each group, as well as the statistic name,
its value, and the associated p-value.
Usage: outputpaireds... | Prints or write to a file stats for two groups, using the name, n,
mean, sterr, min and max for each group, as well as the statistic name,
its value, and the associated p-value.
Usage: outputpairedstats(fname,writemode,
name1,n1,mean1,stderr1,min1,max1,
name2,n2,... | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx_extras/stats.py#L1762-L1816 |
bxlab/bx-python | lib/bx/gene_reader.py | GeneReader | def GeneReader( fh, format='gff' ):
""" yield chrom, strand, gene_exons, name """
known_formats = ( 'gff', 'gtf', 'bed')
if format not in known_formats:
print('%s format not in %s' % (format, ",".join( known_formats )), file=sys.stderr)
raise Exception('?')
if format == 'bed':
... | python | def GeneReader( fh, format='gff' ):
""" yield chrom, strand, gene_exons, name """
known_formats = ( 'gff', 'gtf', 'bed')
if format not in known_formats:
print('%s format not in %s' % (format, ",".join( known_formats )), file=sys.stderr)
raise Exception('?')
if format == 'bed':
... | yield chrom, strand, gene_exons, name | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx/gene_reader.py#L19-L79 |
bxlab/bx-python | lib/bx/gene_reader.py | CDSReader | def CDSReader( fh, format='gff' ):
""" yield chrom, strand, cds_exons, name """
known_formats = ( 'gff', 'gtf', 'bed')
if format not in known_formats:
print('%s format not in %s' % (format, ",".join( known_formats )), file=sys.stderr)
raise Exception('?')
if format == 'bed':
f... | python | def CDSReader( fh, format='gff' ):
""" yield chrom, strand, cds_exons, name """
known_formats = ( 'gff', 'gtf', 'bed')
if format not in known_formats:
print('%s format not in %s' % (format, ",".join( known_formats )), file=sys.stderr)
raise Exception('?')
if format == 'bed':
f... | yield chrom, strand, cds_exons, name | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx/gene_reader.py#L81-L155 |
bxlab/bx-python | lib/bx/gene_reader.py | FeatureReader | def FeatureReader( fh, format='gff', alt_introns_subtract="exons", gtf_parse=None):
"""
yield chrom, strand, cds_exons, introns, exons, name
gtf_parse Example:
# parse gene_id from transcript_id "AC073130.2-001"; gene_id "TES";
gene_name = lambda s: s.split(';')[1].split()[1].strip('"')
for c... | python | def FeatureReader( fh, format='gff', alt_introns_subtract="exons", gtf_parse=None):
"""
yield chrom, strand, cds_exons, introns, exons, name
gtf_parse Example:
# parse gene_id from transcript_id "AC073130.2-001"; gene_id "TES";
gene_name = lambda s: s.split(';')[1].split()[1].strip('"')
for c... | yield chrom, strand, cds_exons, introns, exons, name
gtf_parse Example:
# parse gene_id from transcript_id "AC073130.2-001"; gene_id "TES";
gene_name = lambda s: s.split(';')[1].split()[1].strip('"')
for chrom, strand, cds_exons, introns, exons, name in FeatureReader( sys.stdin, format='gtf', gtf_pars... | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx/gene_reader.py#L157-L284 |
bxlab/bx-python | lib/bx/intervals/random_intervals.py | throw_random_gap_list | def throw_random_gap_list( lengths, mask, save_interval_func, allow_overlap=False ):
"""
Generates a set of non-overlapping random intervals from a length
distribution.
`lengths`: list containing the length of each interval to be generated.
We expect this to be sorted by decreasing ... | python | def throw_random_gap_list( lengths, mask, save_interval_func, allow_overlap=False ):
"""
Generates a set of non-overlapping random intervals from a length
distribution.
`lengths`: list containing the length of each interval to be generated.
We expect this to be sorted by decreasing ... | Generates a set of non-overlapping random intervals from a length
distribution.
`lengths`: list containing the length of each interval to be generated.
We expect this to be sorted by decreasing length to minimize
the chance of failure (MaxtriesException) and for some
... | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx/intervals/random_intervals.py#L25-L54 |
bxlab/bx-python | lib/bx/intervals/random_intervals.py | throw_random_intervals | def throw_random_intervals( lengths, regions, save_interval_func=None, allow_overlap=False ):
"""
Generates a set of non-overlapping random intervals from a length
distribution.
