cli package

The main idea of this package is to emulate the terminal, but doing all of that inside Python itself. So this bash statement:

cat file.txt | head -5 > headerFile.txt

Turns into this statement:

cat("file.txt") | head(5) > file("headerFile.txt")

Here, “cat”, “head” and “file” are all classes extended from BaseCli. All of them implements the “reverse or” operation, or __ror__. Essentially, these 2 statements are equivalent:

3 | obj
obj.__ror__(3)

Also, a lot of these tools assume that we are operating on a table. So this table:

col1	col2	col3
1	2	3
4	5	6

Is equivalent to this list:

[["col1", "col2", "col3"], [1, 2, 3], [4, 5, 6]]

Also, the expected way to use these tools is to import everything directly into the current environment, like this:

from k1lib.bioinfo.cli import *

Besides operating on string iterators alone, this package can also be extra meta, and operate on streams of strings, or streams of streams of anything. I think this is one of the most powerful concept of the cli workflow. If this interests you, check over this:

• Cli streams

Submodules

bio module

This is for functions that are actually biology-related

k1lib.bioinfo.cli.bio.go(term: int)

Looks up a GO term

class k1lib.bioinfo.cli.bio.transcribe

Bases: k1lib.bioinfo.cli.init.BaseCli

Transcribes (DNA -> RNA) incoming rows

__ror__(it: Union[Iterator[str], str])

class k1lib.bioinfo.cli.bio.complement

Bases: k1lib.bioinfo.cli.init.BaseCli

__ror__(it: Union[Iterator[str], str])

class k1lib.bioinfo.cli.bio.translate(length: int = 0)

Bases: k1lib.bioinfo.cli.init.BaseCli

__init__(length: int = 0)

Translates incoming rows.

Parameters

length – 0 for short (L), 1 for med (Leu), 2 for long (Leucine)

__ror__(it: Iterator[str])

class k1lib.bioinfo.cli.bio.medAa

Bases: k1lib.bioinfo.cli.init.BaseCli

Converts short aa sequence to medium one

__ror__(it: Iterator[str])

class k1lib.bioinfo.cli.bio.longAa

Bases: k1lib.bioinfo.cli.init.BaseCli

Converts short aa sequence to long one

__ror__(it: Iterator[str])

entrez module

This module is not really fleshed out, not that useful/elegant, and I just use cmd instead

k1lib.bioinfo.cli.entrez.esearch(db: str = 'nucleotide', query: str = 'PRJNA257197')

k1lib.bioinfo.cli.entrez.efetch(db: Optional[str] = None, ids: Optional[Union[str, List[str]]] = None, format: Optional[str] = None)

mgi module

class k1lib.bioinfo.cli.mgi.batch(headless=True)

Bases: k1lib.bioinfo.cli.init.BaseCli

Queries MGI database, convert list of genes to MGI ids

__init__(headless=True)

Parameters

headless – whether to run this operation headless, or actually display the browser

__ror__(it: List[str])

filt module

This is for functions that cuts out specific parts of the table

class k1lib.bioinfo.cli.filt.filt(predicate: Callable[[str], bool], column: Optional[int] = None)

Bases: k1lib.bioinfo.cli.init.BaseCli

__init__(predicate: Callable[[str], bool], column: Optional[int] = None)

Filters out lines.

Parameters

column –

• if integer, then predicate(row[column])

• if None, then predicate(line)

__ror__(it: Iterator[str])

__invert__()

Negate the condition

k1lib.bioinfo.cli.filt.isValue(value, column: Optional[int] = None)

Filters out lines that is different from the given value

k1lib.bioinfo.cli.filt.inSet(values: Set[Any], column: Optional[int] = None)

Filters out lines that is not in the specified set

k1lib.bioinfo.cli.filt.contains(s: str, column: Optional[int] = None)

Filters out lines that don’t contain the specified substring

class k1lib.bioinfo.cli.filt.nonEmptyStream

Bases: k1lib.bioinfo.cli.init.BaseCli

Filters out streams that have no rows

__ror__(streams: Iterator[Iterator[Any]]) → Iterator[Iterator[Any]]

k1lib.bioinfo.cli.filt.startswith(s: str, column: Optional[int] = None)

