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simon-anders / htseq

HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
https://htseq.readthedocs.io/en/release_0.11.1/
GNU General Public License v3.0
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iv.chrom AttributeError #56

Closed maiher closed 6 years ago

maiher commented 6 years ago

Hi there,

I just installed HTSeq 0.10.0 and checked out your guide, using the example data. Whenever I try to print aln.iv.chrom for non-aligned reads, I get this error message:

Traceback (most recent call last): File "/home/hermi/workspace/Coverage/HTseq/ReadCounts.py", line 46, in print aln.iv.chrom AttributeError: 'NoneType' object has no attribute 'chrom'

I get this both when I use the example data and my own files. I wonder if this might cause any problems downstream?

Cheers, Maike

iosonofabio commented 6 years ago

Hi Maike, I'd say an unmapped read has no chromosome, that's expected. Whether that's what you want depends on what you mean by "downstream": just catch the exception and do whatever you want with it ;-)

Cheers, Fabio

On June 8, 2018 7:37:06 AM PDT, maiher notifications@github.com wrote:

Hi there,

I just intalled HTSeq 0.10.0 and checked out your guide, using the example data. Whenever I try to print aln.iv.chrom for non-aligned reads, I get this error message:

Traceback (most recent call last): File "/home/hermi/workspace/Coverage/HTseq/ReadCounts.py", line 46, in

print aln.iv.chrom AttributeError: 'NoneType' object has no attribute 'chrom' I get this both when I use the example data and my own files. I wonder if this might cause any problems downstream? Cheers, Maike -- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/simon-anders/htseq/issues/56
maiher commented 6 years ago

Dear Fabio,

yeah, after searching everywhere, I just saw that it's even mentioned in the guide! I wanted to delete the issue, but you were faster ;) Thanks for the fast reply and sorry for bothering you.

Maike