`lengths`: list containing the length of each interval to be generated.
We expect this to be sorted by de... | python | def throw_random_intervals( lengths, regions, save_interval_func=None, allow_overlap=False ):
"""
Generates a set of non-overlapping random intervals from a length
distribution.
`lengths`: list containing the length of each interval to be generated.
We expect this to be sorted by de... | Generates a set of non-overlapping random intervals from a length
distribution.
`lengths`: list containing the length of each interval to be generated.
We expect this to be sorted by decreasing length to minimize
the chance of failure (MaxtriesException) and for some
... | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx/intervals/random_intervals.py#L56-L89 |
bxlab/bx-python | lib/bx/intervals/random_intervals.py | throw_random_private | def throw_random_private( lengths, regions, save_interval_func, allow_overlap=False, three_args=True ):
"""
(Internal function; we expect calls only through the interface functions
above)
`lengths`: A list containing the length of each interval to be generated.
`regions`: A list of regions in ... | python | def throw_random_private( lengths, regions, save_interval_func, allow_overlap=False, three_args=True ):
"""
(Internal function; we expect calls only through the interface functions
above)
`lengths`: A list containing the length of each interval to be generated.
`regions`: A list of regions in ... | (Internal function; we expect calls only through the interface functions
above)
`lengths`: A list containing the length of each interval to be generated.
`regions`: A list of regions in which intervals can be placed, sorted by
decreasing length. Elements are triples of the form (length... | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx/intervals/random_intervals.py#L98-L212 |
bxlab/bx-python | lib/bx/seq/seq.py | SeqFile.get | def get(self, start, length):
"""
Fetch subsequence starting at position `start` with length `length`.
This method is picky about parameters, the requested interval must
have non-negative length and fit entirely inside the NIB sequence,
the returned string will contain exactly ... | python | def get(self, start, length):
"""
Fetch subsequence starting at position `start` with length `length`.
This method is picky about parameters, the requested interval must
have non-negative length and fit entirely inside the NIB sequence,
the returned string will contain exactly ... | Fetch subsequence starting at position `start` with length `length`.
This method is picky about parameters, the requested interval must
have non-negative length and fit entirely inside the NIB sequence,
the returned string will contain exactly 'length' characters, or an
AssertionError ... | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx/seq/seq.py#L74-L94 |
bxlab/bx-python | lib/bx/align/score.py | read_scoring_scheme | def read_scoring_scheme( f, gap_open, gap_extend, gap1="-", gap2=None, **kwargs ):
"""
Initialize scoring scheme from a file containint a blastz style text blob.
f can be either a file or the name of a file.
"""
close_it = False
if (type(f) == str):
f = file(f,"rt")
close_it = Tr... | python | def read_scoring_scheme( f, gap_open, gap_extend, gap1="-", gap2=None, **kwargs ):
"""
Initialize scoring scheme from a file containint a blastz style text blob.
f can be either a file or the name of a file.
"""
close_it = False
if (type(f) == str):
f = file(f,"rt")
close_it = Tr... | Initialize scoring scheme from a file containint a blastz style text blob.
f can be either a file or the name of a file. | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx/align/score.py#L91-L103 |
bxlab/bx-python | lib/bx/align/score.py | build_scoring_scheme | def build_scoring_scheme( s, gap_open, gap_extend, gap1="-", gap2=None, **kwargs ):
"""
Initialize scoring scheme from a blastz style text blob, first line
specifies the bases for each row/col, subsequent lines contain the
corresponding scores. Slaw extensions allow for unusual and/or
asymmetric al... | python | def build_scoring_scheme( s, gap_open, gap_extend, gap1="-", gap2=None, **kwargs ):
"""
Initialize scoring scheme from a blastz style text blob, first line
specifies the bases for each row/col, subsequent lines contain the
corresponding scores. Slaw extensions allow for unusual and/or
asymmetric al... | Initialize scoring scheme from a blastz style text blob, first line
specifies the bases for each row/col, subsequent lines contain the
corresponding scores. Slaw extensions allow for unusual and/or
asymmetric alphabets. Symbols can be two digit hex, and each row
begins with symbol. Note that a row co... | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx/align/score.py#L105-L196 |
bxlab/bx-python | lib/bx/align/score.py | accumulate_scores | def accumulate_scores( scoring_scheme, text1, text2, skip_ref_gaps=False ):
"""
Return cumulative scores for each position in alignment as a 1d array.