Filters out lines that don’t start with s

k1lib.bioinfo.cli.filt.endswith(s: str, column: Optional[int] = None)

Filters out lines that don’t end with s

k1lib.bioinfo.cli.filt.isNumeric(column: Optional[int] = None)

Filters out a line if that column is not a number

k1lib.bioinfo.cli.filt.inRange(min: Optional[float] = None, max: Optional[float] = None, column: Optional[int] = None)

Checks whether a column is in range or not

class k1lib.bioinfo.cli.filt.head(n: int = 10)

Bases: k1lib.bioinfo.cli.init.BaseCli

__init__(n: int = 10)

Only outputs first n lines. You can also negate it (like ~head(5)), which then only outputs after first n lines. Examples:

"abcde" | head(2) | dereference() # returns ["a", "b"]
"abcde" | ~head(2) | dereference() # returns ["c", "d", "e"]
"0123456" | head(-3) | dereference() # returns ['0', '1', '2', '3']
"0123456" | ~head(-3) | dereference() # returns ['4', '5', '6']

__ror__(it: Iterator[T]) → Iterator[T]

__invert__()

class k1lib.bioinfo.cli.filt.columns(*columns: List[int])

Bases: k1lib.bioinfo.cli.init.BaseCli

__init__(*columns: List[int])

Cuts out specific columns, sliceable. Examples:

["0123456789"] | cut(5, 8) | dereference() # returns [['5', '8']]
["0123456789"] | cut(2) | dereference() # returns ['2']
["0123456789"] | cut(5, 8) | dereference() # returns [['5', '8']]
["0123456789"] | ~cut()[:7:2] | dereference() # returns [['1', '3', '5', '7', '8', '9']]

If you’re selecting only 1 column, then Iterator[T] will be returned, not Table[T].

__ror__(it: k1lib.bioinfo.cli.init.MetaObj) → k1lib.bioinfo.cli.init.MetaObj

__invert__()

k1lib.bioinfo.cli.filt.cut

alias of k1lib.bioinfo.cli.filt.columns

class k1lib.bioinfo.cli.filt.rows(*rows: List[int])

Bases: k1lib.bioinfo.cli.init.BaseCli

__init__(*rows: List[int])

Cuts out specific rows. Space complexity O(1) as a list is not constructed (unless you’re using some really weird slices).

Parameters

rows – ints for the row indices

Example:

"0123456789" | rows(2) | dereference() # returns ["2"]
"0123456789" | rows(5, 8) | dereference() # returns ["5", "8"]
"0123456789" | rows()[2:5] | dereference() # returns ["2", "3", "4"]
"0123456789" | ~rows()[2:5] | dereference() # returns ["0", "1", "5", "6", "7", "8", "9"]
"0123456789" | ~rows()[:7:2] | dereference() # returns ['1', '3', '5', '7', '8', '9']
"0123456789" | rows()[:-4] | dereference() # returns ['0', '1', '2', '3', '4', '5']
"0123456789" | ~rows()[:-4] | dereference() # returns ['6', '7', '8', '9']

__invert__()

__ror__(it: Iterator[str])

class k1lib.bioinfo.cli.filt.intersection

Bases: k1lib.bioinfo.cli.init.BaseCli

Returns the intersection of multiple streams. Example:

[[1, 2, 3, 4, 5], [7, 2, 4, 6, 5]] | intersection() # will return set([2, 4, 5])

__ror__(its: Iterator[Iterator[Any]]) → Set[Any]

gb module

class k1lib.bioinfo.cli.gb.feats

Bases: k1lib.bioinfo.cli.init.BaseCli

Fetches features, each on a separate stream

__ror__(it)

static filt(term: str) → k1lib.bioinfo.cli.init.BaseCli

Filters for a specific term in all the features texts

static tag(tag: str) → k1lib.bioinfo.cli.init.BaseCli

Gets a single tag out. Applies this on a single feature only

class k1lib.bioinfo.cli.gb.origin

Bases: k1lib.bioinfo.cli.init.BaseCli

Return the origin section of the genbank file

__ror__(it)

grep module

class k1lib.bioinfo.cli.grep.grep(pattern: str, before: int = 0, after: int = 0)

