Moderator: Peter

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Peter5.6k
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Location:
Scotland, UK
Website:
http://blastedbio.blog...
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Google Scholar Page
Last seen:
1 week, 4 days ago
Joined:
8 years, 4 months ago
Email:
p*********@googlemail.com

I contribute to a number of open source bioinformatics projects, including Biopython and Galaxy. I have written a number of Galaxy tools & wrappers, co-ordinate the Galaxy BLAST+ wrappers, and currently serve on the Intergalactic Utilities Commission (aka the Galaxy ToolShed Police).

Posts by Peter

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Comment: C: Arrow Assembly polishing Error "KeyError: 'BASECALLERVERSION'"
... It seems you can't use a BAM file made by mapping a FASTA file in this way as it is missing PacBio meta-data which is expected (e.g. the ``BASECALLERVERSION`` information). You should be able to map the raw unaligned PacBio BAM file, or use the ``*.subreadset.xml`` file which also has metadata. ...
written 11 days ago by Peter5.6k
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Comment: C: Arrow Assembly polishing Error "KeyError: 'BASECALLERVERSION'"
... It seems from reading https://github.com/PacificBiosciences/pitchfork/issues/316 that the ``KeyError 'BASECALLERVERSION'`` problem is to do with missing PacBio headers in the aligned BAM file. I've logged an issue as https://github.com/PacificBiosciences/pbcore/issues/117 using pbalign and arrow ...
written 12 days ago by Peter5.6k
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Comment: C: Arrow Assembly polishing Error "KeyError: 'BASECALLERVERSION'"
... I just hit something similar, logged as https://github.com/PacificBiosciences/pbcore/issues/117 ...
written 12 days ago by Peter5.6k
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Comment: C: Reverse complement for multiple fastq files
... The annotation will not in general apply to the RC sequence, so in the ``.reverse_complement(...)`` arguments you can provide new values (as in the updated original question) or use ``True`` to preserve a value. See the method's documentation: http://biopython.org/DIST/docs/api/Bio.SeqRecord.SeqRec ...
written 4 months ago by Peter5.6k
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Answer: A: Is the order of descriptions and alignments identical while iterating over the B
... In the legacy human readable plain text BLAST output, there was a summary table which is where the descriptions came from, followed by pairwise alignments. You could control the max number of entries to show in each at the BLAST command line. So, it made sense to parse them separately. In the BLAST ...
written 8 months ago by Peter5.6k
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Comment: C: Parsing fasta file using seqIO
... BioPerl's SeqIO? Biopython's SeqIO? Some other seqIO? (Only clear from the tags you've added) ...
written 8 months ago by Peter5.6k
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Answer: A: Blast-XML and Biopython: extract query-anchored results (i.e. MSA)
... There is indeed a ``.multiple_alignment`` attribute in the BLAST record object, and there is code in ``Bio.Blast.NCBIStandalone`` (the plain text BLAST parser) which should populate it. There is an example of sorts in one test within ``Tests/test_NCBITextParser.py`` which might be useful. As a self ...
written 8 months ago by Peter5.6k
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Comment: C: AttributeError: 'Hit' object has no attribute 'sacc_ver'
... What version of Biopython do you have? If updating does not fix this you might want to report this at https://github.com/biopython/biopython/issues ...
written 9 months ago by Peter5.6k
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Comment: C: biopython esearch not giving all children taxIDs
... Oh good. I should have tried the example myself really to confirm my hunch. Thanks! ...
written 9 months ago by Peter5.6k
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Comment: C: biopython esearch not giving all children taxIDs
... Unfortunately, I think you might have to list all the child taxon identifiers explicitly - but try exploring the web interface for building an advanced query first in case that shows a better solution. ...
written 10 months ago by Peter5.6k

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