If `skip_ref_gaps` is False positions in returned array correspond to each
column in alignment, if True they correspond to each non-gap position (ea... | python | def accumulate_scores( scoring_scheme, text1, text2, skip_ref_gaps=False ):
"""
Return cumulative scores for each position in alignment as a 1d array.
If `skip_ref_gaps` is False positions in returned array correspond to each
column in alignment, if True they correspond to each non-gap position (ea... | Return cumulative scores for each position in alignment as a 1d array.
If `skip_ref_gaps` is False positions in returned array correspond to each
column in alignment, if True they correspond to each non-gap position (each
base) in text1. | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx/align/score.py#L245-L287 |
bxlab/bx-python | lib/bx/align/core.py | shuffle_columns | def shuffle_columns( a ):
"""Randomize the columns of an alignment"""
mask = range( a.text_size )
random.shuffle( mask )
for c in a.components:
c.text = ''.join( [ c.text[i] for i in mask ] ) | python | def shuffle_columns( a ):
"""Randomize the columns of an alignment"""
mask = range( a.text_size )
random.shuffle( mask )
for c in a.components:
c.text = ''.join( [ c.text[i] for i in mask ] ) | Randomize the columns of an alignment | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx/align/core.py#L403-L408 |
bxlab/bx-python | lib/bx/align/core.py | Alignment.slice_by_component | def slice_by_component( self, component_index, start, end ):
"""
Return a slice of the alignment, corresponding to an coordinate interval in a specific component.
component_index is one of
an integer offset into the components list
a string indicating the src of the desi... | python | def slice_by_component( self, component_index, start, end ):
"""
Return a slice of the alignment, corresponding to an coordinate interval in a specific component.
component_index is one of
an integer offset into the components list
a string indicating the src of the desi... | Return a slice of the alignment, corresponding to an coordinate interval in a specific component.
component_index is one of
an integer offset into the components list
a string indicating the src of the desired component
a component
start and end are relative to the ... | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx/align/core.py#L122-L146 |
bxlab/bx-python | lib/bx/align/core.py | Alignment.remove_all_gap_columns | def remove_all_gap_columns( self ):
"""
Remove any columns containing only gaps from alignment components,
text of components is modified IN PLACE.
"""
seqs = []
for c in self.components:
try:
seqs.append( list( c.text ) )
except Ty... | python | def remove_all_gap_columns( self ):
"""
Remove any columns containing only gaps from alignment components,
text of components is modified IN PLACE.
"""
seqs = []
for c in self.components:
try:
seqs.append( list( c.text ) )
except Ty... | Remove any columns containing only gaps from alignment components,
text of components is modified IN PLACE. | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx/align/core.py#L160-L188 |
bxlab/bx-python | lib/bx/align/core.py | Component.slice_by_coord | def slice_by_coord( self, start, end ):
"""
Return the slice of the component corresponding to a coordinate interval.
start and end are relative to the + strand, regardless of the component's strand.
"""
start_col = self.coord_to_col( start )
end_col = self.coord_to_col... | python | def slice_by_coord( self, start, end ):
"""
Return the slice of the component corresponding to a coordinate interval.
start and end are relative to the + strand, regardless of the component's strand.
"""
start_col = self.coord_to_col( start )
end_col = self.coord_to_col... | Return the slice of the component corresponding to a coordinate interval.
start and end are relative to the + strand, regardless of the component's strand. | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx/align/core.py#L307-L318 |
bxlab/bx-python | lib/bx/align/core.py | Component.coord_to_col | def coord_to_col( self, pos ):
"""
Return the alignment column index corresponding to coordinate pos.
pos is relative to the + strand, regardless of the component's strand.
"""
start,end = self.get_forward_strand_start(),self.get_forward_strand_end()
if pos < start or p... | python | def coord_to_col( self, pos ):
"""
Return the alignment column index corresponding to coordinate pos.
pos is relative to the + strand, regardless of the component's strand.
