PatternCounter#

Features#

This tool allows to count patterns in lists of sequential groups using rules and variables.

For the following examples, consider the following file (sequences.txt):

A -1 -2
B -1 -2
A B -1 -2
A -1 B C -1 -2
B -1 A B -1 A -1 C -1 -2

Example 1: Count how many sequences contain both the elements A and B:

$ patterncounter count "A B" -n -f sequences.txt
Supp((A B)) = 0.6 | 3 lines: 2, 3, 4

Example 2: Count how many sequences contain elements A and B at the same group:

$ patterncounter count "A & B" -n -f sequences.txt
Supp(A & B) = 0.4 | 2 lines: 2, 4

Example 3: Count how many sequences have an element B that after after A:

$ patterncounter count "A -> B" -n -f sequences.txt
Supp(A -> B) = 0.2 | 1 lines: 3

Example 4: Count in how many sequences the element B was removed within an interval of A:

$ patterncounter count "[A OutB]" -n -f sequences.txt
Supp([A OutB]) = 0.2 | 1 lines: 4

Example 5: Count in how many sequences there is an element C that occurs after an interval of A:

$ patterncounter count "[A] -> C" -n -f sequences.txt
Supp([A] -> C) = 0.4 | 2 lines: 3, 4

Example 6: Show results even when the pattern does not exist:

$ patterncounter count "Z" -n -f sequences.txt -z
Supp(Z) = 0.0 | 0 lines

In addition to using simple rules, it is possible to define multiple rules and calculated association rules metrics among them:

Example 7: Count both how many sequences have an interval of A, and how many sequences have an interval of A with an element B inside:

$ patterncounter count "[A]" "[A B]" -n -f sequences.txt
Supp([A], [A B]) = 0.4 | 2 lines: 2, 4
Association Rule: [A] ==> [A B]
  Supp([A]) = 0.8 | 4 lines: 0, 2, 3, 4
  Supp([A B]) = 0.4 | 2 lines: 2, 4
  Conf = 0.5
  Lift = 1.25
Association Rule: [A B] ==> [A]
  Supp([A B]) = 0.4 | 2 lines: 2, 4
  Supp([A]) = 0.8 | 4 lines: 0, 2, 3, 4
  Conf = 1.0
  Lift = 1.25

It is also possible to define variables.

Example 8: Count how many sequences have groups with two distinct elements:

$ patterncounter count "x & y" -v "x" -v "y" -n -f sequences.txt -z
Supp(x & y) = 0.6 | 3 lines: 2, 3, 4

[BINDING: x = B; y = A]
  Supp(B & A) = 0.4 | 2 lines: 2, 4

[BINDING: x = A; y = B]
  Supp(A & B) = 0.4 | 2 lines: 2, 4

[BINDING: x = B; y = C]
  Supp(B & C) = 0.2 | 1 lines: 3

[BINDING: x = A; y = C]
  Supp(A & C) = 0.0 | 0 lines

[BINDING: x = C; y = B]
  Supp(C & B) = 0.2 | 1 lines: 3

[BINDING: x = C; y = A]
  Supp(C & A) = 0.0 | 0 lines

Note that the result first shows the combined metrics (union).

Finally, given a file of sequences, it is also possible to select its lines (0-indexes):

$ patterncounter select -f sequences.txt -n 4
A -1 -2
A B -1 -2
B -1 A B -1 A -1 C -1 -2

Installation#

You can install PatternCounter via pip from PyPI:

$ pip install patterncounter

Usage#

Please see the Command-line Reference for details.

Contributing#

Contributions are very welcome. To learn more, see the Contributor Guide.

License#

Distributed under the terms of the MIT license, PatternCounter is free and open source software.

Issues#

If you encounter any problems, please file an issue along with a detailed description.

Credits#

This project was generated from @cjolowicz’s Hypermodern Python Cookiecutter template.

Usage#

patterncounter#

PatternCounter. This tool counts patterns from lists of sequences.

patterncounter [OPTIONS] COMMAND [ARGS]...

