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volkansevim / alpha-CENTAURI

A python package from Pacific Biosciences to analyze centromeric sequences
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KeyError #1

Open hendersi opened 5 years ago

hendersi commented 5 years ago

Hi,

I am using alpha-CENTAURI on nanopore reads from Arabidopsis thaliana. I am trying to use your program to annotate centromere satellites. I am using Python2.7 on a MacOS Mojave.

When I run chop_to_monomers.py I get the error pasted below. The KeyError refers to one of the read names. Do you have any suggestions on what might be going wrong and how to fix it??

Best wishes, Ian Henderson

Traceback (most recent call last): File "/Users/ian/Desktop/CEN/Naish/alpha-CENTAURI-master/src/chop_to_monomers.py", line 79, in parseHMMout("hmmoutF.out", "inferred_monomers_F.zzz", "F") File "/Users/ian/Desktop/CEN/Naish/alpha-CENTAURI-master/src/chop_to_monomers.py", line 24, in parseHMMout if low != 0 and high < len(seq_db[ID]) - 1: KeyError: '9dd87eb3-2ee7-4095-8259-11414934b389'

hendersi commented 5 years ago

I have fixed the problem. It was caused by reads having names like this:

9fb046eb-5946-4eec-8834-872f4755c9d1 runid=c0d9bf1e25f81816c32813953da0a77e5b46d5c1 sampleid=Nanobind_ext1 read=15875 ch=89 start_time=2019-07-26T03:29:31Z

Once I truncated read names to this format everything works fine!

9fb046eb-5946-4eec-8834-872f4755c9d1

volkansevim commented 5 years ago

Glad you could work it out, Ian. :)

On Fri, Oct 11, 2019 at 7:49 AM hendersi notifications@github.com wrote:

I have fixed the problem. It was caused by reads having names like this:

9fb046eb-5946-4eec-8834-872f4755c9d1 runid=c0d9bf1e25f81816c32813953da0a77e5b46d5c1 sampleid=Nanobind_ext1 read=15875 ch=89 start_time=2019-07-26T03:29:31Z

Once I truncated read names to this format everything works fine!

9fb046eb-5946-4eec-8834-872f4755c9d1

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hendersi commented 5 years ago

Thanks - I’m enjoying looking into the output!!!

On 11 Oct 2019, at 19:17, Volkan Sevim notifications@github.com wrote:

Glad you could work it out, Ian. :)

On Fri, Oct 11, 2019 at 7:49 AM hendersi notifications@github.com wrote:

I have fixed the problem. It was caused by reads having names like this:

9fb046eb-5946-4eec-8834-872f4755c9d1 runid=c0d9bf1e25f81816c32813953da0a77e5b46d5c1 sampleid=Nanobind_ext1 read=15875 ch=89 start_time=2019-07-26T03:29:31Z

Once I truncated read names to this format everything works fine!

9fb046eb-5946-4eec-8834-872f4755c9d1

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/volkansevim/alpha-CENTAURI/issues/1?email_source=notifications&email_token=AB7YVP63PLICTDNX56XSB5DQOCG73A5CNFSM4I7YIHKKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEBAHSNY#issuecomment-541096247, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB7YVP3XGOW2GTO6WJLOJRDQOCG73ANCNFSM4I7YIHKA .

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