"""
start,end = self.get_forward_strand_start(),self.get_forward_strand_end()
if pos < start or p... | Return the alignment column index corresponding to coordinate pos.
pos is relative to the + strand, regardless of the component's strand. | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx/align/core.py#L320-L351 |
bxlab/bx-python | lib/bx/align/tools/thread.py | thread | def thread( mafs, species ):
"""
Restrict an list of alignments to a given list of species by:
1) Removing components for any other species
2) Remove any columns containing all gaps
Example:
>>> import bx.align.maf
>>> block1 = bx.align.maf.from_string( '''... | python | def thread( mafs, species ):
"""
Restrict an list of alignments to a given list of species by:
1) Removing components for any other species
2) Remove any columns containing all gaps
Example:
>>> import bx.align.maf
>>> block1 = bx.align.maf.from_string( '''... | Restrict an list of alignments to a given list of species by:
1) Removing components for any other species
2) Remove any columns containing all gaps
Example:
>>> import bx.align.maf
>>> block1 = bx.align.maf.from_string( '''
... a score=4964.0
... s hg18.ch... | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx/align/tools/thread.py#L10-L66 |
bxlab/bx-python | lib/bx/align/tools/thread.py | get_components_for_species | def get_components_for_species( alignment, species ):
"""Return the component for each species in the list `species` or None"""
# If the number of components in the alignment is less that the requested number
# of species we can immediately fail
if len( alignment.components ) < len( species ): return No... | python | def get_components_for_species( alignment, species ):
"""Return the component for each species in the list `species` or None"""
# If the number of components in the alignment is less that the requested number
# of species we can immediately fail
if len( alignment.components ) < len( species ): return No... | Return the component for each species in the list `species` or None | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx/align/tools/thread.py#L68-L76 |
bxlab/bx-python | lib/bx/align/tools/thread.py | remove_all_gap_columns | def remove_all_gap_columns( components ):
"""
Remove any columns containing only gaps from a set of alignment components,
text of components is modified IN PLACE.
TODO: Optimize this with Pyrex.
"""
seqs = [ list( c.text ) for c in components ]
i = 0
text_size = len( seqs[0]... | python | def remove_all_gap_columns( components ):
"""
Remove any columns containing only gaps from a set of alignment components,
text of components is modified IN PLACE.
TODO: Optimize this with Pyrex.
"""
seqs = [ list( c.text ) for c in components ]
i = 0
text_size = len( seqs[0]... | Remove any columns containing only gaps from a set of alignment components,
text of components is modified IN PLACE.
TODO: Optimize this with Pyrex. | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx/align/tools/thread.py#L78-L98 |
bxlab/bx-python | lib/bx/align/maf.py | read_next_maf | def read_next_maf( file, species_to_lengths=None, parse_e_rows=False ):
"""
Read the next MAF block from `file` and return as an `Alignment`
instance. If `parse_i_rows` is true, empty components will be created
when e rows are encountered.
"""
alignment = Alignment(species_to_lengths=species_t... | python | def read_next_maf( file, species_to_lengths=None, parse_e_rows=False ):
"""
Read the next MAF block from `file` and return as an `Alignment`
instance. If `parse_i_rows` is true, empty components will be created
when e rows are encountered.
"""
alignment = Alignment(species_to_lengths=species_t... | Read the next MAF block from `file` and return as an `Alignment`
instance. If `parse_i_rows` is true, empty components will be created
when e rows are encountered. | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx/align/maf.py#L133-L201 |
bxlab/bx-python | lib/bx/align/maf.py | readline | def readline( file, skip_blank=False ):
"""Read a line from provided file, skipping any blank or comment lines"""
while 1:
line = file.readline()
#print "every line: %r" % line
if not line: return None
if line[0] != '#' and not ( skip_blank and line.isspace() ):
retu... | python | def readline( file, skip_blank=False ):
"""Read a line from provided file, skipping any blank or comment lines"""
while 1:
line = file.readline()
#print "every line: %r" % line
if not line: return None
if line[0] != '#' and not ( skip_blank and line.isspace() ):
retu... | Read a line from provided file, skipping any blank or comment lines | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx/align/maf.py#L203-L210 |
bxlab/bx-python | lib/bx/align/maf.py | parse_attributes | def parse_attributes( fields ):
"""Parse list of key=value strings into a dict"""
attributes = {}
for field in fields:
pair = field.split( '=' )
attributes[ pair[0] ] = pair[1]
return attributes | python | def parse_attributes( fields ):
"""Parse list of key=value strings into a dict"""
attributes = {}
for field in fields:
pair = field.split( '=' )
attributes[ pair[0] ] = pair[1]
return attributes | Parse list of key=value strings into a dict | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx/align/maf.py#L212-L218 |
bxlab/bx-python | lib/bx/motif/io/transfac.py | TransfacReader.as_dict | def as_dict( self, key="id" ):
"""
Return a dictionary containing all remaining motifs, using `key`
as the dictionary key.