Bases: k1lib.bioinfo.cli.init.BaseCli

__init__(pattern: str, before: int = 0, after: int = 0)

Find lines that has the specified pattern. Example: .. code-block:

# returns ['c', 'd', '2', 'd']
"abcde12d34" | grep("d", 1) | dereference()
# returns ['d', 'e', 'd', '3', '4']
"abcde12d34" | grep("d", 0, 3).till("e") | dereference()

Parameters

• pattern – regex pattern to search for in a line

• before – lines before the hit. Outputs independent lines

• after – lines after the hit. Outputs independent lines

till(pattern: str)

Greps until some other pattern appear. Before lines will be honored, but after lines will be set to inf. Inclusive.

__ror__(it: Iterator[str]) → Iterator[str]

class k1lib.bioinfo.cli.grep.grepToTable(pattern: str, before: int = 0, after: int = 0)

Bases: k1lib.bioinfo.cli.init.BaseCli

__init__(pattern: str, before: int = 0, after: int = 0)

Searches for a pattern. If found, then put all the before and after lines in different columns. Example:

# returns [['2', 'b'], ['5', 'b']]
"1a\n 2b\n 3c\n 4d\n 5b\n 6c\n f" | grepToTable("b", 1) | dereference()

__ror__(it: Iterator[str]) → k1lib.bioinfo.cli.init.MetaObj

class k1lib.bioinfo.cli.grep.grepTemplate(pattern: str, template: str)

Bases: k1lib.bioinfo.cli.init.BaseCli

__init__(pattern: str, template: str)

Searches over all lines, pick out the match, and expands it to the templateand yields

__ror__(it: Iterator[str])

init module

cli.bioinfoSettings = {'defaultDelim': '\t', 'defaultIndent': '  ', 'lookupImgs': True, 'oboFile': None, 'strict': False}

Main settings of k1lib.bioinfo.cli. When using:

from k1lib.bioinfo.cli import *

…you can just set the settings like this:

bioinfoSettings["defaultIndent"] = "\t"

There are a few settings:

• defaultDelim: default delimiter used in-between columns when creating tables

• defaultIndent: default indent used for displaying nested structures

• lookupImgs: whether to automatically look up images when exploring something

• oboFile: gene ontology obo file location

• strict: whether strict mode is on. Turning it on can help you debug stuff, but could also be a pain to work with

k1lib.bioinfo.cli.init.patchDefaultDelim(s: str)

Parameters

s –

• if not None, returns self

• else returns the default delimiter in settings

k1lib.bioinfo.cli.init.patchDefaultIndent(s: str)

Parameters

s –

• if not None, returns self

• else returns the default indent character in settings

k1lib.bioinfo.cli.init.newTypeHint(name, docs='')

Creates a new type hint that can be sliced and yet still looks fine in sphinx. Crudely written by my poorly understood idea of Python’s metaclasses. Seriously, this shit is bonkers, read over it https://stackoverflow.com/questions/100003/what-are-metaclasses-in-python

Example:

Table = newTypeHint("Table", "some docs")
Table[int] # prints out as "Table[int]", and sphinx fell for it too
Table[Table[str], float] # prints out as "Table[Table[str], float]"

class k1lib.bioinfo.cli.init.Table

Bases: object

Essentially just Iterator[List[T]]. This class is just here so that I can generate the docs with nicely formatted types like “Table[str]”.

class k1lib.bioinfo.cli.init.Row(iterable=(), /)

Bases: list

Not really used currently. Just here for potential future feature

class k1lib.bioinfo.cli.init.BaseCli

Bases: object

all() → k1lib.bioinfo.cli.init.BaseCli

Applies this BaseCli to all incoming streams

f()

Creates a normal function \(f(x)\) which is equivalent to x | self.

class k1lib.bioinfo.cli.init.serial(*clis: List[k1lib.bioinfo.cli.init.BaseCli])

