From replacement data table (below on the image), I am trying to incorporate the solbox product replace in time series data format(above on the image). I need to extract out the number of consumers per day from the information.
What I need to find out:
On a specific date, which number of solbox product was active
On a specific date, which number of solbox product (which was a consumer) was active
I have used this line of code in excel but cannot implement this on python properly.
=SUMPRODUCT((Record_Solbox_Replacement!$O$2:$O$1367 = "consumer") * (A475>=Record_Solbox_Replacement!$L$2:$L$1367)*(A475<Record_Solbox_Replacement!$M$2:$M$1367))
I tried in python -
timebase_df['date'] = pd.date_range(start = replace_table_df['solbox_started'].min(), end = replace_table_df['solbox_started'].max(), freq = frequency)
timebase_df['date_unix'] = timebase_df['date'].astype(np.int64) // 10**9
timebase_df['no_of_solboxes'] = ((timebase_df['date_unix']>=replace_table_df['started'].to_numpy()) & (timebase_df['date_unix'] < replace_table_df['ended'].to_numpy() & replace_table_df['customer_type'] == 'customer']))
ERROR:
~\Anaconda3\Anaconda4\lib\site-packages\pandas\core\ops\array_ops.py in comparison_op(left, right, op)
232 # The ambiguous case is object-dtype. See GH#27803
233 if len(lvalues) != len(rvalues):
--> 234 raise ValueError("Lengths must match to compare")
235
236 if should_extension_dispatch(lvalues, rvalues):
ValueError: Lengths must match to compare
Can someone help me please? I can explain in comment section if I have missed something.
Related
so I want to do a fisher exact test (one sided) on every row of a 3000+ row table with a format matching the below example
gene
sample_alt
sample_ref
population_alt
population_ref
One
4
556
770
37000
Two
5
555
771
36999
Three
6
554
772
36998
I would ideally like to make another column of the table equivalent to
[(4+556)!(4+770)!(770+37000)!(556+37000)!]/[4!(556!)770!(37000!)(4+556+770+37000)!]
for the first row of data, and so on and so forth for each row of the table.
I know how to do a fisher test in R for simple 2x2 tables, but I wouldn't know how I would apply the fisher.test() function to each row of a large table. I also can't use an excel formula because the numbers get so big with the factorials that they reach excel's digit limit and result in a #NUM error. What's the best way to simply complete this? Thanks in advance!
Beginning with a tab-delimited text file on desktop (table.txt) with the same format as shown in the stem question
if(!require(psych)){install.packages("psych")}
multiFisher = function(file="Desktop/table.txt", saveit=TRUE,
outfile="Desktop/table.csv", progress=T,
verbose=FALSE, digits=3, ... )
{
require(psych)
Data = read.table(file, skip=1, header=F,
col.names=c("Gene", "MD", "WTD", "MC", "WTC"), ...)
if(verbose){print(str(Data))}
Data$Fisher.p = NA
Data$phi = NA
Data$OR1 = format(0.123, nsmall=3)
Data$OR2 = NA
if(progress){cat("\n")}
for(i in 1:length(Data$Gene)){
Matrix = matrix(c(Data$WTC[i],Data$MC[i],Data$WTD[i],Data$MD[i]), nrow=2)
Fisher = fisher.test(Matrix, alternative = 'greater')
Data$Fisher.p[i] = signif(Fisher$p.value, digits=digits)
Data$phi[i] = phi(Matrix, digits=digits)
OR1 = (Data$WTC[i]*Data$MD[i])/(Data$MC[i]*Data$WTD[i])
OR2 = 1 / OR1
Data$OR1[i] = format(signif(OR1, digits=digits), nsmall=3)
Data$OR2[i] = signif(OR2, digits=digits)
if(progress) {cat(".")}
}
if(progress){cat("\n"); cat("\n")}
if(saveit){write.csv(Data, outfile)}
return(Data)
}
multiFisher()
I've been trying to optimise a bokeh server to calculate live stats by selected country on Covid19.