"""
rval = {}
for motif in self:
rval[ getattr( motif, key ) ] = motif
return rval | python | def as_dict( self, key="id" ):
"""
Return a dictionary containing all remaining motifs, using `key`
as the dictionary key.
"""
rval = {}
for motif in self:
rval[ getattr( motif, key ) ] = motif
return rval | Return a dictionary containing all remaining motifs, using `key`
as the dictionary key. | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx/motif/io/transfac.py#L52-L60 |
bxlab/bx-python | lib/bx/motif/io/transfac.py | TransfacReader.parse_record | def parse_record( self, lines ):
"""
Parse a TRANSFAC record out of `lines` and return a motif.
"""
# Break lines up
temp_lines = []
for line in lines:
fields = line.rstrip( "\r\n" ).split( None, 1 )
if len( fields ) == 1:
fields.ap... | python | def parse_record( self, lines ):
"""
Parse a TRANSFAC record out of `lines` and return a motif.
"""
# Break lines up
temp_lines = []
for line in lines:
fields = line.rstrip( "\r\n" ).split( None, 1 )
if len( fields ) == 1:
fields.ap... | Parse a TRANSFAC record out of `lines` and return a motif. | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx/motif/io/transfac.py#L90-L174 |
bxlab/bx-python | scripts/bed_rand_intersect.py | bit_clone | def bit_clone( bits ):
"""
Clone a bitset
"""
new = BitSet( bits.size )
new.ior( bits )
return new | python | def bit_clone( bits ):
"""
Clone a bitset
"""
new = BitSet( bits.size )
new.ior( bits )
return new | Clone a bitset | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/scripts/bed_rand_intersect.py#L35-L41 |
bxlab/bx-python | scripts/bed_rand_intersect.py | throw_random | def throw_random( lengths, mask ):
"""
Try multiple times to run 'throw_random'
"""
saved = None
for i in range( maxtries ):
try:
return throw_random_bits( lengths, mask )
except MaxtriesException as e:
saved = e
continue
raise e | python | def throw_random( lengths, mask ):
"""
Try multiple times to run 'throw_random'
"""
saved = None
for i in range( maxtries ):
try:
return throw_random_bits( lengths, mask )
except MaxtriesException as e:
saved = e
continue
raise e | Try multiple times to run 'throw_random' | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/scripts/bed_rand_intersect.py#L43-L54 |
bxlab/bx-python | scripts/bed_rand_intersect.py | as_bits | def as_bits( region_start, region_length, intervals ):
"""
Convert a set of intervals overlapping a region of a chromosome into
a bitset for just that region with the bits covered by the intervals
set.
"""
bits = BitSet( region_length )
for chr, start, stop in intervals:
bits.set_r... | python | def as_bits( region_start, region_length, intervals ):
"""
Convert a set of intervals overlapping a region of a chromosome into
a bitset for just that region with the bits covered by the intervals
set.
"""
bits = BitSet( region_length )
for chr, start, stop in intervals:
bits.set_r... | Convert a set of intervals overlapping a region of a chromosome into
a bitset for just that region with the bits covered by the intervals
set. | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/scripts/bed_rand_intersect.py#L56-L65 |
bxlab/bx-python | scripts/bed_rand_intersect.py | interval_lengths | def interval_lengths( bits ):
"""
Get the length distribution of all contiguous runs of set bits from
"""
end = 0
while 1:
start = bits.next_set( end )
if start == bits.size: break
end = bits.next_clear( start )
yield end - start | python | def interval_lengths( bits ):
"""
Get the length distribution of all contiguous runs of set bits from
"""
end = 0
while 1:
start = bits.next_set( end )
if start == bits.size: break
end = bits.next_clear( start )
yield end - start | Get the length distribution of all contiguous runs of set bits from | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/scripts/bed_rand_intersect.py#L67-L76 |
bxlab/bx-python | scripts/bed_rand_intersect.py | count_overlap | def count_overlap( bits1, bits2 ):
"""
Count the number of bits that overlap between two sets
"""
b = BitSet( bits1.size )
b |= bits1
b &= bits2
return b.count_range( 0, b.size ) | python | def count_overlap( bits1, bits2 ):
"""
Count the number of bits that overlap between two sets
"""
b = BitSet( bits1.size )
b |= bits1
b &= bits2
return b.count_range( 0, b.size ) | Count the number of bits that overlap between two sets | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/scripts/bed_rand_intersect.py#L78-L85 |
bxlab/bx-python | scripts/bed_rand_intersect.py | overlapping_in_bed | def overlapping_in_bed( fname, r_chr, r_start, r_stop ):
"""
Get from a bed all intervals that overlap the region defined by
r_chr, r_start, r_stop.
