Moderator: Peter
Peter ♦ 5.6k
- Reputation:
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- Location:
- Scotland, UK
- Website:
- http://blastedbio.blog...
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- Google Scholar Page
- Last seen:
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- Joined:
- 8 years, 6 months ago
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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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... I was just looking at this for a sample where FASTQC reported lots of the Illumina Universal Adapter present. Looking in the files included with FASTQC, this is defined in Configuration/adapter_list.txt (under the conda opt folder if you use conda), and says:
Illumina Universal Adapter AGAT ...
written 28 days ago by
Peter ♦ 5.6k
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... 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 10 weeks ago by
Peter ♦ 5.6k
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... 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 10 weeks ago by
Peter ♦ 5.6k
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... I just hit something similar, logged as https://github.com/PacificBiosciences/pbcore/issues/117 ...
written 10 weeks ago by
Peter ♦ 5.6k
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... 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 6 months ago by
Peter ♦ 5.6k
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... 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 10 months ago by
Peter ♦ 5.6k
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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 10 months ago by
Peter ♦ 5.6k
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... 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 10 months ago by
Peter ♦ 5.6k
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... 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 11 months ago by
Peter ♦ 5.6k
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... Oh good. I should have tried the example myself really to confirm my hunch. Thanks! ...
written 11 months ago by
Peter ♦ 5.6k
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