Bioinformatics

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8:59 AM

@terdon Hi

I have sent a modified description after discussiong with the team. Sorry for all troubles im giving. i thing your previous scrip posted there is working fine but i need few modifications

terdon

9:25 AM

@SafinaA.R Hi. Do me a favor, please edit your question so that it explains what yu currently need. Don't add "edit", just make it so it asks what you need. Also, it would be really great if you could give an example of each of the categories as I asked for yesterday

You show an example that isn't in your file, SRR1270146. That is just confusing. Could you pelase clean the question up a bit? And in the meantime I'll have a look at your new requirement.

So, you said:

HI. I think it is now running fine. So now i have the proper classification verified by my team. So any thing that is resistant to ISONIASID and RIfampicin is mdr but it can also be mdr if these two are there plus any of these or all of these: Pyrazinamid, Ethambutal, Streptomycin, ETHIONAMIDE. like these are the few example of mdr from the list:

ERR038736 ERR038737 ERR038738 ERR038739 ERR038740 ERR038742 ERR038743 ERR038744 ERR038745 ERR038746 ERR038747 ERR038748 ERR038749 ERR038750 ERR038752 ERR046855

— Safina A.R 29 mins ago

Does this mean that MDR only requires resistance to ISONIASID and RIFAMPICIN? So if it is resistant to any other drug as well we don't care? Or if it is resistant to one of Pyrazinamid, Ethambutal, Streptomycin, ETHIONAMIDE specifically we don't care?

Of those examples you show, only 1 is actually in your drug.csv file. Please give me examples I can use!

Anyway, I edited again. Have a look. But please fix your question. It looks like I'm answering another one now.

Safina A.R

9:41 AM

@terdon Yea a strain must be resistant to isoniazid and rifampicin to be an mdr. but if is resisatnt to any of these or all of these(Pyrazinamid, Ethambutal, Streptomycin, ETHIONAMIDE) in addition to Iso and rif it is again an mdr

im editing my question. okay

terdon

@SafinaA.R OK, the updated answer should work then.

Safina A.R

10:03 AM

So for XDR and PreXDR it should be MDR than it must be resisatnt to CIPROFLOXACIN|MOXIFLOXACIN|OFLOXACIN|LEVOFLOXACIN - Pre-XDR and in XDR it should be MDR+ AMYCACIN/CAPREOMYCIN/KANAMYCIN

i have uploaded the new file with all the ids i posted here as an example.

terdon

@SafinaA.R Wait, it should be MDR or it should just be resistant to ISONIAZID and RIFAMPICIN?

Have you looked at my code? Have you tried to modify it yourself?

And I see you have still not added the examples I asked for. So I ask again, for the third time: add an example of each of the categories from your file. Like this:

20 hours ago, by terdon

ERS389418	OTHER
ERS458130	SUSCEPTIBLE
ERR046903	PRE-XDR
SRR1269497	XDR
ERR046855	MDR

Anyway, I edited again. Try this one.

If it doesn't work, please try and understand the code and fix it yourself though, I'm sorry, but I can't spend more time on this.

Safina A.R

I have put the example of MDR and looking for XDR and Pre-XDR manually it is taking time.

I m trying your code. It is not generating any output.

ERR038280 Susc
ERR038281 Susc
ERR038282 Susc
ERR038283 Susc
ERR038284 Susc
ERR038285 Susc
ERR038286 Susc
ERR038287 Susc
ERR038288 Susc

ERR038736 MDR
ERR038737 MDR
ERR038738 MDR
ERR038739 MDR
ERR038740 MDR
ERR038742 MDR
ERR038743 MDR
ERR038744 MDR
ERR038745 MDR

ERR038741 Others
ERR038294 Others
ERR038751 Others

SRS553990 XDR

ERR133879 Pre-XDR

@terdon im getting tese errors in the script :

./foo.pl: line 1: use: command not found
./foo.pl: line 1: $'\r': command not found
./foo.pl: line 2: use: command not found
./foo.pl: line 2: $'\r': command not found
./foo.pl: line 3: $'\r': command not found
./foo.pl: line 5: my: command not found
./foo.pl: line 5: $'\r': command not found
./foo.pl: line 6: $'\r': command not found
./foo.pl: line 8: sub: command not found
./foo.pl: line 9: my: command not found
./foo.pl: line 9: $'\r': command not found
./foo.pl: line 10: my: command not found

terdon

10:24 AM

@SafinaA.R please run it as I explain in the answer: perl foo.pl file.csv

Safina A.R

Oh i forget to write perl. thank you so much terdon for all your help. (y)

terdon

Glad it finally works! :)

Safina A.R

10:46 AM

Yes.

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