"""
rval = []
for line in open( fname ):
if line.startswith( "#" ) or line.startswith( "track" ):
continue
fields = lin... | python | def overlapping_in_bed( fname, r_chr, r_start, r_stop ):
"""
Get from a bed all intervals that overlap the region defined by
r_chr, r_start, r_stop.
"""
rval = []
for line in open( fname ):
if line.startswith( "#" ) or line.startswith( "track" ):
continue
fields = lin... | Get from a bed all intervals that overlap the region defined by
r_chr, r_start, r_stop. | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/scripts/bed_rand_intersect.py#L87-L100 |
bxlab/bx-python | lib/bx/align/tools/tile.py | tile_interval | def tile_interval( sources, index, ref_src, start, end, seq_db=None ):
"""
Tile maf blocks onto an interval. The resulting block will span the interval
exactly and contain the column from the highest scoring alignment at each
position.
`sources`: list of sequence source names to include in final bl... | python | def tile_interval( sources, index, ref_src, start, end, seq_db=None ):
"""
Tile maf blocks onto an interval. The resulting block will span the interval
exactly and contain the column from the highest scoring alignment at each
position.
`sources`: list of sequence source names to include in final bl... | Tile maf blocks onto an interval. The resulting block will span the interval
exactly and contain the column from the highest scoring alignment at each
position.
`sources`: list of sequence source names to include in final block
`index`: an instnace that can return maf blocks overlapping intervals
`... | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx/align/tools/tile.py#L13-L71 |
bxlab/bx-python | lib/bx/pwm/pwm_score_maf.py | MafMotifSelect | def MafMotifSelect(mafblock,pwm,motif=None,threshold=0):
if motif != None and len(motif) != len(pwm):
raise Exception("pwm and motif must be the same length")
# generic alignment
alignlist = [ c.text for c in mafblock.components ]
align = pwmx.Align( alignlist )
nrows,ncols = align.dims
... | python | def MafMotifSelect(mafblock,pwm,motif=None,threshold=0):
if motif != None and len(motif) != len(pwm):
raise Exception("pwm and motif must be the same length")
# generic alignment
alignlist = [ c.text for c in mafblock.components ]
align = pwmx.Align( alignlist )
nrows,ncols = align.dims
... | for ir in range(nrows):
# scan alignment row for motif subsequences
for start in range(ncols):
if align.rows[ir][start] == '-': continue
elif align.rows[ir][start] == 'n': continue
elif align.rows[ir][start] == 'N': continue
# gather enough subseq for moti... | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx/pwm/pwm_score_maf.py#L79-L170 |
bxlab/bx-python | lib/bx/phylo/newick.py | create_parser | def create_parser():
"""
Create a 'pyparsing' parser for newick format trees roughly based on the
grammar here:
http://evolution.genetics.washington.edu/phylip/newick_doc.html
Problems:
- Is a single leaf a valid tree?
- Branch length on root? Doesn't make sense to me, and force... | python | def create_parser():
"""
Create a 'pyparsing' parser for newick format trees roughly based on the
grammar here:
http://evolution.genetics.washington.edu/phylip/newick_doc.html
Problems:
- Is a single leaf a valid tree?
- Branch length on root? Doesn't make sense to me, and force... | Create a 'pyparsing' parser for newick format trees roughly based on the
grammar here:
http://evolution.genetics.washington.edu/phylip/newick_doc.html
Problems:
- Is a single leaf a valid tree?