Bases: k1lib.bioinfo.cli.init.BaseCli

__init__(*clis: List[k1lib.bioinfo.cli.init.BaseCli])

Merges clis into 1, feeding end to end. Used in chaining clis together without a prime iterator. Meaning, without this, stuff like this fails to run:

[1, 2] | a() | b() # runs
c = a() | b(); [1, 2] | c # doesn't run if this class doesn't exist

__ror__(it: Iterator[Any]) → Iterator[Any]

class k1lib.bioinfo.cli.init.oneToMany(*clis: List[k1lib.bioinfo.cli.init.BaseCli])

Bases: k1lib.bioinfo.cli.init.BaseCli

__init__(*clis: List[k1lib.bioinfo.cli.init.BaseCli])

Duplicates 1 stream into multiple streams, each for a cli in the list. Used in the “a & b” joining operator

__ror__(it: Iterator[Any]) → Iterator[Iterator[Any]]

class k1lib.bioinfo.cli.init.manyToMany(cli)

Bases: k1lib.bioinfo.cli.init.BaseCli

__init__(cli)

Applies multiple streams to a single cli. Used in the “a.all()” operator.

__ror__(it: Iterator[Iterator[Any]]) → Iterator[Iterator[Any]]

class k1lib.bioinfo.cli.init.manyToManySpecific(*clis: List[k1lib.bioinfo.cli.init.BaseCli])

Bases: k1lib.bioinfo.cli.init.BaseCli

__init__(*clis: List[k1lib.bioinfo.cli.init.BaseCli])

Applies multiple streams to multiple clis independently. Used in the “a + b” joining operator

__ror__(its: Iterator[Any]) → Iterator[Any]

input module

k1lib.bioinfo.cli.input.cat(fileName: Optional[str] = None)

Reads a file line by line.

Parameters

fileName – if None, then return a BaseCli that accepts a file name and outputs Iterator[str]

class k1lib.bioinfo.cli.input.cats

Bases: k1lib.bioinfo.cli.init.BaseCli

Like cat(), but opens multiple files at once, returning streams. Looks something like this:

apply(lambda s: cat(s))

__ror__(fileNames: Iterator[str]) → Iterator[Iterator[str]]

k1lib.bioinfo.cli.input.curl(url: str) → Iterator[str]

Gets file from url

k1lib.bioinfo.cli.input.wget(url: str, fileName: Optional[str] = None)

Downloads a file

Parameters

• url – The url of the file

• fileName – if None, then tries to infer it from the url

class k1lib.bioinfo.cli.input.cmd(cmd: str)

Bases: k1lib.bioinfo.cli.init.BaseCli

__init__(cmd: str)

Runs a command, and returns the output line by line.

property err

Error from the last command

__ror__(it: Optional[Iterator[str]]) → Iterator[str]

Pipes in lines of input, or if there’s nothing to pass, then pass None

k1lib.bioinfo.cli.input.requireCli(cliTool: str)

Searches for a particular cli tool (eg. “ls”), throws ImportError if not found, else do nothing

kcsv module

This module is for dealing with csv stuff

k1lib.bioinfo.cli.kcsv.cat(file: str) → Iterator[str]

Opens a csv file, and turns them into nice row elements

kxml module

This module is for dealing with xml stuff

class k1lib.bioinfo.cli.kxml.node

Bases: k1lib.bioinfo.cli.init.BaseCli

Turns lines into a single node

__ror__(it: Iterator[str]) → Iterator[xml.etree.ElementTree.Element]

class k1lib.bioinfo.cli.kxml.maxDepth(depth: Optional[int] = None, copy: bool = True)

Bases: k1lib.bioinfo.cli.init.BaseCli

__init__(depth: Optional[int] = None, copy: bool = True)

Filters out too deep nodes

Parameters

• depth – max depth to include in

• copy – whether to limit the nodes itself, or limit a copy

__ror__(nodes: Iterator[xml.etree.ElementTree.Element]) → Iterator[xml.etree.ElementTree.Element]

class k1lib.bioinfo.cli.kxml.tag(tag: str)