Options

--version#: Show the version and exit.

convert#

Convert spmf dictionary to sequence list.

patterncounter convert [OPTIONS]

Options

-l, --line-sep <line_sep>#: line separator

-i, --interval-sep <interval_sep>#: interval separator

-e, --element-sep <element_sep>#: element separator

-r, --remove <remove>#: remove elements that start with prefix

-f, --file <file>#: load input from file

-s, --stop-on-failures#: stop on failures

count#

Count patterns in file.

patterncounter count [OPTIONS] [PATTERN_DEFINITIONS]...

Options

-l, --line-sep <line_sep>#: line separator

-i, --interval-sep <interval_sep>#: interval separator

-e, --element-sep <element_sep>#: element separator

--in-prefix <in_prefix>#: prefix that is added to elements when they enter a slice

--out-prefix <out_prefix>#: prefix that is added to elements when they exit a slice

-z, --show-support-zero#: show rule when support is zero

-b, --hide-bindings#: hide bindings

-n, --line-number#: show line numbers

-t, --line-text#: show line text

-f, --file <file>#: load input from file

-c, --csv#: display result as csv

Arguments

PATTERN_DEFINITIONS#: Optional argument(s)

select#

Select lines from file.

patterncounter select [OPTIONS] [LINES]...

Options

-l, --line-sep <line_sep>#: line separator

-f, --file <file>#: load input from file

-n, --line-number#: show line numbers

Arguments

LINES#: Optional argument(s)

show#

Show sequence list with In and Out.

patterncounter show [OPTIONS]

Options

-l, --line-sep <line_sep>#: line separator

-i, --interval-sep <interval_sep>#: interval separator

-e, --element-sep <element_sep>#: element separator

--in-prefix <in_prefix>#: prefix that is added to elements when they enter a slice

--out-prefix <out_prefix>#: prefix that is added to elements when they exit a slice

-n, --line-number#: show line numbers

-f, --file <file>#: load input from file

Rules#

This document defines the syntax of the pattern rules. There are 4 types of constructs in the syntax: Elements, Unary Operators, Binary Operators, and Groups.

Elements#

To define a pattern with elements, just write the element name. For instance to find the element A, the rule is just A. Suppose the sequence A ... A B ... C D ... A, this rule matches the first, second, and last groups.

In addition to simple elements, it is possible to find the group where the element was inserted. In this case, the rule that matches the insertion of an element A is InA. Suppose the sequence A ... A B ... C D ... A, this rule matches the first and last groups.

Similarly, it is possible to find the first group that the element does not appear anymore after appearing once. In this case, the rule that matches the removal of an element A is OutA. Suppose the sequence A ... A B ... C D ... A, this rule matches the third group.

Summary:

Element: A
Insertion: InA
Removal: OutA

Unary Operators#

Unary operators can be applied to rules. Currently, three operators are supported: First (^), Last ($), and Not (~).

The operator First (^) makes the rule only match if it is at the beginning of the sequence. The rule ^A only matches the first group in the sequence A ... A B ... C D ... A.

The operator Last ($) is similar, but it only matches at the end of the sequence. The rule $A only matches the last group in the sequence A ... A B ... C D ... A.

The operator Not (~) inverts matches. The rul ~A does not match the sequence A ... A B ... C D ... A, because A has at least one match. Howerver ~E matches the sequence.

Summary:

First: ^A
Last: $A
Not: ~A

Binary Operators#

Binary operators apply to sets of rules. Currently, five operators are supported: And ( ), Intersect (&), Or (|), Sequence (->), LooseSequence (=>).

Every rule separated by space is treated as using the And operator. Hence, the rule A C matches the sequence A ... A B ... C D ... A. Note that the individual rules do not need to match in the same group: C matches the third group, while A matches the other. Since, both rules matches the sequence, A C also matches it. However, rules such as A E or A $C do not match the sequence.

If you want to match the rule at the same position, it is possible to use the Intersect operator (&). In this case, A & B matches only the second group of the sequence A ... A B ... C D ... A.

The operator Or (|) matches the sequence if either one of its subrules matches the sequence. The rule E | C matches the sequence A ... A B ... C D ... A because C matches it, even though E does not match it.

