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terdon
terdon
1:54 PM
@SafinaA.R come into this room if you want to debug your issue.
 
Safina A.R
Safina A.R
@terdon Hi
 
terdon
terdon
Hi! So, can you give me a specific example from the drugs.csv file that should be MDR and isn't or that shouldn't be MDR and is?
MDR should be susceptible to ISONIAZID and RIFAMPICIN, correct?
 
Safina A.R
Safina A.R
So i want to extract Strains if they are resistant to ISONIAZID and RIFAMPICIN. In your code we are getting MDR - ERS389515 which is susceptible to these so it is not MDR
 
terdon
terdon
Ah! Hang on, I had understood the opposite (my bad, your question is correct)
Give me a second.
 
Safina A.R
Safina A.R
MDR eg from drug.csv are:
 
terdon
terdon
1:58 PM
SRR1269683 for example?
OK, @SafinaA.R try the updated answer. Does that work as you need it to?
 
Safina A.R
Safina A.R
No SRR129683 are not MDR
MDR should be only resistant to ISONIAZID and RIFAMPICIN
 
terdon
terdon
Ah, but not to the rest?
I had understood that if it is resistant to those two, then it is MDR irrespective of the rest. OK, I need to rewrite again.
 
Safina A.R
Safina A.R
Yes to rest it should be susceptible
Similarly, For Pre-XDR it is resistant to: ISONIAZID + RIFAMPICIN + CIPROFLOXACIN/MOXIFLOXACIN/OFLOXACIN/LEVOFLOXACIN -> (out of CIPROFLOXACIN/MOXIFLOXACIN/OFLOXACIN/LEVOFLOXACIN it can be any one or two or all + ISONIAZID + RIFAMPICIN)
In case of this ERS458727
ERS458727 ETHAMBUTOL SUSCEPTIBLE
ERS458727 ISONIAZID RESISTANT
ERS458727 PYRAZINAMIDE SUSCEPTIBLE
ERS458727 RIFAMPICIN SUSCEPTIBLE
ERS458727 STREPTOMYCIN SUSCEPTIBLE

It is monoresistant to Isoniazid o we will classify it as Isoniazid mono-resisatnt
@terdon
 
terdon
terdon
OK, hang on
No, wait, what is " Isoniazid mono-resisatnt "? Is that a new category?
 
Safina A.R
Safina A.R
Yeah just to explain you because there are these types of entries as well in the file.
So for these types of exception Others category will work
 
terdon
terdon
2:11 PM
OK. Can you give me an example strain for each of the categories MDR, XDR, Pre-XDR, Susceptible and OTHER?
That way I can test and make sure I get it right.
So, ERS458727 should be other. Can you give me one strain from each of the rest?
 
Safina A.R
Safina A.R
ERS458757 ETHAMBUTOL SUSCEPTIBLE
ERS458757 ISONIAZID SUSCEPTIBLE
ERS458757 PYRAZINAMIDE SUSCEPTIBLE
ERS458757 RIFAMPICIN SUSCEPTIBLE
ERS458757 STREPTOMYCIN RESISTANT

So this is Mono-resistant to Streptomycin
 
terdon
terdon
Just give me the name of a strain and the category you want it to be in please.
@SafinaA.R ?
 
Safina A.R
Safina A.R
@terdon im leaving for home please send me your email and i will brief you with few examples from the list at night. Thank you
 
terdon
terdon
@SafinaA.R Hang on, try the updated answer it might be OK now.
And when you have the examples, just add them to your question and then ping me here to let me know.
Just something like this: 
ERS389418	OTHER
ERS458130	SUSCEPTIBLE
ERR046903	PRE-XDR
SRR1269497	XDR
ERR046855	MDR
 

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