From f0d2dbc52d9aab2684aff4ddec039c4d58a28587 Mon Sep 17 00:00:00 2001 From: sepandhaghighi Date: Tue, 19 Nov 2024 17:06:21 +0330 Subject: [PATCH 01/20] doc : TOC removed --- README.md | 14 -------------- 1 file changed, 14 deletions(-) diff --git a/README.md b/README.md index e87966f..52d64e4 100644 --- a/README.md +++ b/README.md @@ -18,20 +18,6 @@ ---------- -## Table of contents - -* [Overview](https://github.com/openscilab/opr#overview) -* [Installation](https://github.com/openscilab/opr#installation) -* [Usage](https://github.com/openscilab/opr#usage) -* [Issues & Bug Reports](https://github.com/openscilab/opr#issues--bug-reports) -* [Todo](https://github.com/openscilab/opr/blob/main/TODO.md) -* [Contribution](https://github.com/openscilab/opr/blob/main/.github/CONTRIBUTING.md) -* [Authors](https://github.com/openscilab/opr/blob/main/AUTHORS.md) -* [License](https://github.com/openscilab/opr/blob/main/LICENSE) -* [Show Your Support](https://github.com/openscilab/opr#show-your-support) -* [Changelog](https://github.com/openscilab/opr/blob/main/CHANGELOG.md) -* [Code of Conduct](https://github.com/openscilab/opr/blob/main/.github/CODE_OF_CONDUCT.md) - ## Overview

From 96bb93fab5a3d3de9473594ed6c645e64424f405 Mon Sep 17 00:00:00 2001 From: sepandhaghighi Date: Tue, 19 Nov 2024 17:15:11 +0330 Subject: [PATCH 02/20] doc : discord badge fixed --- README.md | 16 ++++------------ 1 file changed, 4 insertions(+), 12 deletions(-) diff --git a/README.md b/README.md index 52d64e4..7a13457 100644 --- a/README.md +++ b/README.md @@ -2,18 +2,10 @@

- - Codecov - - - PyPI version - - - built with Python3 - - - Discord Channel - + Codecov + PyPI version + built with Python3 + Discord Channel ---------- From 83bad556b362434ad851358ceaa613f4b6f5bfc5 Mon Sep 17 00:00:00 2001 From: sepandhaghighi Date: Tue, 19 Nov 2024 17:16:20 +0330 Subject: [PATCH 03/20] doc : pypi badge fixed --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 7a13457..e37a38b 100644 --- a/README.md +++ b/README.md @@ -3,7 +3,7 @@

Codecov - PyPI version + PyPI version built with Python3 Discord Channel From 2e90f3a3c118dda0f65e0ed0bc171c3b549779c3 Mon Sep 17 00:00:00 2001 From: sepandhaghighi Date: Tue, 19 Nov 2024 17:25:10 +0330 Subject: [PATCH 04/20] doc : logo added --- README.md | 4 ++-- otherfiles/logo.png | Bin 0 -> 19965 bytes 2 files changed, 2 insertions(+), 2 deletions(-) create mode 100644 otherfiles/logo.png diff --git a/README.md b/README.md index e37a38b..a4e37bc 100644 --- a/README.md +++ b/README.md @@ -1,8 +1,8 @@

- +

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TODO PyPI Counter - - + + @@ -28,7 +28,7 @@ OPR is an open source Python package that provides ... TODO Github Stars - + @@ -42,10 +42,10 @@ OPR is an open source Python package that provides ... TODO CI - + - + @@ -71,8 +71,8 @@ Just fill an issue and describe it. We'll check it ASAP! or send an email to [op You can also join our discord server - - Discord Channel + + Discord Channel From c59c5994a85f1de31d562ae1ac8e993a01ee3816 Mon Sep 17 00:00:00 2001 From: sepandhaghighi Date: Tue, 19 Nov 2024 18:31:30 +0330 Subject: [PATCH 06/20] doc : overview section updated --- README.md | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index bcceac6..18f2f52 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@
-
+

OPR: Optimized Primer


Codecov PyPI version @@ -13,7 +13,7 @@ ## Overview

-OPR is an open source Python package that provides ... TODO +OPR is an open-source Python package designed to simplify and streamline primer design and analysis for biologists and bioinformaticians. OPR enables users to design, validate, and optimize primers with ease, catering to a wide range of applications such as PCR, qPCR, and sequencing. With a focus on user-friendliness and efficiency, OPR aims to bridge the gap between biological research and computational tools, making primer-related workflows faster and more reliable.