Bases: k1lib.bioinfo.cli.init.BaseCli

__init__(tag: str)

Finds all tags that have a particular name. If found, then don’t search deeper

__ror__(nodes: Iterator[xml.etree.ElementTree.Element]) → Iterator[xml.etree.ElementTree.Element]

class k1lib.bioinfo.cli.kxml.pretty(indent: Optional[str] = None)

Bases: k1lib.bioinfo.cli.init.BaseCli

__ror__(it: Iterator[xml.etree.ElementTree.Element]) → Iterator[str]

class k1lib.bioinfo.cli.kxml.display(depth: int = 3, lines: int = 20)

Bases: k1lib.bioinfo.cli.init.BaseCli

__init__(depth: int = 3, lines: int = 20)

Convenience method for getting head, make it pretty and print it out

__ror__(it: Iterator[xml.etree.ElementTree.Element], lines=10)

modifier module

This is for quick modifiers, think of them as changing formats

class k1lib.bioinfo.cli.modifier.apply(f: Callable[[str], str], column: Optional[int] = None)

Bases: k1lib.bioinfo.cli.init.BaseCli

__init__(f: Callable[[str], str], column: Optional[int] = None)

Applies a function f to every line

Parameters

column – if not None, then applies the function to that column only

__ror__(it: Iterator[str])

k1lib.bioinfo.cli.modifier.lstrip(column: Optional[int] = None, char: Optional[str] = None)

Strips left of every line

k1lib.bioinfo.cli.modifier.rstrip(column: Optional[int] = None, char: Optional[str] = None)

Strips right of every line

k1lib.bioinfo.cli.modifier.strip(column: Optional[int] = None, char: Optional[str] = None)

Strips both sides of every line

k1lib.bioinfo.cli.modifier.upper(column: Optional[int] = None)

Make all characters uppercase

k1lib.bioinfo.cli.modifier.lower(column: Optional[int] = None)

Make all characters lowercase

k1lib.bioinfo.cli.modifier.replace(s: str, target: Optional[str] = None, column: Optional[int] = None)

Replaces substring s with target for each line.

k1lib.bioinfo.cli.modifier.remove(s: str, column: Optional[int] = None)

Removes a specific substring in each line.

k1lib.bioinfo.cli.modifier.toFloat(column: Optional[int] = None)

Converts every row into a float. Excludes non numbers if not in strict mode.

k1lib.bioinfo.cli.modifier.toInt(column: Optional[int] = None)

Converts every row into an integer. Excludes non numbers if not in strict mode.

class k1lib.bioinfo.cli.modifier.sort(column: int = 0, numeric=True, reverse=False)

Bases: k1lib.bioinfo.cli.init.BaseCli

__init__(column: int = 0, numeric=True, reverse=False)

Sorts all lines based on a specific column.

Parameters

• numeric – whether to treat column as float

• reverse – False for smaller to bigger, True for bigger to smaller. Use __invert__() to quickly reverse the order instead of using this param

__ror__(it: Iterator[str])

__invert__()

Creates a clone that has the opposite sort order

output module

For operations that feel like the termination

class k1lib.bioinfo.cli.output.file(fileName: str)

Bases: k1lib.bioinfo.cli.init.BaseCli

__ror__(it: Iterator[str]) → None

class k1lib.bioinfo.cli.output.pretty

Bases: k1lib.bioinfo.cli.init.BaseCli

Pretty prints a table

__ror__(it: k1lib.bioinfo.cli.init.MetaObj) → Iterator[str]

k1lib.bioinfo.cli.output.display(lines: int = 10)

Convenience method for displaying a table

k1lib.bioinfo.cli.output.headOut(lines: int = 10)

Convenience method for head() | stdout

sam module

This is for functions that are .sam or .bam related

k1lib.bioinfo.cli.sam.cat(bamFile: str)

Get sam file outputs from bam file

class k1lib.bioinfo.cli.sam.header(long=True)

Bases: k1lib.bioinfo.cli.init.BaseCli

__init__(long=True)

Adds a header to the table.

Parameters

long – whether to use a long descriptive header, or a short one

__ror__(it)

class k1lib.bioinfo.cli.sam.quality(log=True)

Bases: k1lib.bioinfo.cli.init.BaseCli

__init__(log=True)

Get numeric quality of sequence.