- Branch length on root? Doesn't make sense to me, and forces the root
to be an edg... | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx/phylo/newick.py#L52-L89 |
bxlab/bx-python | scripts/maf_tile_2bit.py | get_fill_char | def get_fill_char( maf_status ):
"""
Return the character that should be used to fill between blocks
having a given status
"""
## assert maf_status not in ( maf.MAF_CONTIG_NESTED_STATUS, maf.MAF_NEW_NESTED_STATUS,
## maf.MAF_MAYBE_NEW_NESTED_STATUS ), \
## "Ne... | python | def get_fill_char( maf_status ):
"""
Return the character that should be used to fill between blocks
having a given status
"""
## assert maf_status not in ( maf.MAF_CONTIG_NESTED_STATUS, maf.MAF_NEW_NESTED_STATUS,
## maf.MAF_MAYBE_NEW_NESTED_STATUS ), \
## "Ne... | Return the character that should be used to fill between blocks
having a given status | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/scripts/maf_tile_2bit.py#L72-L90 |
bxlab/bx-python | scripts/maf_tile_2bit.py | guess_fill_char | def guess_fill_char( left_comp, right_comp ):
"""
For the case where there is no annotated synteny we will try to guess it
"""
# No left component, obiously new
return "*"
# First check that the blocks have the same src (not just species) and
# orientation
if ( left_comp.src == right_co... | python | def guess_fill_char( left_comp, right_comp ):
"""
For the case where there is no annotated synteny we will try to guess it
"""
# No left component, obiously new
return "*"
# First check that the blocks have the same src (not just species) and
# orientation
if ( left_comp.src == right_co... | For the case where there is no annotated synteny we will try to guess it | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/scripts/maf_tile_2bit.py#L92-L107 |
bxlab/bx-python | scripts/maf_tile_2bit.py | remove_all_gap_columns | def remove_all_gap_columns( texts ):
"""
Remove any columns containing only gaps from alignment texts
"""
seqs = [ list( t ) for t in texts ]
i = 0
text_size = len( texts[0] )
while i < text_size:
all_gap = True
for seq in seqs:
if seq[i] not in ( '-', '#', '*', '... | python | def remove_all_gap_columns( texts ):
"""
Remove any columns containing only gaps from alignment texts
"""
seqs = [ list( t ) for t in texts ]
i = 0
text_size = len( texts[0] )
while i < text_size:
all_gap = True
for seq in seqs:
if seq[i] not in ( '-', '#', '*', '... | Remove any columns containing only gaps from alignment texts | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/scripts/maf_tile_2bit.py#L109-L127 |
bxlab/bx-python | lib/bx/cookbook/__init__.py | cross_lists | def cross_lists(*sets):
"""Return the cross product of the arguments"""
wheels = [iter(_) for _ in sets]
digits = [next(it) for it in wheels]
while True:
yield digits[:]
for i in range(len(digits)-1, -1, -1):
try:
digits[i] = next(wheels[i])
br... | python | def cross_lists(*sets):
"""Return the cross product of the arguments"""
wheels = [iter(_) for _ in sets]
digits = [next(it) for it in wheels]
while True:
yield digits[:]
for i in range(len(digits)-1, -1, -1):
try:
digits[i] = next(wheels[i])
br... | Return the cross product of the arguments | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx/cookbook/__init__.py#L16-L30 |
bxlab/bx-python | lib/bx/misc/readlengths.py | read_lengths_file | def read_lengths_file( name ):
"""
Returns a hash from sequence name to length.
"""
chrom_to_length = {}
f = file ( name, "rt" )
for line in f:
line = line.strip()
if line == '' or line[0] == '#': continue
try:
fields = line.split()
if len(fields)... | python | def read_lengths_file( name ):
"""
Returns a hash from sequence name to length.
"""
chrom_to_length = {}
f = file ( name, "rt" )
for line in f:
line = line.strip()
if line == '' or line[0] == '#': continue
try:
fields = line.split()
if len(fields)... | Returns a hash from sequence name to length. | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx/misc/readlengths.py#L7-L28 |
bxlab/bx-python | lib/bx/wiggle.py | IntervalReader | def IntervalReader( f ):
"""
Iterator yielding chrom, start, end, strand, value.
Values are zero-based, half-open.
Regions which lack a score are ignored.
"""
current_chrom = None
current_pos = None
current_step = None
# always for wiggle data
strand = '+'
mode = "bed"
... | python | def IntervalReader( f ):
"""
Iterator yielding chrom, start, end, strand, value.
Values are zero-based, half-open.
Regions which lack a score are ignored.
"""
current_chrom = None
current_pos = None
current_step = None
# always for wiggle data
strand = '+'
mode = "bed"
... | Iterator yielding chrom, start, end, strand, value.
Values are zero-based, half-open.
Regions which lack a score are ignored. | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx/wiggle.py#L14-L63 |
bxlab/bx-python | lib/bx/misc/binary_file.py | BinaryFileReader.read_and_unpack | def read_and_unpack( self, format, byte_count=None ):
"""
Read enough bytes to unpack according to `format` and return the
tuple of unpacked values.