@@ -54,7 +54,6 @@ OPR is an open source Python package that provides ... TODO ## Installation ### PyPI - - Check [Python Packaging User Guide](https://packaging.python.org/installing/) - Run `pip install opr==0.1` ### Source code From c89c4c20f5e36feb533c4a24099016b13450d4d5 Mon Sep 17 00:00:00 2001 From: sepandhaghighi Date: Tue, 19 Nov 2024 18:51:08 +0330 Subject: [PATCH 07/20] doc : usage section updated --- README.md | 42 +++++++++++++++++++++++++++++++++++++++++- 1 file changed, 41 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 18f2f52..fb5126b 100644 --- a/README.md +++ b/README.md @@ -62,6 +62,46 @@ OPR is an open-source Python package designed to simplify and streamline primer ## Usage +### Load +```pycon +>>> from opr import Primer +>>> primer1 = Primer(sequence="CTGGAGGACGGAAGAGGAAGTAA") +>>> primer1.sequence +'CTGGAGGACGGAAGAGGAAGTAA' +``` + +### Properties + +#### Molecular weight +```pycon +>>> primer1.molecular_weight +7235.79 +``` +#### GC content +```pycon +>>> primer1.gc_content +0.5217391304347826 +``` +#### Melting temperature +```pycon +>>> primer1.melting_temperature() +57.056521739130446 +``` +### Operations + +#### Reverse +```pycon +>>> primer1_reversed = primer1.reverse() +>>> primer1_reversed.sequence +'AATGAAGGAGAAGGCAGGAGGTC' +``` +#### Complement +```pycon +>>> primer1_complemented = primer1.complement() +>>> primer1_complemented.sequence +'GACCTCCTGCCTTCTCCTTCATT' +``` + ## Issues & bug reports Just fill an issue and describe it. We'll check it ASAP! or send an email to [opr@openscilab.com](mailto:opr@openscilab.com "opr@openscilab.com"). @@ -75,7 +115,7 @@ You can also join our discord server -## Show Your Support +## Show your support ### Star this repo From c5b13dcdf1f85501ca8e2df7f371371536516831 Mon Sep 17 00:00:00 2001 From: sepandhaghighi Date: Tue, 19 Nov 2024 18:54:42 +0330 Subject: [PATCH 08/20] doc : AUTHORS.md updated --- AUTHORS.md | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/AUTHORS.md b/AUTHORS.md index 683ee58..04e7641 100644 --- a/AUTHORS.md +++ b/AUTHORS.md @@ -1,12 +1,16 @@ # Core Developers - ---------- - Sepand Haghighi - Open Science Laboratory ([Github](https://github.com/sepandhaghighi)) ** - AmirHosein Rostami - Open Science Laboratory ([Github](https://github.com/AHReccese)) ** - Sadra Sabouri - Open Science Laboratory ([Github](https://github.com/sadrasabouri)) +- Mojtaba Moghadam - University of Zanjan ([Github](https://github.com/mojtaba-moghadam) ** **Maintainer** # Other Contributors ---------- +- [@boreshnavard](https://github.com/boreshnavard) ++ + + +++ **Graphic designer** From 3778c86d52d38bac09f18daf0e4edc1c6b25288d Mon Sep 17 00:00:00 2001 From: sepandhaghighi Date: Tue, 19 Nov 2024 19:00:07 +0330 Subject: [PATCH 09/20] fix : setup.py updated --- setup.py | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/setup.py b/setup.py index 7377a85..dae3664 100644 --- a/setup.py +++ b/setup.py @@ -23,7 +23,7 @@ def read_description(): description += c.read() return description except Exception: - return '''TODO''' + return '''OPR is an open-source Python package designed to simplify and streamline primer design and analysis for biologists and bioinformaticians. OPR enables users to design, validate, and optimize primers with ease, catering to a wide range of applications such as PCR, qPCR, and sequencing. With a focus on user-friendliness and efficiency, OPR aims to bridge the gap between biological research and computational tools, making primer-related workflows faster and more reliable.''' setup( @@ -31,7 +31,7 @@ def read_description(): packages=[ 'opr', ], version='0.1', - description='TODO', + description='OPR: Optimized Primer', long_description=read_description(), long_description_content_type='text/markdown', author='OPR Development Team', @@ -46,7 +46,6 @@ def read_description(): python_requires='>=3.6', classifiers=[ 'Development Status :: 3 - Alpha', - 'Intended Audience :: Developers', 'Natural Language :: English', 'License :: OSI Approved :: MIT License', 'Operating System :: OS Independent', @@ -63,13 +62,12 @@ def read_description(): 'Intended Audience :: End Users/Desktop', 'Intended Audience :: Manufacturing', 'Intended Audience :: Science/Research', - 'Topic :: Scientific/Engineering :: Information Analysis', 'Topic :: Education', 'Topic :: Scientific/Engineering', + 'Topic :: Scientific/Engineering :: Information Analysis', 'Topic :: Scientific/Engineering :: Artificial Intelligence', - 'Topic :: Scientific/Engineering :: Human Machine Interfaces', 'Topic :: Scientific/Engineering :: Mathematics', - 'Topic :: Scientific/Engineering :: Physics', + 'Topic :: Scientific/Engineering :: Bio-Informatics', ], license='MIT', ) From 09097422fbcaa5f96f35197ff7b1ea4798f3d6c2 Mon Sep 17 00:00:00 2001 From: sepandhaghighi Date: Tue, 19 Nov 2024 19:00:58 +0330 Subject: [PATCH 10/20] doc : logo size updated --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index fb5126b..8f2a983 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,5 @@
- +