The Sequence operator (->) only matches the sequence when the second rule appears after the first one. The rule A -> C matches A ... A B ... C D ... A because C appears after a group that contains A. Note that C -> D does not match the sequence, since C and D are on the same group. However, A -> B matches the sequence because A matches at least a group in the sequence (the first) that appears before B.

The LooseSequence operator (=>) allows to match elements as “sequence” when they are also on the same groups. It matches everythin that the Sequence operator matches in addition to the same-group situations. In this case, C => D matches the sequence A ... A B ... C D ... A. The order within the same group does not matter. Hence, D => C also matches the sequence.

Summary:

And: A B C
Intersect: A & B
Or: A | B
Sequence: A -> B
LooseSequence: A => B

Groups#

Finally, the last type of construct in the rules are groups. There are two types of groups: Parentheses (()) and Slices ([], {}, [}, {]).

Parentheses allow nesting operators and building complex rules without worrying about operator precedences. For instance, the rule (E | C) -> A matches the sequence A ... A B ... C D ... A because it first evaluates (E | C) and founds that C matches the sequence, and then it found that C -> A matches the sequence. Parentheses with internal rules can be used in place of any other rule.

Slices matches sequential groups in the sequence. The rule [A] matches the first two groups of the A ... A B ... C D ... A and the last group too (slices can have size 1). In this simple form, the slice is not much more interesting than element rules. However, slices also allow finding rules within them. The rule [A B] matches the sequence because it finds a slice of A that contains B as well.

Is it possible to have complex rules with slices. For instance the rule [A $B ~C] matches a slice that does not have C and that ends with B. Hence, it matches the sequence A ... A B ... C D ... A. Note that the within slices, the unary operators refer to the slice groups. Hence ^ matches the first element of the slice, $ matches the last, and ~ only considers the slice in the negative.

Square bracket slices consider all of the groups of the slices. It is also possible to match “open” slices using braces. The rule {A B] only matches slices of A that contain B in a position that is not the first. Similarly, the rule [A B} matches slices of A that contain B in a position that is not the last. Finally, the rule {A B} matches slices of A that contain B in a position that is neither the first nor the last.

Summary:

Parenthesis: (A B)
Closed slice: [A B]
Left-open slice: {A B]
Right-open slice: [A B}
Open slice: {A B}

Variables#

This document describes the syntax of variable definitions (argument -v of command line).

There are three types of variable definitions:

Simple (-v "X"): If you just define the name of the variable, the tool will try to bind it to all names that appear in your input file
Exclusive (-v "X~A,B"): If you define a list of comma-separated elements after ~, the tool will try to bind the variable to all names that appear in your input file, except the ones on the list
Inclusive (-v "X:A,B"): If you define a list of comma-separated elements after :, the tool will only bind the variable to the elements you defined.

It is not necessary to define In and Out variables. If you have a variable X bound to Element, not only the rule X will match Element, but the rule InX will match InElement and the rule OutX will match OutElement.

Reference#

patterncounter#

Pattern Counter.

patterncounter.parse(text)#

Parses text and returns a Rule.

Parameters: text (str) –
Return type: Rule

Contributor Guide#

Thank you for your interest in improving this project. This project is open-source under the MIT license and welcomes contributions in the form of bug reports, feature requests, and pull requests.

Here is a list of important resources for contributors:

How to report a bug#

Report bugs on the Issue Tracker.

When filing an issue, make sure to answer these questions:

Which operating system and Python version are you using?
Which version of this project are you using?
What did you do?
What did you expect to see?
What did you see instead?

The best way to get your bug fixed is to provide a test case, and/or steps to reproduce the issue.

How to request a feature#

Request features on the Issue Tracker.

How to set up your development environment#

You need Python 3.8+ and the following tools:

Install the package with development requirements:

$ poetry install

You can now run an interactive Python session, or the command-line interface:

$ poetry run python
$ poetry run patterncounter

How to test the project#

Run the full test suite:

$ nox

List the available Nox sessions:

$ nox --list-sessions

You can also run a specific Nox session. For example, invoke the unit test suite like this:

$ nox --session=tests

Unit tests are located in the tests directory, and are written using the pytest testing framework.

How to submit changes#

Open a pull request to submit changes to this project.

