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+--- Thread: panda, excel - script pauses and doesn't continue running, no error message (/thread-14311.html)
panda, excel - script pauses and doesn't continue running, no error message - william - Nov-24-2018
Hi, I'm having some trouble with a script I created to essentially run down an excel column, and if it found a particular string to replace that string. It runs great... up until something like row 200.
I wondered if it was something to do with the memory my system allows python, but I would expect for the program to quit and give me an error message. Nothing like that?
I've posted my script below - as you can see it has a number of if statements and the design is to clean up some data (column name is 'culture1') and replace the names of bacteria with cleaner names so they can be categorised more easily.
The output is something like this here... it has no error message and the script does not stop running - it just stays on "row 230 done".
Output:.... row 170 done
row 177 done
row 182 done
row 187 done
row 188 done
row 195 done
row 197 done
row 199 done
row 214 done
row 230 done...import pandas as pd
i=0
df=pd.read_excel('*location of data*') #insert info
while (i < df.shape[0]):
t = df.ix[i, 'culture1']
length = -1
if str(type(t))=='<class \'float\'>':
i+=1
elif t.find('Coag.neg.Staph.') > length:
df.at[[i], ['culture1']] = 'Coag. neg. Staph.'
elif t.find('Staph.aureus') > length:
df.at[[i], ['culture1']] = 'Staph. Aureus'
elif t.find('Enterococcussp.')>length:
df.at[[i], ['culture1']] = 'Enterococcus Sp.'
elif t.find('Pseud.aeruginosa')>length:
df.at[[i], ['culture1']] = 'Pseud. Aeruginosa'
elif t.find('Pseudomonas.putida')>length:
df.at[[i], ['culture1']] = 'Pseud. Putida'
elif t.find('Candida.albicans')>length:
df.at[[i], ['culture1']] = 'Candida Albicans'
elif t.find('Enterobacter.cloacae')>length:
df.at[[i], ['culture1']] = 'Enterobacter Cloacae'
elif t.find('Candida.parapsilosis')>length:
df.at[[i], ['culture1']] = 'Candida Parapsilosis'
elif t.find('Kleb.pneumoniae')>length:
df.at[[i], ['culture1']] = 'Kleb. Pneumoniae'
elif t.find('Aci.baumanni')>length:
df.at[[i], ['culture1']] = 'Aci. baumanni'
elif t.find('Candida.glabrata')>length:
df.at[[i], ['culture1']] = 'Candida Glabrata'
elif t.find('Candida. glabrata')>length:
df.at[[i], ['culture1']] = 'Candida Glabrata'
elif t.find('Enterococcus.sp.')>length:
df.at[[i], ['culture1']] = 'Enterococcus Sp.'
elif t.find('VRE')>length:
df.at[[i], ['culture1']] = 'VRE'
elif t.find('Klebsiella.oxytoca')>length:
df.at[[i], ['culture1']] = 'Klebsiella Oxytoca'
elif t.find('E\'coccus.faecalis')>length:
df.at[[i], ['culture1']] = 'Enterococcus Faecalis'
elif t.find('Eggerthellalenta')>length:
df.at[[i], ['culture1']] = 'Eggerthella lenta'
elif t.find('Enterococcusfaecium')>length:
df.at[[i], ['culture1']] = 'Enterococcus Faecium'
elif t.find('Corynebacteriumsp.')>length:
df.at[[i], ['culture1']] = 'Corynebacterium Sp.'
elif t.find('Propionibacteriumsp')>length:
df.at[[i], ['culture1']] = 'Cutibacterium acnes'
elif t.find('Escherichiacoli')>length:
df.at[[i], ['culture1']] = 'Escherichia coli'
elif t.find('MRSA')>length:
df.at[[i], ['culture1']] = 'MRSA'
elif t.find('Candidaalbicans')>length:
df.at[[i], ['culture1']] = 'Candida Albicans'
elif t.find('strepmitis/oralis')>length:
df.at[[i], ['culture1']] = 'Strep. Mitis'
elif t.find('Bacillussp.')>length:
df.at[[i], ['culture1']] = 'Bacillus sp.'
elif t.find('Staph.haemolyticus')>length:
df.at[[i], ['culture1']] = 'Staph. Haemolyticus'
elif t.find('Staphepidermidis')>length:
df.at[[i], ['culture1']] = 'Staph. Epidermidis'
elif t.find('E\'coccusfaecalis')>length:
df.at[[i], ['culture1']] = 'Enterococcus Faecalis'
elif t.find('Klebsiellaoxytoca')>length:
df.at[[i], ['culture1']] = 'Klebsiella Oxytoca'
elif t.find('Staphschleiferi')>length:
df.at[[i], ['culture1']] = 'Staph. Schleiferi'
elif t.find('Proteusmirabilis')>length:
df.at[[i], ['culture1']] = 'Proteus Mirabilis'
elif t.find('Candidaparapsilosis')>length:
df.at[[i], ['culture1']] = 'Candida Parapsilosis'
elif t.find('Enterobactercloacae')>length:
df.at[[i], ['culture1']] = 'Enterobacter Cloacae'
elif t.find('Sten.maltophilia')>length:
df.at[[i], ['culture1']] = 'Sten. Maltophilia'
elif t.find('VancresEnterococci')>length:
df.at[[i], ['culture1']] = 'VRE'
elif t.find('Burkholderiacepacia')>length:
df.at[[i], ['culture1']] = 'Burkholderia cepacia'
elif t.find('Brev.vesicularis')>length:
df.at[[i], ['culture1']] = 'B. vesicularis'
elif t.find('Micrococcussp.')>length:
df.at[[i], ['culture1']] = 'Micrococcus sp.'
elif t.find('Candidasp.')>length:
df.at[[i], ['culture1']] = 'Candida Sp.'
elif t.find(':Coag.neg.Staph.')>length:
df.at[[i], ['culture1']] = 'Coag. neg. Staph.'
elif t.find('Achromobactersp')>length:
df.at[[i], ['culture1']] = 'Achromobacter Sp.'
elif t.find('Strep.intermedius')>length:
df.at[[i], ['culture1']] = 'Strep. Intermedius'
elif t.find('Enterob.sakazaki')>length:
df.at[[i], ['culture1']] = 'Enterob. Sakazaki'
elif t.find('Enterob.aerogenes')>length:
df.at[[i], ['culture1']] = 'Enterob. Aerogenes'
elif t.find('E.coli')>length:
df.at[[i], ['culture1']] = 'Escherichia coli'
elif t.find('Str.parasanguinis')>length:
df.at[[i], ['culture1']] = 'Strep. Parasanguinis'
else:
print('row ', i, 'done')
i+=1
df.to_excel('*location*', sheet_name='*NAME*') #insert info
RE: panda, excel - script pauses and doesn't continue running, no error message - ichabod801 - Nov-24-2018
Well, i is only incremented if t is a float (I would use
isinstance(t, float) there) or if none of the text searches trigger. So if one of the text searches triggers, what prevents it from becoming an infinite loop?