OPR: Optimized Primer


Codecov From 32abe920942407bffbea17fb9871238156fed2dd Mon Sep 17 00:00:00 2001 From: sepandhaghighi Date: Tue, 19 Nov 2024 19:18:50 +0330 Subject: [PATCH 11/20] doc : references section added --- README.md | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/README.md b/README.md index 8f2a983..2505595 100644 --- a/README.md +++ b/README.md @@ -114,6 +114,16 @@ You can also join our discord server Discord Channel +## References + +
1- Oligo Calc: Oligonucleotide Properties Calculator
+ +
2- Marmur, Julius, and Paul Doty. "Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature." Journal of molecular biology 5.1 (1962): 109-118.
+ +
3- Wallace, R. Bruce, et al. "Hybridization of synthetic oligodeoxyribonucleotides to Φ X 174 DNA: the effect of single base pair mismatch." Nucleic acids research 6.11 (1979): 3543-3558.
+ +
4- Panjkovich, Alejandro, and Francisco Melo. "Comparison of different melting temperature calculation methods for short DNA sequences." Bioinformatics 21.6 (2005): 711-722.
+ ## Show your support From bf7464893ec866e3e529aab8759ca1008511bd18 Mon Sep 17 00:00:00 2001 From: sepandhaghighi Date: Tue, 19 Nov 2024 19:45:22 +0330 Subject: [PATCH 12/20] doc : Logo link fixed --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 2505595..0f2d2ec 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,5 @@
- +

OPR: Optimized Primer


Codecov From b6fb8f7d1a3fb6a25c69b6dc7fe87ced5ecf017f Mon Sep 17 00:00:00 2001 From: sepandhaghighi Date: Tue, 19 Nov 2024 19:48:15 +0330 Subject: [PATCH 13/20] fix : setup.py tags updated --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index dae3664..dc9e256 100644 --- a/setup.py +++ b/setup.py @@ -38,7 +38,7 @@ def read_description(): author_email='opr@openscilab.com', url='https://github.com/openscilab/opr', download_url='https://github.com/openscilab/opr/tarball/v0.1', - keywords="python3 python machine_learning ML", + keywords="primer biology bioinformatics genome dna", project_urls={ 'Source': 'https://github.com/openscilab/opr', }, From c87a80d7aa792483f214b7cc744e40db2a01e293 Mon Sep 17 00:00:00 2001 From: sepandhaghighi Date: Tue, 19 Nov 2024 19:50:07 +0330 Subject: [PATCH 14/20] doc : CHANGELOG.md updated --- CHANGELOG.md | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 1673157..3ee76b9 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,9 +5,7 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html). ## [Unreleased] -### Added -### Changed -## [0.1] - 2024-06-05 +## [0.1] - 2024-11-xx ### Added - `MeltingTemperature` enum - Basic melting temperature calculation From 09d183abd91e130c4d0cc17f002ceb01a5c43203 Mon Sep 17 00:00:00 2001 From: sepandhaghighi Date: Tue, 19 Nov 2024 19:54:53 +0330 Subject: [PATCH 15/20] doc : meta.yaml updated --- otherfiles/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/otherfiles/meta.yaml b/otherfiles/meta.yaml index b8194c8..89fbc91 100644 --- a/otherfiles/meta.yaml +++ b/otherfiles/meta.yaml @@ -24,7 +24,7 @@ about: license_family: MIT summary: Python library for machine learning input and output description: | - OPR is an open source Python package that provides... TODO + OPR is an open-source Python package designed to simplify and streamline primer design and analysis for biologists and bioinformaticians. OPR enables users to design, validate, and optimize primers with ease, catering to a wide range of applications such as PCR, qPCR, and sequencing. With a focus on user-friendliness and efficiency, OPR aims to bridge the gap between biological research and computational tools, making primer-related workflows faster and more reliable. Website: https://openscilab.com From ba744bf68c49d3e5541bbdb38c1df9940b5fea7f Mon Sep 17 00:00:00 2001 From: sepandhaghighi Date: Tue, 19 Nov 2024 19:57:13 +0330 Subject: [PATCH 16/20] fix : minor space bug in README.md fixed --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 0f2d2ec..6196d6b 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@
-

