agutil 0.2.2a0

SEARCH_RANGE

The agutil module includes the class, search_range. A search_range class instance keeps track of a set of numerical ranges. Any number of ranges can be included or excluded from the instance. A single point, or range of points can be checked against the instance for intersection. Multiple instances can be combined with union, difference, and intersection operators to produce new search_range instances. The set of points in the search range is implemented as a bitset for efficiency

API

• search_range(start=0, stop=0, fill=True) (constructor) Creates a new search_range instance with the range [start, stop) included search_range.check(i) will return True for any point within [start, stop)

• search_range.add_range(start, stop) Adds the range [start, stop) to the set of points in the search range

• search_range.remove_range(start, stop) Removes the range [s_tart_, stop) from the set of points in the search range

• search_range.check(coord) Returns True if coord exists within the set of points included in the search range. Returns False otherwise

• search_range.check_range(start, stop) Returns True if any point within the range [start, stop) is included in the search range. Returns False otherwise

• search_range.union(other)

• search_range.difference(other)

• search_range.intersection(other) Returns a new search_range whose set of points is the result of the union, difference, or intersection (respectively) of this search_range and other. These methods can also be accessed through the following binary operators:

  • Union: a|b a+b

  • Difference: a-b

  • Intersection: a&b _a*b_

• search_range.__iter__() (iteration) search_ranges support iteration, which produces a sequence of points included in the range

• search_range.gen_ranges() Returns a generator which yields pairs of [start, stop) coordinates for each continuous set of points in the range

• search_range.range_count() Returns the number of points included in the range

• search_range.__str__() Produces a string which lists the ranges produced by gen_ranges()

• search_range.__repr__() Produces a string which lists each point included in the range

• search_range.__bool__() Returns True if there is at least one point included in the range

STATUS_BAR

The agutil module includes the class, status_bar. A status_bar instance provides a status indicator which can be updated at any time. The display is only updated when necessary, so there is minimal drawback for updating the instance frequently

API

• status_bar(maximum, show_percent = False, init=True, prepend=””, append=””, cols=int(get_terminal_size()[0]/2), update_threshold=.00005, debugging=False, transcript=None) (constructor) Creates a new status_bar instance ranging from 0 to maximum

show_percent toggles whether or not a percentage meter should be displayed to the right of the bar

init sets whether or not the status_bar should immediately display. If set to false, the bar is displayed at the first update

prepend is text to be prepended to the left of the bar. It will always remain to the left of the bar as the display updates. WARNING Prepended text offsets the bar. If any part of the bar (including prepended or appended text) extends beyond a single line on the console, the status bar will not display properly. Prepended text should be kept short

append is text to be appended to the right of the bar. It will always remain to the right of the bar as the display updates. WARNING Appended text extends the display. If any part of the bar (including prepended or appended text) extends beyond a single line of the console, the status bar will not display properly. Appended text should be kept short

cols sets how long the bar should be. It defaults to half the terminal size

update_threshold sets the minimum change in percentage to trigger an update to the percentage meter

debugging triggers the status_bar to never print to stdout. If set true, no output will be produced, but exact string of what would be displayed is maintained at all times in the display attribute

transcript is a filepath to where the status bar should keep a log of all changes to the display. If transcript is None (the default value) or False, logging is disabled. WARNING Using the transcript will slow down performance by requiring the status bar to make frequent i/o every time the display is modified. Useful for debugging issues with prepended or appended text, but not recommended if the transcript is not needed

• status_bar.update(value) updates the display iff value would require a change in the length of the progress bar, or if it changes the percentage readout by at least update_threshold

• status_bar.clear(erase=False) Clears the readout from stdout. If erase is true, the readout is cleared entirely. Otherwise, the cursor position is simply reset to the front of the bar, which will overwrite characters in the readout with subsequent output to stdout by any source

• status_bar.prepend(text, updateText=True) Displays text to the left of the bar. It will always remain to the left of the bar as the display updates. WARNING Prepended text offsets the bar. If any part of the bar (including prepended or appended text) extends beyond a single line on the console, the status bar will not display properly. Prepended text should be kept short. If updateText is True, the display is immediately re-drawn to reflect the new text. Otherwise, the display will wait until the next time update() is called before updating the text

• status_bar.append(text, updateText=True) Displays text to the right of the bar. It will always remain to the right of the bar as the display updates. WARNING Appended text extends the display. If any part of the bar (including prepended or appended text) extends beyond a single line of the console, the status bar will not display properly. Appended text should be kept short. If updateText is True, the display is immediately re-drawn to reflect the new text. Otherwise, the display will wait until the next time update() is called before updating the text

bio.MAF2BED

The agutil.bio.maf2bed module provides a command line interface for converting maf files into bed files. To follow the bed format, and to reduce the size of the bed itself, maf2bed generates two files by default. A .bed file with entries in the format of: Chromosome Start Stop Key and a .key file with entries in the format of: Key <All fields present in the original maf>

COMMAND USAGE

• $ maf2bed convert <input> <output> [--exclude-silent] [--skip-keyfile] Converts the file input to output and output.key files. If –exclude-silent is set, silent mutations are not included in the output. If –skip-keyfile is set, the program only generates a single file, output which is identical to the input file, except that start and stop coordinates have been shifted to 0-based

• $ maf2bed lookup <input> <keys...> Looks up the entries for each key listed in keys in the keyfile input

bio.TSVMANIP

The agutil.tsvManip module provides a command line interface for modifying large tsv files. While not strictly biology oriented, its original purpose was to parse and rearrange different fields of bed files

COMMAND USAGE

• $ tsvmanip <input> <output> [--no-headers] [-c COLUMN] [-d DELIMITER] [--i0 COL] [-s COL] [-m IN:OUT] [-v]

Parses input according to the following arguments, and writes to output

Optional arguments:

–no-headers Flag indicating that there are is no header row

-c COLUMN, –col COLUMN Column containing input data to parse (0-indexed). Multiple columns can be selected by providing the option multiple times (Ex: –col 0 –col 5 –col 6). All columns are selected by default

-d DELIMITER, –delim DELIMITER Delimiters for splitting input columns into multiple new columns for output Delimiters can be specified for multiple columns by providing the option multiple times Delimiters are matched to colums by order provided. For example, the first delimiter provided matches to the first column parsed for input. An underscore (_) indicates no delimiter for that column. To use a delimiter consisting entirely of one or more underscores, append a single underscore to the end of the delimiter string. (Ex: ‘–delim __’ (two underscores) indicates a delimiter of ‘_’ (one underscore) ). Multiple delimiters can be provided for the same column by prefixing the delimiters for the string with : Delimiters for the same column are applied in the order provided to all resulting columns from subsequent splits. Prefixed delimiter inputs will not affect the matching of unprefixed delimiters to columns. (Ex: –col 0 –col 1 –delim –delim ) (Ex: –col 1 –col 4 –delim –delim –delim 1:)

–i0 COL Selected columns should be shifted from 1 to 0 index. This is applied after selected columns are plucked from the input, and split by delimiters. Provided column numbers match the indecies of columns after those steps. Multiple columns can be selected by supplying the argument multiple times

-s COL, –strip-commas COL Strip commas from the specified columns. Column numbers reference before mapping, but after splitting

-m IN:OUT, –map IN:OUT Mappings to map plucked columns to output columns. Use to change the order of columns. Maps are in the format of: <input column #>:<output column #> This is the last step in parsing, so input column #’s should be relative to any changes made by plucking and splitting

-v Provide verbose output