Your pull request needs to meet the following guidelines for acceptance:

The Nox test suite must pass without errors and warnings.
Include unit tests. This project maintains 100% code coverage.
If your changes add functionality, update the documentation accordingly.

Feel free to submit early, though—we can always iterate on this.

To run linting and code formatting checks before committing your change, you can install pre-commit as a Git hook by running the following command:

$ nox --session=pre-commit -- install

It is recommended to open an issue before starting work on anything. This will allow a chance to talk it over with the owners and validate your approach.

Contributor Covenant Code of Conduct#

Our Pledge#

We as members, contributors, and leaders pledge to make participation in our community a harassment-free experience for everyone, regardless of age, body size, visible or invisible disability, ethnicity, sex characteristics, gender identity and expression, level of experience, education, socio-economic status, nationality, personal appearance, race, caste, color, religion, or sexual identity and orientation.

We pledge to act and interact in ways that contribute to an open, welcoming, diverse, inclusive, and healthy community.

Our Standards#

Examples of behavior that contributes to a positive environment for our community include:

Demonstrating empathy and kindness toward other people
Being respectful of differing opinions, viewpoints, and experiences
Giving and gracefully accepting constructive feedback
Accepting responsibility and apologizing to those affected by our mistakes, and learning from the experience
Focusing on what is best not just for us as individuals, but for the overall community

Examples of unacceptable behavior include:

The use of sexualized language or imagery, and sexual attention or advances of any kind
Trolling, insulting or derogatory comments, and personal or political attacks
Public or private harassment
Publishing others’ private information, such as a physical or email address, without their explicit permission
Other conduct which could reasonably be considered inappropriate in a professional setting

Enforcement Responsibilities#

Community leaders are responsible for clarifying and enforcing our standards of acceptable behavior and will take appropriate and fair corrective action in response to any behavior that they deem inappropriate, threatening, offensive, or harmful.

Community leaders have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, and will communicate reasons for moderation decisions when appropriate.

Scope#

This Code of Conduct applies within all community spaces, and also applies when an individual is officially representing the community in public spaces. Examples of representing our community include using an official e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event.

Enforcement#

Instances of abusive, harassing, or otherwise unacceptable behavior may be reported to the community leaders responsible for enforcement at joaofelipenp@gmail.com. All complaints will be reviewed and investigated promptly and fairly.

All community leaders are obligated to respect the privacy and security of the reporter of any incident.

Enforcement Guidelines#

Community leaders will follow these Community Impact Guidelines in determining the consequences for any action they deem in violation of this Code of Conduct:

1. Correction#

Community Impact: Use of inappropriate language or other behavior deemed unprofessional or unwelcome in the community.

Consequence: A private, written warning from community leaders, providing clarity around the nature of the violation and an explanation of why the behavior was inappropriate. A public apology may be requested.

2. Warning#

Community Impact: A violation through a single incident or series of actions.

Consequence: A warning with consequences for continued behavior. No interaction with the people involved, including unsolicited interaction with those enforcing the Code of Conduct, for a specified period of time. This includes avoiding interactions in community spaces as well as external channels like social media. Violating these terms may lead to a temporary or permanent ban.

3. Temporary Ban#

Community Impact: A serious violation of community standards, including sustained inappropriate behavior.

Consequence: A temporary ban from any sort of interaction or public communication with the community for a specified period of time. No public or private interaction with the people involved, including unsolicited interaction with those enforcing the Code of Conduct, is allowed during this period. Violating these terms may lead to a permanent ban.

4. Permanent Ban#

Community Impact: Demonstrating a pattern of violation of community standards, including sustained inappropriate behavior, harassment of an individual, or aggression toward or disparagement of classes of individuals.

Consequence: A permanent ban from any sort of public interaction within the community.

Attribution#

This Code of Conduct is adapted from the Contributor Covenant, version 2.1, available at https://www.contributor-covenant.org/version/2/1/code_of_conduct.html.

Community Impact Guidelines were inspired by Mozilla’s code of conduct enforcement ladder.

For answers to common questions about this code of conduct, see the FAQ at https://www.contributor-covenant.org/faq. Translations are available at https://www.contributor-covenant.org/translations.

License#

MIT License

Copyright © 2022 Joao Felipe Pimentel

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.