OPR: Optimized Primer

+

OPR: Optimized Primer


Codecov PyPI version From 75d87f95bb1b9b2de9ff4b19f441ee88ac3a959c Mon Sep 17 00:00:00 2001 From: sepandhaghighi Date: Tue, 19 Nov 2024 20:34:40 +0330 Subject: [PATCH 17/20] fix : setup.py tags updated --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index dc9e256..8e7be5f 100644 --- a/setup.py +++ b/setup.py @@ -38,7 +38,7 @@ def read_description(): author_email='opr@openscilab.com', url='https://github.com/openscilab/opr', download_url='https://github.com/openscilab/opr/tarball/v0.1', - keywords="primer biology bioinformatics genome dna", + keywords="primer biology bioinformatics genome dna pcr", project_urls={ 'Source': 'https://github.com/openscilab/opr', }, From 0c07e5c6d2c1c9b75ba25c90a28142ec10ea11a5 Mon Sep 17 00:00:00 2001 From: sepandhaghighi Date: Tue, 19 Nov 2024 20:54:08 +0330 Subject: [PATCH 18/20] doc : minor edit in AUTHORS.md --- AUTHORS.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/AUTHORS.md b/AUTHORS.md index 04e7641..9805200 100644 --- a/AUTHORS.md +++ b/AUTHORS.md @@ -3,7 +3,7 @@ - Sepand Haghighi - Open Science Laboratory ([Github](https://github.com/sepandhaghighi)) ** - AmirHosein Rostami - Open Science Laboratory ([Github](https://github.com/AHReccese)) ** - Sadra Sabouri - Open Science Laboratory ([Github](https://github.com/sadrasabouri)) -- Mojtaba Moghadam - University of Zanjan ([Github](https://github.com/mojtaba-moghadam) +- Mojtaba Moghadam - University of Zanjan ([Github](https://github.com/mojtaba-moghadam)) ** **Maintainer** From eb7c835f6e81564de25c8992072a40f8ecf408b0 Mon Sep 17 00:00:00 2001 From: sepandhaghighi Date: Tue, 19 Nov 2024 21:00:35 +0330 Subject: [PATCH 19/20] doc : bold OPR --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 6196d6b..fb2c1df 100644 --- a/README.md +++ b/README.md @@ -13,7 +13,7 @@ ## Overview

-OPR is an open-source Python package designed to simplify and streamline primer design and analysis for biologists and bioinformaticians. OPR enables users to design, validate, and optimize primers with ease, catering to a wide range of applications such as PCR, qPCR, and sequencing. With a focus on user-friendliness and efficiency, OPR aims to bridge the gap between biological research and computational tools, making primer-related workflows faster and more reliable. +**OPR** is an open-source Python package designed to simplify and streamline primer design and analysis for biologists and bioinformaticians. **OPR** enables users to design, validate, and optimize primers with ease, catering to a wide range of applications such as PCR, qPCR, and sequencing. With a focus on user-friendliness and efficiency, **OPR** aims to bridge the gap between biological research and computational tools, making primer-related workflows faster and more reliable.

From cbd77abf32aeb05d270338c805bd2cfe1dfc2c52 Mon Sep 17 00:00:00 2001 From: sepandhaghighi Date: Tue, 19 Nov 2024 21:24:21 +0330 Subject: [PATCH 20/20] doc : bold OPR fixed --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index fb2c1df..d36c297 100644 --- a/README.md +++ b/README.md @@ -13,7 +13,7 @@ ## Overview

-**OPR** is an open-source Python package designed to simplify and streamline primer design and analysis for biologists and bioinformaticians. **OPR** enables users to design, validate, and optimize primers with ease, catering to a wide range of applications such as PCR, qPCR, and sequencing. With a focus on user-friendliness and efficiency, **OPR** aims to bridge the gap between biological research and computational tools, making primer-related workflows faster and more reliable. +OPR is an open-source Python package designed to simplify and streamline primer design and analysis for biologists and bioinformaticians. OPR enables users to design, validate, and optimize primers with ease, catering to a wide range of applications such as PCR, qPCR, and sequencing. With a focus on user-friendliness and efficiency, OPR aims to bridge the gap between biological research and computational tools, making primer-related workflows faster and more reliable.