Parameters

log – whether to use log scale (0 -> 40), or linear scale (1 -> 0.0001)

__ror__(line)

structural module

This is for functions that sort of changes the table structure in a dramatic way. They’re the core transformations

class k1lib.bioinfo.cli.structural.joinColumns(fillValue=None)

Bases: k1lib.bioinfo.cli.init.BaseCli

__init__(fillValue=None)

Join multiple columns and loop through all rows. Aka transpose.

Parameters

fillValue – if not None, then will try to zip longest with this fill value

Example:

# returns [[1, 4], [2, 5], [3, 6]]
[[1, 2, 3], [4, 5, 6]] | joinColumns() | dereference()
# returns [[1, 4], [2, 5], [3, 6], [0, 7]]
[[1, 2, 3], [4, 5, 6, 7]] | joinColumns(0) | dereference()

__ror__(it: Iterator[Iterator[T]]) → k1lib.bioinfo.cli.init.MetaObj

k1lib.bioinfo.cli.structural.transpose

alias of k1lib.bioinfo.cli.structural.joinColumns

k1lib.bioinfo.cli.structural.splitColumns

alias of k1lib.bioinfo.cli.structural.joinColumns

class k1lib.bioinfo.cli.structural.joinList(element=None, begin=True)

Bases: k1lib.bioinfo.cli.init.BaseCli

__init__(element=None, begin=True)

Join element into list.

Parameters

element – the element to insert. If None, then takes the input [e, […]], else takes the input […] as usual

Example:

# returns [5, 2, 6, 8]
[5, [2, 6, 8]] | joinList()
# also returns [5, 2, 6, 8]
[2, 6, 8] | joinList(5)

__ror__(it: Tuple[T, Iterator[T]]) → Iterator[T]

class k1lib.bioinfo.cli.structural.joinStreams

Bases: k1lib.bioinfo.cli.init.BaseCli

Join multiple streams. Example:

# returns [1, 2, 3, 4, 5]
[[1, 2, 3], [4, 5]] | joinStreams() | dereference()

__ror__(streams: Iterator[Iterator[T]]) → Iterator[T]

k1lib.bioinfo.cli.structural.insertRow(*row: List[T])

Inserts a row right before every other rows. See also: joinList().

k1lib.bioinfo.cli.structural.insertColumn(*column, begin=True, fillValue='')

Inserts a column at beginning or end. Example:

# returns [['a', 1, 2], ['b', 3, 4]]
[[1, 2], [3, 4]] | insertColumn("a", "b") | dereference()

k1lib.bioinfo.cli.structural.insertIdColumn(table=False, begin=True, fillValue='')

Inserts an id column at the beginning (or end).

Parameters

table – if False, then insert column to an Iterator[str], else treat input as a full fledged table

Example:

# returns [[0, 'a', 2], [1, 'b', 4]]
[["a", 2], ["b", 4]] | insertIdColumn(True) | dereference()
# returns [[0, 'a'], [1, 'b']]
"ab" | insertIdColumn()

class k1lib.bioinfo.cli.structural.toDict(keyF: Optional[Callable[[Any], str]] = None, valueF: Optional[Callable[[Any], Any]] = None)

Bases: k1lib.bioinfo.cli.init.BaseCli

__init__(keyF: Optional[Callable[[Any], str]] = None, valueF: Optional[Callable[[Any], Any]] = None)

Transform an incoming stream into a dict using a function for values. Example:

names = ["wanda", "vision", "loki", "mobius"]
names | toDict(valueF=lambda s: len(s)) # will return {"wanda": 5, "vision": 6, ...}
names | toDict(lambda s: s.title(), lambda s: len(s)) # will return {"Wanda": 5, "Vision": 6, ...}

__ror__(keys: Iterator[Any]) → Dict[Any, Any]

class k1lib.bioinfo.cli.structural.split(delim: Optional[str] = None, idx: Optional[int] = None)

Bases: k1lib.bioinfo.cli.init.BaseCli

__init__(delim: Optional[str] = None, idx: Optional[int] = None)

Splits each line using a delimiter, and outputs the parts as a separate line.

