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Update README.md
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3 changes: 3 additions & 0 deletions README.md
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# project_spring_2020

[![CircleCI](https://circleci.com/gh/biof309/project_spring_2020/tree/master.svg?style=shield)](https://circleci.com/gh/biof309/project_spring_2020/tree/master)

This package aims to calculate the volume of samples needed to get 700 ng of DNA after measurment of these samples using the nanodrop
The input file is a modified csv file (obtained directly fron the Nanodrop) where only the samples of interest are kept
28 changes: 28 additions & 0 deletions get_volumes/Data.csv
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 ID,Sample Time,Type,Conc.,Units,Factor,A260 (10 mm),A280 (10 mm),A3rd (10 mm),A260/A280,BlankTime,Calibration Time,Note,Diagnostic Code
1,18/03/2020 10:42,dsDNA,10,ng/µl,50,0.199,0.121,0.036,1.64,18/03/2020 10:42,01/01/2010 00:00,,0x00000000
2,18/03/2020 10:42,dsDNA,10.1,ng/µl,50,0.202,0.124,0.044,1.62,18/03/2020 10:42,01/01/2010 00:00,,0x00000000
3,18/03/2020 10:43,dsDNA,12.2,ng/µl,50,0.245,0.146,0.043,1.68,18/03/2020 10:42,01/01/2010 00:00,,0x00000000
4,18/03/2020 10:43,dsDNA,13.4,ng/µl,50,0.268,0.161,0.047,1.66,18/03/2020 10:42,01/01/2010 00:00,,0x00000000
5,18/03/2020 10:43,dsDNA,10.8,ng/µl,50,0.216,0.145,0.018,1.49,18/03/2020 10:42,01/01/2010 00:00,,0x00000000
6,18/03/2020 10:43,dsDNA,10.8,ng/µl,50,0.216,0.134,0.041,1.61,18/03/2020 10:42,01/01/2010 00:00,,0x00000000
7,18/03/2020 10:44,dsDNA,13.7,ng/µl,50,0.274,0.151,0.024,1.82,18/03/2020 10:42,01/01/2010 00:00,,0x00000000
8,18/03/2020 10:44,dsDNA,14.8,ng/µl,50,0.297,0.16,0.012,1.86,18/03/2020 10:42,01/01/2010 00:00,,0x00000000
9,18/03/2020 10:44,dsDNA,15.3,ng/µl,50,0.306,0.172,0.014,1.78,18/03/2020 10:42,01/01/2010 00:00,,0x00000000
10,18/03/2020 10:44,dsDNA,20.8,ng/µl,50,0.416,0.224,0.013,1.86,18/03/2020 10:42,01/01/2010 00:00,,0x00000000
11,18/03/2020 10:45,dsDNA,7.1,ng/µl,50,0.143,0.083,0.037,1.72,18/03/2020 10:42,01/01/2010 00:00,,0x00000000
12,18/03/2020 10:45,dsDNA,7.7,ng/µl,50,0.154,0.091,0.028,1.68,18/03/2020 10:42,01/01/2010 00:00,,0x00000000
13,18/03/2020 10:45,dsDNA,9.5,ng/µl,50,0.19,0.132,0.086,1.43,18/03/2020 10:42,01/01/2010 00:00,,0x00000000
14,18/03/2020 10:46,dsDNA,8.9,ng/µl,50,0.177,0.104,0.011,1.71,18/03/2020 10:42,01/01/2010 00:00,,0x00000000
15,18/03/2020 10:46,dsDNA,8.1,ng/µl,50,0.162,0.081,-0.031,2.01,18/03/2020 10:42,01/01/2010 00:00,,0x00000000
16,18/03/2020 10:46,dsDNA,10.2,ng/µl,50,0.204,0.128,0.016,1.6,18/03/2020 10:42,01/01/2010 00:00,,0x00000000
17,18/03/2020 10:46,dsDNA,10.4,ng/µl,50,0.207,0.136,0.048,1.53,18/03/2020 10:42,01/01/2010 00:00,,0x00000000
18,18/03/2020 10:46,dsDNA,4.7,ng/µl,50,0.093,0.09,-0.432,1.03,18/03/2020 10:42,01/01/2010 00:00,,0x00000000
19,18/03/2020 10:47,dsDNA,12,ng/µl,50,0.24,0.131,0.012,1.83,18/03/2020 10:42,01/01/2010 00:00,,0x00000000
20,18/03/2020 10:47,dsDNA,15.3,ng/µl,50,0.305,0.168,0.031,1.82,18/03/2020 10:42,01/01/2010 00:00,,0x00000000
,18/03/2020 10:47,Blank,,,,,,,,,01/01/2010 00:00,,0x00000000
21,18/03/2020 10:48,dsDNA,775,ng/µl,50,15.499,8.283,0.031,1.87,18/03/2020 10:47,01/01/2010 00:00,,0x00000000
22,18/03/2020 10:48,dsDNA,777.4,ng/µl,50,15.548,8.308,0.034,1.87,18/03/2020 10:47,01/01/2010 00:00,,0x00000000
23,18/03/2020 10:48,dsDNA,784.8,ng/µl,50,15.696,8.386,0.041,1.87,18/03/2020 10:47,01/01/2010 00:00,,0x00000000
24,18/03/2020 10:48,dsDNA,1925.6,ng/µl,50,38.512,22.107,0.024,1.74,18/03/2020 10:47,01/01/2010 00:00,,0x00000000
25,18/03/2020 10:48,dsDNA,1916.3,ng/µl,50,38.327,21.934,0.022,1.75,18/03/2020 10:47,01/01/2010 00:00,,0x00000000
26,18/03/2020 10:48,dsDNA,1925.8,ng/µl,50,38.516,22.093,0.023,1.74,18/03/2020 10:47,01/01/2010 00:00,,0x00000000
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9 changes: 9 additions & 0 deletions get_volumes/core_function.py
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import pandas as pd
def get_volumes(input):
data = pd.read_csv(input) #if UnicodeDecodeError open csv file in Sublime Text and Save with UTF-8 encoding
data.head()
clean_data = data.copy()[['Sample Time','Type', 'Conc.']]
clean_data.head()
clean_data["Volume"] = 700/clean_data["Conc."]
clean_data.head()
return clean_data
1 change: 0 additions & 1 deletion project_spring_2020/sample_file.py
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25 changes: 25 additions & 0 deletions setup.py
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import setuptools
from pathlib import Path

