Moderator: Peter

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Peter5.6k
Reputation:
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Location:
Scotland, UK
Website:
http://blastedbio.blog...
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Last seen:
4 weeks ago
Joined:
8 years, 6 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

<prev • 616 results • page 1 of 62 • next >
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Comment: C: Trimming TruSeq Universal Adapter (Trimmomatic)
... 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 Peter5.6k
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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 10 weeks 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 10 weeks 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 10 weeks 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 6 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 10 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 10 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 10 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 11 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 11 months ago by Peter5.6k

Latest awards to Peter

Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Is There A Way To Sort A Biopython Alignment By A Feature Other Then Id?
Commentator 12 months ago, created a comment with at least 3 up-votes. For C: Is There A Way To Sort A Biopython Alignment By A Feature Other Then Id?
Scholar 15 months ago, created an answer that has been accepted. For A: The Longest Chromosome > Sizeof(Int32)
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Good Answer 18 months ago, created an answer that was upvoted at least 5 times. For A: Speed Of Efetch In Biopython
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Is There A Way To Sort A Biopython Alignment By A Feature Other Then Id?
Appreciated 2.1 years ago, created a post with more than 5 votes. For A: Speed Of Efetch In Biopython
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: How To Have Only Id And Sequence Printed In Output After Parse Sequences From A
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: Is There A Way To Sort A Biopython Alignment By A Feature Other Then Id?
Epic Question 2.4 years ago, created a question with more than 10,000 views. For Bash $@ (Dollar At Variable) Loses Quote Characters
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Is There A Way To Sort A Biopython Alignment By A Feature Other Then Id?
Scholar 2.5 years ago, created an answer that has been accepted. For A: The Longest Chromosome > Sizeof(Int32)
Good Answer 2.7 years ago, created an answer that was upvoted at least 5 times. For A: Biopython Embl Parser Only Reads One Entry
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: Is There A Way To Sort A Biopython Alignment By A Feature Other Then Id?
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: Is There A Way To Sort A Biopython Alignment By A Feature Other Then Id?
Scholar 2.8 years ago, created an answer that has been accepted. For A: The Longest Chromosome > Sizeof(Int32)
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: Is There A Way To Sort A Biopython Alignment By A Feature Other Then Id?
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: Is There A Way To Sort A Biopython Alignment By A Feature Other Then Id?
Appreciated 3.4 years ago, created a post with more than 5 votes. For A: Biopython Embl Parser Only Reads One Entry
Scholar 3.4 years ago, created an answer that has been accepted. For A: The Longest Chromosome > Sizeof(Int32)
Teacher 3.4 years ago, created an answer with at least 3 up-votes. For A: Is There A Way To Sort A Biopython Alignment By A Feature Other Then Id?
Scholar 3.4 years ago, created an answer that has been accepted. For A: BioPython: convert fasta to fastq without quality score input file
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Scholar 3.5 years ago, created an answer that has been accepted. For A: BioPython: convert fasta to fastq without quality score input file

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