bx_extras.pstat module

pstat.py module

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This module provides some useful list and array manipulation routines modeled after those found in the |Stat package by Gary Perlman, plus a number of other useful list/file manipulation functions. The list-based functions include:

abut (source,*args) simpleabut (source, addon) colex (listoflists,cnums) collapse (listoflists,keepcols,collapsecols,fcn1=None,fcn2=None,cfcn=None) dm (listoflists,criterion) flat (l) linexand (listoflists,columnlist,valuelist) linexor (listoflists,columnlist,valuelist) linedelimited (inlist,delimiter) lineincols (inlist,colsize) lineincustcols (inlist,colsizes) list2string (inlist) makelol(inlist) makestr(x) printcc (lst,extra=2) printincols (listoflists,colsize) pl (listoflists) printl(listoflists) replace (lst,oldval,newval) recode (inlist,listmap,cols=’all’) remap (listoflists,criterion) roundlist (inlist,num_digits_to_round_floats_to) sortby(listoflists,sortcols) unique (inlist) duplicates(inlist) writedelimited (listoflists, delimiter, file, writetype=’w’)

Some of these functions have alternate versions which are defined only if Numeric (NumPy) can be imported. These functions are generally named as above, with an ‘a’ prefix.

aabut (source, *args) acolex (a,indices,axis=1) acollapse (a,keepcols,collapsecols,sterr=0,ns=0) adm (a,criterion) alinexand (a,columnlist,valuelist) alinexor (a,columnlist,valuelist) areplace (a,oldval,newval) arecode (a,listmap,col=’all’) arowcompare (row1, row2) arowsame (row1, row2) asortrows(a,axis=0) aunique(inarray) aduplicates(inarray)

Currently, the code is all but completely un-optimized. In many cases, the array versions of functions amount simply to aliases to built-in array functions/methods. Their inclusion here is for function name consistency.

bx_extras.pstat.abut(source, *args)

Like the |Stat abut command. It concatenates two lists side-by-side and returns the result. ‘2D’ lists are also accomodated for either argument (source or addon). CAUTION: If one list is shorter, it will be repeated until it is as long as the longest list. If this behavior is not desired, use pstat.simpleabut().

Usage: abut(source, args) where args=any # of lists Returns: a list of lists as long as the LONGEST list past, source on the

‘left’, lists in <args> attached consecutively on the ‘right’

bx_extras.pstat.cmp(x, y)

Replacement for built-in function cmp that was removed in Python 3

bx_extras.pstat.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 (listoflists,cnums) Returns: a list-of-lists corresponding to the columns from listoflists

specified by cnums, in the order the column numbers appear in cnums

bx_extras.pstat.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 to a function rather than None (e.g., stats.sterr, len) will append those results (e.g., the sterr, N) after each calculated mean. cfcn is the collapse function to apply (defaults to mean, defined here in the pstat module to avoid circular imports with stats.py, but harmonicmean or others could be passed).

Usage: collapse (listoflists,keepcols,collapsecols,fcn1=None,fcn2=None,cfcn=None) Returns: a list of lists with all unique permutations of entries appearing in

columns (“conditions”) specified by keepcols, abutted with the result of cfcn (if cfcn=None, defaults to the mean) of each column specified by collapsecols.

bx_extras.pstat.dm(listoflists, criterion)

Returns rows from the passed list of lists that meet the criteria in the passed criterion expression (a string as a function of x; e.g., ‘x[3]>=9’ will return all rows where the 4th column>=9 and “x[2]==’N’” will return rows with column 2 equal to the string ‘N’).

Usage: dm (listoflists, criterion) Returns: rows from listoflists that meet the specified criterion.

bx_extras.pstat.duplicates(inlist)

Returns duplicate items in the FIRST dimension of the passed list.

Usage: duplicates (inlist)

bx_extras.pstat.flat(l)

Returns the flattened version of a ‘2D’ list. List-correlate to the a.flat() method of NumPy arrays.

Usage: flat(l)

bx_extras.pstat.linedelimited(inlist, delimiter)

Returns a string composed of elements in inlist, with each element separated by ‘delimiter.’ Used by function writedelimited. Use ‘ ‘ for tab-delimiting.

Usage: linedelimited (inlist,delimiter)

bx_extras.pstat.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

bx_extras.pstat.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) Returns: formatted string created from inlist

bx_extras.pstat.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 listoflists where columnlist[i]=valuelist[i] for ALL i

bx_extras.pstat.linexor(listoflists, columnlist, valuelist)

Returns the rows of a list of lists where col (from columnlist) = val (from valuelist) for ANY pair of values (colunmlist[i],valuelist[i[). One value is required for each column in columnlist. If only one value exists for columnlist but multiple values appear in valuelist, the valuelist values are all assumed to pertain to the same column.

Usage: linexor (listoflists,columnlist,valuelist) Returns: the rows of listoflists where columnlist[i]=valuelist[i] for ANY i

bx_extras.pstat.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

bx_extras.pstat.makelol(inlist)

Converts a 1D list to a 2D list (i.e., a list-of-lists). Useful when you want to use put() to write a 1D list one item per line in the file.

Usage: makelol(inlist) Returns: if l = [1,2,’hi’] then returns [[1],[2],[‘hi’]] etc.

bx_extras.pstat.makestr(x)

bx_extras.pstat.nonrepeats(inlist)

Returns items that are NOT duplicated in the first dim of the passed list.

Usage: nonrepeats (inlist)

bx_extras.pstat.pl(listoflists)

Prints a list of lists, 1 list (row) at a time.

Usage: pl(listoflists) Returns: None

bx_extras.pstat.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

bx_extras.pstat.printincols(listoflists, colsize)

Prints a list of lists in columns of (fixed) colsize width, where colsize is an integer.

Usage: printincols (listoflists,colsize) Returns: None

bx_extras.pstat.printl(listoflists)

Alias for pl.

bx_extras.pstat.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 with the appropriate values replaced with new ones

bx_extras.pstat.remap(listoflists, criterion)

Remaps values in a given column of a 2D list (listoflists). This requires a criterion as a function of ‘x’ so that the result of the following is returned … map(lambda x: ‘criterion’,listoflists).

Usage: remap(listoflists,criterion) criterion=string Returns: remapped version of listoflists

bx_extras.pstat.replace(inlst, oldval, newval)

Replaces all occurrences of ‘oldval’ with ‘newval’, recursively.

Usage: replace (inlst,oldval,newval)

bx_extras.pstat.roundlist(inlist, digits)

Goes through each element in a 1D or 2D inlist, and applies the following function to all elements of float … round(element,digits).

Usage: roundlist(inlist,digits) Returns: list with rounded floats

bx_extras.pstat.simpleabut(source, addon)

Concatenates two lists as columns and returns the result. ‘2D’ lists are also accomodated for either argument (source or addon). This DOES NOT repeat either list to make the 2 lists of equal length. Beware of list pairs with different lengths … the resulting list will be the length of the FIRST list passed.

Usage: simpleabut(source,addon) where source, addon=list (or list-of-lists) Returns: a list of lists as long as source, with source on the ‘left’ and

addon on the ‘right’

bx_extras.pstat.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

bx_extras.pstat.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