with open("README.md", "r") as fh:
long_description = fh.read()

setuptools.setup(
name="get_volumes",
version="0.0.1",
author="Damien Ferhadian",
author_email="[email protected]",
description="Calculate the volume of sample needed to get a certain amount of DNA to do a qPCR after Nanodrop measurement",
long_description=long_description,
long_description_content_type="text/markdown",
url="https://github.com/dferhadian/-project_spring_2020/tree/master/get_volumes",
packages=setuptools.find_packages(),
scripts = ['get_volumes/core_function.py'],
classifiers=[
"Programming Language :: Python :: 3",
"License :: OSI Approved :: MIT License",
"Operating System :: OS Independent",
],
python_requires='>=3.6',

)
28 changes: 28 additions & 0 deletions tests/Data.csv
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 ID,Sample Time,Type,Conc.,Units,Factor,A260 (10 mm),A280 (10 mm),A3rd (10 mm),A260/A280,BlankTime,Calibration Time,Note,Diagnostic Code
1,18/03/2020 10:42,dsDNA,10,ng/µl,50,0.199,0.121,0.036,1.64,18/03/2020 10:42,01/01/2010 00:00,,0x00000000
2,18/03/2020 10:42,dsDNA,10.1,ng/µl,50,0.202,0.124,0.044,1.62,18/03/2020 10:42,01/01/2010 00:00,,0x00000000
3,18/03/2020 10:43,dsDNA,12.2,ng/µl,50,0.245,0.146,0.043,1.68,18/03/2020 10:42,01/01/2010 00:00,,0x00000000
4,18/03/2020 10:43,dsDNA,13.4,ng/µl,50,0.268,0.161,0.047,1.66,18/03/2020 10:42,01/01/2010 00:00,,0x00000000
5,18/03/2020 10:43,dsDNA,10.8,ng/µl,50,0.216,0.145,0.018,1.49,18/03/2020 10:42,01/01/2010 00:00,,0x00000000
6,18/03/2020 10:43,dsDNA,10.8,ng/µl,50,0.216,0.134,0.041,1.61,18/03/2020 10:42,01/01/2010 00:00,,0x00000000
7,18/03/2020 10:44,dsDNA,13.7,ng/µl,50,0.274,0.151,0.024,1.82,18/03/2020 10:42,01/01/2010 00:00,,0x00000000
8,18/03/2020 10:44,dsDNA,14.8,ng/µl,50,0.297,0.16,0.012,1.86,18/03/2020 10:42,01/01/2010 00:00,,0x00000000
9,18/03/2020 10:44,dsDNA,15.3,ng/µl,50,0.306,0.172,0.014,1.78,18/03/2020 10:42,01/01/2010 00:00,,0x00000000
10,18/03/2020 10:44,dsDNA,20.8,ng/µl,50,0.416,0.224,0.013,1.86,18/03/2020 10:42,01/01/2010 00:00,,0x00000000
11,18/03/2020 10:45,dsDNA,7.1,ng/µl,50,0.143,0.083,0.037,1.72,18/03/2020 10:42,01/01/2010 00:00,,0x00000000
12,18/03/2020 10:45,dsDNA,7.7,ng/µl,50,0.154,0.091,0.028,1.68,18/03/2020 10:42,01/01/2010 00:00,,0x00000000
