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Parsing error in SearchIO HMMer 2 parser #198

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kblin opened this Issue Jul 26, 2013 · 8 comments

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kblin commented Jul 26, 2013

Some input files seem to trigger a crash in the hsp parser with an Index error on
otherseq += self.line[19:].split()[0].strip()
I'll try to reproduce this outside of my software pipeline and will provide a fix.

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bow commented Jul 26, 2013

Hm..this sounds like it may be caused by unexpected whitespaces in the otherseq sequence line. Keep us posted on the progress (and if you'd like to attach the problematic file :) ).

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kblin commented Jul 26, 2013

Yeah, that's my guess. Unfortunately I haven't gotten to the point of the crash yet. All in all I guess we're dealing with invalid input, but it'd be nice to handle this more gracefully.

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earldean commented Sep 21, 2013

I was wondering what input files causes the index error. Also, would you want an error message to be printed, or would you want the program to just keep running? I did a try statement and if there is an IndexError a pass.
I pushed it to my repository, but have not done a pull request.

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kblin commented Sep 22, 2013

I was unable to reproduce this so far, but I guess this had to do with hmmer options used. I'll try to dig up the crashing sequence and try again.

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bow commented Feb 26, 2014

@kblin, any update on this :)? If not, I am closing this issue.

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earldean commented Feb 26, 2014

No update on the issue.

Cheers,

Earl

On Feb 26, 2014, at 11:34 AM, Wibowo Arindrarto notifications@github.com wrote:

@kblin, any update on this :)? If not, I am closing this issue.


Reply to this email directly or view it on GitHub.

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kblin commented Mar 12, 2014

Sorry, I don't have the dataset around anymore. I'll just close it and reopen if I ever run across it again.

@kblin kblin closed this Mar 12, 2014

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bow commented Mar 12, 2014

Ok, thank you :)

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