I found myself repeating a groupby function to calculate new columns and was wondering, having selected the groupby, if I could then apply it in a similar way to .agg() on multiple columns ?
For example:
dfall = pd.DataFrame(db("SELECT * FROM C19daily"))
dfall.set_index(['geoId', 'date'], drop=False, inplace=True)
dfall = dfall.sort_index(ascending=True)
dfall.head()
id date geoId cases deaths auid
geoId date
AD 2020-03-03 70119 2020-03-03 AD 1 0 AD03/03/2020
2020-03-14 70118 2020-03-14 AD 1 0 AD14/03/2020
2020-03-16 70117 2020-03-16 AD 3 0 AD16/03/2020
2020-03-17 70116 2020-03-17 AD 9 0 AD17/03/2020
2020-03-18 70115 2020-03-18 AD 0 0 AD18/03/2020
I need to create new columns based on 'cases' and 'deaths' and applying various functions like cumsum(). Currently I do this the long way
dfall['ccases'] = dfall.groupby(level=0)['cases'].cumsum()
dfall['dpc_cases'] = dfall.groupby(level=0)['cases'].pct_change(fill_method='pad', periods=7)
.....
dfall['cdeaths'] = dfall.groupby(level=0)['deaths'].cumsum()
dfall['dpc_deaths'] = dfall.groupby(level=0)['deaths'].pct_change(fill_method='pad', periods=7)
I tried to optimise the groupby call like this:-
with dfall.groupby(level=0) as gr:
gr = g['cases'].cumsum()...
But the error suggest the class doesn't support this
AttributeError: __enter__
I thought I could use .agg({}) and supply dictionary
g = dfall.groupby(level=0).agg({'cc' : 'cumsum', 'cd' : 'cumsum'})
but that produces another error
pandas.core.base.SpecificationError: nested renamer is not supported
I have plenty of other bits to optimise, I thought this python part would be the easiest and save a few ms!
Could anyone nudge me in the right direction?
To avoid repeating dfall.groupby(level=0) you can just save it in a variable:
gb = dfall.groupby(level=0)
gb_cases = gb['cases']
dfall['ccases'] = gb_cases.cumsum()
dfall['dpc_cases'] = gb_cases.pct_change(fill_method='pad', periods=7)
...
And to run multiple aggregations using a single expression, I think you can use named aggregation. But I have no clue whether it will be more performant or not. Either way, it's better to profile the code and improve the actual bottlenecks.
I am trying to parse raw data results from a text file into an organised tuple but having trouble getting it right.
My raw data from the textfile looks something like this:
Episode Cumulative Results
EpisodeXD0281119
Date collected21/10/2019
Time collected10:00
Real time PCR for M. tuberculosis (Xpert MTB/Rif Ultra):
PCR result Mycobacterium tuberculosis complex NOT detected
Bacterial Culture:
Bottle: Type FAN Aerobic Plus
Result No growth after 5 days
EpisodeST32423457
Date collected23/02/2019
Time collected09:00
Gram Stain:
Neutrophils Occasional
Gram positive bacilli Moderate (2+)
Gram negative bacilli Numerous (3+)
Gram negative cocci Moderate (2+)
EpisodeST23423457
Date collected23/02/2019
Time collected09:00
Bacterial Culture:
A heavy growth of
1) Klebsiella pneumoniae subsp pneumoniae (KLEPP)
ensure that this organism does not spread in the ward/unit.
A heavy growth of
2) Enterococcus species (ENCSP)
Antibiotic/Culture KLEPP ENCSP
Trimethoprim-sulfam R
Ampicillin / Amoxic R S
Amoxicillin-clavula R
Ciprofloxacin R
Cefuroxime (Parente R
Cefuroxime (Oral) R
Cefotaxime / Ceftri R
Ceftazidime R
Cefepime R
Gentamicin S
Piperacillin/tazoba R
Ertapenem R
Imipenem S
Meropenem R
S - Sensitive ; I - Intermediate ; R - Resistant ; SDD - Sensitive Dose Dependant
Comment for organism KLEPP:
** Please note: this is a carbapenem-RESISTANT organism. Although some
carbapenems may appear susceptible in vitro, these agents should NOT be used as
MONOTHERAPY in the treatment of this patient. **
Please isolate this patient and practice strict contact precautions. Please
inform Infection Prevention and Control as contact screening might be
indicated.