13,18/03/2020 10:45,dsDNA,9.5,ng/µl,50,0.19,0.132,0.086,1.43,18/03/2020 10:42,01/01/2010 00:00,,0x00000000
14,18/03/2020 10:46,dsDNA,8.9,ng/µl,50,0.177,0.104,0.011,1.71,18/03/2020 10:42,01/01/2010 00:00,,0x00000000
15,18/03/2020 10:46,dsDNA,8.1,ng/µl,50,0.162,0.081,-0.031,2.01,18/03/2020 10:42,01/01/2010 00:00,,0x00000000
16,18/03/2020 10:46,dsDNA,10.2,ng/µl,50,0.204,0.128,0.016,1.6,18/03/2020 10:42,01/01/2010 00:00,,0x00000000
17,18/03/2020 10:46,dsDNA,10.4,ng/µl,50,0.207,0.136,0.048,1.53,18/03/2020 10:42,01/01/2010 00:00,,0x00000000
18,18/03/2020 10:46,dsDNA,4.7,ng/µl,50,0.093,0.09,-0.432,1.03,18/03/2020 10:42,01/01/2010 00:00,,0x00000000
19,18/03/2020 10:47,dsDNA,12,ng/µl,50,0.24,0.131,0.012,1.83,18/03/2020 10:42,01/01/2010 00:00,,0x00000000
20,18/03/2020 10:47,dsDNA,15.3,ng/µl,50,0.305,0.168,0.031,1.82,18/03/2020 10:42,01/01/2010 00:00,,0x00000000
,18/03/2020 10:47,Blank,,,,,,,,,01/01/2010 00:00,,0x00000000
21,18/03/2020 10:48,dsDNA,775,ng/µl,50,15.499,8.283,0.031,1.87,18/03/2020 10:47,01/01/2010 00:00,,0x00000000
22,18/03/2020 10:48,dsDNA,777.4,ng/µl,50,15.548,8.308,0.034,1.87,18/03/2020 10:47,01/01/2010 00:00,,0x00000000
23,18/03/2020 10:48,dsDNA,784.8,ng/µl,50,15.696,8.386,0.041,1.87,18/03/2020 10:47,01/01/2010 00:00,,0x00000000
24,18/03/2020 10:48,dsDNA,1925.6,ng/µl,50,38.512,22.107,0.024,1.74,18/03/2020 10:47,01/01/2010 00:00,,0x00000000
25,18/03/2020 10:48,dsDNA,1916.3,ng/µl,50,38.327,21.934,0.022,1.75,18/03/2020 10:47,01/01/2010 00:00,,0x00000000
26,18/03/2020 10:48,dsDNA,1925.8,ng/µl,50,38.516,22.093,0.023,1.74,18/03/2020 10:47,01/01/2010 00:00,,0x00000000
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12 changes: 12 additions & 0 deletions tests/get_volume_test.py
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import pandas as pd
from get_volumes import core_function
from pathlib import Path

tests_dir = Path(__file__).parent
DATAPATH = tests_dir / 'Data.csv'
def test_get_volumes():
expected = pd.DataFrame({"Conc.":[10.0,10.1,12.2],'Volume':[70,69.3,57.38]})

result = core_function.get_volumes(DATAPATH)
assert (result.head(3)["Conc."].round(1) == expected["Conc."].round(1)).all
assert (result.head(3)["Volume"].round(0) == expected["Volume"].round(0)).all
9 changes: 0 additions & 9 deletions tests/sample_test.py
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