Parameters

idx – if available, only outputs the element at that index

__ror__(it: Iterator[str])

class k1lib.bioinfo.cli.structural.table(delim: Optional[str] = None)

Bases: k1lib.bioinfo.cli.init.BaseCli

__init__(delim: Optional[str] = None)

Splits lines to rows (List[str]) using a delimiter. Example:

# returns [['a', 'bd'], ['1', '2', '3']]
["a|bd", "1|2|3"] | table("|") | dereference()

__ror__(it: Iterator[str]) → k1lib.bioinfo.cli.init.MetaObj

class k1lib.bioinfo.cli.structural.stitch(delim: Optional[str] = None)

Bases: k1lib.bioinfo.cli.init.BaseCli

__init__(delim: Optional[str] = None)

Stitches elements in a row together, so they become a simple string. See also: k1lib.bioinfo.cli.output.pretty

__ror__(it: k1lib.bioinfo.cli.init.MetaObj) → Iterator[str]

k1lib.bioinfo.cli.structural.listToTable()

Turns Iterator[T] into Table[T]

k1lib.bioinfo.cli.structural.tableFromList()

Turns Iterator[T] into Table[T]

class k1lib.bioinfo.cli.structural.count

Bases: k1lib.bioinfo.cli.init.BaseCli

Finds unique elements and returns a table with [frequency, value, percent] columns. Example:

# returns [[1, 'a', '33%'], [2, 'b', '67%']]
['a', 'b', 'b'] | count() | dereference()

__ror__(it: Iterator[str])

class k1lib.bioinfo.cli.structural.accumulate(columnIdx: int = 0, avg=False)

Bases: k1lib.bioinfo.cli.init.BaseCli

__init__(columnIdx: int = 0, avg=False)

Groups lines that have the same row[columnIdx], and add together all other columns, assuming they’re numbers

Parameters

• columnIdx – common column index to accumulate

• avg – calculate average values instead of sum

__ror__(it: Iterator[str])

class k1lib.bioinfo.cli.structural.AA_(*idxs: List[int], wraps=False)

Bases: k1lib.bioinfo.cli.init.BaseCli

__init__(*idxs: List[int], wraps=False)

Returns 2 streams, one that has the selected element, and the other the rest. Example:

[1, 5, 6, 3, 7] | AA_(1) # will return [5, [1, 6, 3, 7]]

You can also put multiple indexes through:

[1, 5, 6] | AA_(0, 2) # will return [[1, [5, 6]], [6, [1, 5]]]

If you put None in, then all indexes will be sliced:

[1, 5, 6] | AA_(0, 2)

# will return:
# [[1, [5, 6]],
#  [5, [1, 6]],
#  [6, [1, 5]]]

As for why the strange name, think of this operation as “AĀ”. In statistics, say you have a set “A”, then “not A” is commonly written as A with an overline “Ā”. So “AA_” represents “AĀ”, and that it first returns the selection A first.

Parameters

wraps – if True, then the first example will return [[5, [1, 6, 3, 7]]] instead, so that A has the same signature as Ā

__ror__(it: List[Any]) → List[List[List[Any]]]

class k1lib.bioinfo.cli.structural.sample

Bases: k1lib.bioinfo.cli.init.BaseCli

Returns (firstRow, iterator). This sort of peaks at the first row, to potentially gain some insights about the internal formats.

__ror__(it)

class k1lib.bioinfo.cli.structural.infinite

Bases: k1lib.bioinfo.cli.init.BaseCli

Yields an infinite amount of the passed in object. Example:

# returns [[1, 2, 3], [1, 2, 3], [1, 2, 3]]
[1, 2, 3] | infinite() | head(3) | toList()

__ror__(o: T) → Iterator[T]

utils module

This is for all short utilities that has the boilerplate feeling

class k1lib.bioinfo.cli.utils.size(idx=None)

Bases: k1lib.bioinfo.cli.init.BaseCli

__init__(idx=None)

Returns number of rows and columns in the input.