For further advice on the treatment of this isolate, please contact.
The currently available laboratory methods for performing colistin
susceptibility results are unreliable and may not predict clinical outcome.
Based on published data and clinical experience, colistin is a suitable
therapeutic alternative for carbapenem resistant Acinetobacter spp, as well as
carbapenem resistant Enterobacteriaceae. If colistin is clinically indicated,
please carefully assess clinical response.
EpisodeST234234057
Date collected23/02/2019
Time collected09:00
Authorised by xxxx on 27/02/2019 at 10:35
MIC by E-test:
Organism Klebsiella pneumoniae (KLEPN)
Antibiotic Meropenem
MIC corrected 4 ug/mL
MIC interpretation Resistant
Antibiotic Imipenem
MIC corrected 1 ug/mL
MIC interpretation Sensitive
Antibiotic Ertapenem
MIC corrected 2 ug/mL
MIC interpretation Resistant
EpisodeST23423493
Date collected18/02/2019
Time collected03:15
Potassium 4.4 mmol/L 3.5 - 5.1
EpisodeST45445293
Date collected18/02/2019
Time collected03:15
Creatinine 32 L umol/L 49 - 90
eGFR (MDRD formula) >60 mL/min/1.73 m2
Creatinine 28 L umol/L 49 - 90
eGFR (MDRD formula) >60 mL/min/1.73 m2
Essentially the pattern is that ALL information starts with a unique EPISODE NUMBER and follows with a DATE and TIME and then the result of whatever test. This is the pattern throughout.
What I am trying to parse into my tuple is the date, time, name of the test and the result - whatever it might be. I have the following code:
with open(filename) as f:
data = f.read()
data = data.splitlines()
DS = namedtuple('DS', 'date time name value')
parsed = list()
idx_date = [i for i, r in enumerate(data) if r.strip().startswith('Date')]
for start, stop in zip(idx_date[:-1], idx_date[1:]):
chunk = data[start:stop]
date = time = name = value = None
for row in chunk:
if not row: continue
row = row.strip()
if row.startswith('Episode'): continue
if row.startswith('Date'):
_, date = row.split()
date = date.replace('collected', '')
elif row.startswith('Time'):
_, time = row.split()
time = time.replace('collected', '')
else:
name, value, *_ = row.split()
print (name)
parsed.append(DS(date, time, name, value))
print(parsed)
My error is that I am unable to find a way to parse the heterogeneity of the test RESULT in a way that I can use later, for example for the tuple DS ('DS', 'date time name value'):
DATE = 21/10/2019
TIME = 10:00
NAME = Real time PCR for M tuberculosis or Potassium
RESULT = Negative or 4.7
Any advice appreciated. I have hit a brick wall.
I have a dataframe which contain a column 'trade_dt' like this
2009/12/1
2009/12/2
2009/12/3
2009/12/4
I got this problem
benchmark['trade_dt'] = pd.to_datetime(benchmark['trade_dt'], format='%Y-&m-%d')
ValueError: time data '2009/12/1' does not match format '%Y-&m-%d' (match)
how to solve it? Thanks~
Need change format for match - replace & and - to % and /:
benchmark['trade_dt'] = pd.to_datetime(benchmark['trade_dt'], format='%Y/%m/%d')
Also working with sample data removing format (but not sure with real data):
benchmark['trade_dt'] = pd.to_datetime(benchmark['trade_dt'])
print (benchmark)
trade_dt
0 2009-12-01
1 2009-12-02
2 2009-12-03
3 2009-12-04
I am currently building a binary classification model and have created an input file for svm-train (svm_input.txt). This input file has 453 lines, 4 No. features and 2 No. classes [0,1].
i.e
0 1:15.0 2:40.0 3:30.0 4:15.0
1 1:22.73 2:40.91 3:36.36 4:0.0
1 1:31.82 2:27.27 3:22.73 4:18.18
0 1:22.73 2:13.64 3:36.36 4:27.27
1 1:30.43 2:39.13 3:13.04 4:17.39 ......................