"""
pattern = "%s%s" % ( self.endian_code, format )
if byte_count is None:
byte_count = struct.calcsize( patter... | python | def read_and_unpack( self, format, byte_count=None ):
"""
Read enough bytes to unpack according to `format` and return the
tuple of unpacked values.
"""
pattern = "%s%s" % ( self.endian_code, format )
if byte_count is None:
byte_count = struct.calcsize( patter... | Read enough bytes to unpack according to `format` and return the
tuple of unpacked values. | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx/misc/binary_file.py#L59-L67 |
bxlab/bx-python | lib/bx/misc/binary_file.py | BinaryFileReader.read_c_string | def read_c_string( self ):
"""
Read a zero terminated (C style) string
"""
rval = []
while 1:
ch = self.file.read(1)
assert len( ch ) == 1, "Unexpected end of file"
if ch == b'\0':
break
rval.append( ch )
ret... | python | def read_c_string( self ):
"""
Read a zero terminated (C style) string
"""
rval = []
while 1:
ch = self.file.read(1)
assert len( ch ) == 1, "Unexpected end of file"
if ch == b'\0':
break
rval.append( ch )
ret... | Read a zero terminated (C style) string | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx/misc/binary_file.py#L69-L80 |
bxlab/bx-python | lib/bx/misc/binary_file.py | BinaryFileWriter.pack_and_write | def pack_and_write( self, format, value ):
"""
Read enough bytes to unpack according to `format` and return the
tuple of unpacked values.
"""
pattern = "%s%s" % ( self.endian_code, format )
return self.file.write( struct.pack( pattern, value ) ) | python | def pack_and_write( self, format, value ):
"""
Read enough bytes to unpack according to `format` and return the
tuple of unpacked values.
"""
pattern = "%s%s" % ( self.endian_code, format )
return self.file.write( struct.pack( pattern, value ) ) | Read enough bytes to unpack according to `format` and return the
tuple of unpacked values. | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx/misc/binary_file.py#L137-L143 |
bxlab/bx-python | lib/bx/misc/binary_file.py | BinaryFileWriter.write_c_string | def write_c_string( self, value ):
"""
Read a zero terminated (C style) string
"""
self.file.write( value )
self.file.write( b'\0' ) | python | def write_c_string( self, value ):
"""
Read a zero terminated (C style) string
"""
self.file.write( value )
self.file.write( b'\0' ) | Read a zero terminated (C style) string | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx/misc/binary_file.py#L145-L150 |
bxlab/bx-python | lib/bx/align/tools/fuse.py | fuse_list | def fuse_list( mafs ):
"""
Try to fuse a list of blocks by progressively fusing each adjacent pair.
"""
last = None
for m in mafs:
if last is None:
last = m
else:
fused = fuse( last, m )
if fused:
last = fused
else:
... | python | def fuse_list( mafs ):
"""
Try to fuse a list of blocks by progressively fusing each adjacent pair.
"""
last = None
for m in mafs:
if last is None:
last = m
else:
fused = fuse( last, m )
if fused:
last = fused
else:
... | Try to fuse a list of blocks by progressively fusing each adjacent pair. | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx/align/tools/fuse.py#L8-L24 |
bxlab/bx-python | lib/bx/align/tools/fuse.py | fuse | def fuse( m1, m2 ):
"""
Attempt to fuse two blocks. If they can be fused returns a new block,
otherwise returns None.
Example:
>>> import bx.align.maf
>>> block1 = bx.align.maf.from_string( '''
... a score=0.0
... s hg18.chr10 52686 44 + 135374737 GTGCTAACTTACTGCTCC... | python | def fuse( m1, m2 ):
"""
Attempt to fuse two blocks. If they can be fused returns a new block,
otherwise returns None.
Example:
>>> import bx.align.maf
>>> block1 = bx.align.maf.from_string( '''
... a score=0.0
... s hg18.chr10 52686 44 + 135374737 GTGCTAACTTACTGCTCC... | Attempt to fuse two blocks. If they can be fused returns a new block,
otherwise returns None.
Example:
>>> import bx.align.maf
>>> block1 = bx.align.maf.from_string( '''
... a score=0.0
... s hg18.chr10 52686 44 + 135374737 GTGCTAACTTACTGCTCCACAGAAAACATCAATTCTGCTCATGC
.... | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx/align/tools/fuse.py#L26-L67 |
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