Parameters

idx – if idx is None return (rows, columns). If 0 or 1, then rows or columns

__ror__(it: Iterator[str])

k1lib.bioinfo.cli.utils.shape

alias of k1lib.bioinfo.cli.utils.size

class k1lib.bioinfo.cli.utils.item

Bases: k1lib.bioinfo.cli.init.BaseCli

Returns the first row

__ror__(it: Iterator[str])

class k1lib.bioinfo.cli.utils.identity

Bases: k1lib.bioinfo.cli.init.BaseCli

Yields whatever the input is. Useful for multiple streams

__ror__(it: Iterator[Any])

class k1lib.bioinfo.cli.utils.toStr

Bases: k1lib.bioinfo.cli.init.BaseCli

__init__()

Converts every line (possibly just a number) to a string.

__ror__(it: Iterator[str])

class k1lib.bioinfo.cli.utils.to1Str(delim: Optional[str] = None)

Bases: k1lib.bioinfo.cli.init.BaseCli

__init__(delim: Optional[str] = None)

Merges all strings into 1, with delim in the middle

__ror__(it: Iterator[str])

class k1lib.bioinfo.cli.utils.toNumpy

Bases: k1lib.bioinfo.cli.init.BaseCli

Converts generator to numpy array

__ror__(it: Iterator[float])

class k1lib.bioinfo.cli.utils.toList

Bases: k1lib.bioinfo.cli.init.BaseCli

Converts generator to list. list would do the same, but this is just to maintain the style

__ror__(it: Iterator[Any]) → List[Any]

class k1lib.bioinfo.cli.utils.wrapList

Bases: k1lib.bioinfo.cli.init.BaseCli

Wraps inputs inside a list

__ror__(it: Any) → List[Any]

class k1lib.bioinfo.cli.utils.toSet

Bases: k1lib.bioinfo.cli.init.BaseCli

Converts generator to set. set would do the same, but this is just to maintain the style

__ror__(it: Iterator[Any]) → Set[Any]

class k1lib.bioinfo.cli.utils.toIter

Bases: k1lib.bioinfo.cli.init.BaseCli

Converts object to iterator. iter() would do the same, but this is just to maintain the style

__ror__(it) → Iterator[Any]

class k1lib.bioinfo.cli.utils.toRange

Bases: k1lib.bioinfo.cli.init.BaseCli

Returns iter(range(len(it))), effectively

__ror__(it: Iterator[Any]) → Iterator[int]

class k1lib.bioinfo.cli.utils.equals

Bases: object

Checks if all incoming columns/streams are identical

__ror__(streams: Iterator[Iterator[str]])

class k1lib.bioinfo.cli.utils.reverse

Bases: k1lib.bioinfo.cli.init.BaseCli

Prints last line first, first line last

__ror__(it: Iterator[str]) → List[str]

class k1lib.bioinfo.cli.utils.ignore

Bases: k1lib.bioinfo.cli.init.BaseCli

Just executes everything, ignoring the output

__ror__(it: Iterator[Any])

class k1lib.bioinfo.cli.utils.toSum

Bases: k1lib.bioinfo.cli.init.BaseCli

Calculates the sum of list of numbers

__ror__(it: Iterator[float])

class k1lib.bioinfo.cli.utils.toAvg

Bases: k1lib.bioinfo.cli.init.BaseCli

Calculates average of list of numbers

__ror__(it: Iterator[float])

k1lib.bioinfo.cli.utils.headerIdx()

Cuts out first line, put an index column next to it, and prints it out. Useful when you want to know what your column’s index is to cut it out. Example:

# returns [[0, 'a'], [1, 'b'], [2, 'c']]
["abc"] | headerIdx() | dereference()

class k1lib.bioinfo.cli.utils.dereference

Bases: k1lib.bioinfo.cli.init.BaseCli

Recursively converts any iterator into a list. Only str, numbers.Number are not converted. Example:

iter(range(5)) # returns something like "<range_iterator at 0x7fa8c52ca870>"
iter(range(5)) | deference() # returns [0, 1, 2, 3, 4]

__ror__(it: Iterator[Any]) → List[Any]