My problem is that when I count the number of lines in the output model generated by svm-train (svm_train_model.txt), this has 12 fewer lines than that of the input file. The line count here shows 450, although there are obviously also 9 lines at the beginning showing the various parameters generated
i.e.
svm_type c_svc
kernel_type rbf
gamma 1
nr_class 2
total_sv 441
rho -0.156449
label 0 1
nr_sv 228 213
SV
Therefore 12 lines in total from the original input of 453 have gone. I am new to svm and was hoping that someone could shed some light on why this might have happened?
Thanks in advance
Updated.........
I now believe that in generating the model, it has removed lines whereby the labels and all the parameters are exactly the same.
To explain............... My input is a set of miRNAs which have been classified as 1 and 0 depending on their involvement in a particular process or not (i.e 1=Yes & 0=No). The input file looks something like.......
0 1:22 2:30 3:14 4:16
1 1:26 2:15 3:17 4:25
0 1:22 2:30 3:14 4:16
Whereby, lines one and three are exactly the same and as a result will be removed from the output model. My question is then both why the output model would do this and how I can get around this (whilst using the same features)?
Whilst both SOME OF the labels and their corresponding feature values are identical within the input file, these are still different miRNAs.
NOTE: The Input file does not have a feature for miRNA name (and this would clearly show the differences in each line) however, in terms of the features used (i.e Nucleotide Percentage Content), some of the miRNAs do have exactly the same percentage content of A,U,G & C and as a result are viewed as duplicates and then removed from the output model as it obviously views them as duplicates even though they are not (hence there are less lines in the output model).
the format of the input file is:
Where:
Column 0 - label (i.e 1 or 0): 1=Yes & 0=No
Column 1 - Feature 1 = Percentage Content "A"
Column 2 - Feature 2 = Percentage Content "U"
Column 3 - Feature 3 = Percentage Content "G"
Column 4 - Feature 4 = Percentage Content "C"
The input file actually looks something like (See the very first two lines below), as they appear identical, however each line represents a different miRNA):
1 1:23 2:36 3:23 4:18
1 1:23 2:36 3:23 4:18
0 1:36 2:32 3:5 4:27
1 1:14 2:41 3:36 4:9
1 1:18 2:50 3:18 4:14
0 1:36 2:23 3:23 4:18
0 1:15 2:40 3:30 4:15
In terms of software, I am using libsvm-3.22 and python 2.7.5
Align your input file properly, is my first observation. The code for libsvm doesnt look for exactly 4 features. I identifies by the string literals you have provided separating the features from the labels. I suggest manually converting your input file to create the desired input argument.
Try the following code in python to run
Requirements - h5py, if your input is from matlab. (.mat file)
pip install h5py
import h5py
f = h5py.File('traininglabel.mat', 'r')# give label.mat file for training
variables = f.items()
labels = []
c = []
import numpy as np
for var in variables:
data = var[1]
lables = (data.value[0])
trainlabels= []
for i in lables:
trainlabels.append(str(i))
finaltrain = []
trainlabels = np.array(trainlabels)
for i in range(0,len(trainlabels)):
if trainlabels[i] == '0.0':
trainlabels[i] = '0'
if trainlabels[i] == '1.0':
trainlabels[i] = '1'
print trainlabels[i]
f = h5py.File('training_features.mat', 'r') #give features here
variables = f.items()
lables = []
file = open('traindata.txt', 'w+')
for var in variables:
data = var[1]
lables = data.value
for i in range(0,1000): #no of training samples in file features.mat
file.write(str(trainlabels[i]))
file.write(' ')
for j in range(0,49):
file.write(str(lables[j][i]))
file.write(' ')
file.write('\n')