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Bio.Align.Alignment doesn't contain chromosome data? #4704

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royjacobson opened this issue Apr 15, 2024 · 1 comment
Open

Bio.Align.Alignment doesn't contain chromosome data? #4704

royjacobson opened this issue Apr 15, 2024 · 1 comment
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@royjacobson
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Setup

I am reporting a problem with Biopython version, Python version, and operating
system as follows:

3.9.18 (main, Sep 11 2023, 13:41:44) 
[GCC 11.2.0]
CPython
Linux-5.14.0-162.6.1.el9_1.x86_64-x86_64-with-glibc2.34
1.83

I'm reading a BED alignment file using Align.bed.AlignmentReader, and the resulting Alignment objects don't seem to contain the chrom column anywhere except in the id field inside the first sequence. Is this the intended way to read this information?

@mdehoon
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mdehoon commented Apr 15, 2024

@royjacobson Please show your code.

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