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Moderator: Peter

gravatar for Peter
Peter ♦ 5.6k
Reputation:
5,600
Status:
Trusted
Location:
Scotland, UK
Website:
http://blastedbio.blog...
Scholar ID:
Google Scholar Page
Last seen:
2 months ago
Joined:
8 years, 2 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: 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 9 weeks ago by Peter ♦ 5.6k
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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 6 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 6 months ago by Peter ♦ 5.6k
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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 6 months ago by Peter ♦ 5.6k
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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 7 months ago by Peter ♦ 5.6k
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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 7 months ago by Peter ♦ 5.6k
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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 8 months ago by Peter ♦ 5.6k
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Comment: C: Refseq Proteins For A Given Taxid
... It might be best to email the NCBI Entrez team with the full details - it sounds like something on their server is failing. ...
written 8 months ago by Peter ♦ 5.6k
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Comment: C: extract list of positions from fasta file biopython
... Does you FASTA file have one sequence in it, or many? If one, you only need to open the FASTA file once, and you should use ``SeqIO.read`` for that. If many, you need to know which sequence each of the values `x` refers to. Perhaps ``SeqIO.index`` would be useful here for loading the relevant reco ...
written 9 months ago by Peter ♦ 5.6k
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Comment: C: tool_dependencies.xml Not Working - Why?
... Did you open this on the Galaxy Q&A site? Could you add the link here please. ...
written 9 months ago by Peter ♦ 5.6k

Latest awards to Peter

Teacher 5 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 8 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 11 months ago, created an answer that has been accepted. For A: The Longest Chromosome > Sizeof(Int32)
Appreciated 13 months ago, created a post with more than 5 votes. For A: Speed Of Efetch In Biopython
Appreciated 14 months ago, created a post with more than 5 votes. For A: Speed Of Efetch In Biopython
Good Answer 14 months ago, created an answer that was upvoted at least 5 times. For A: Speed Of Efetch In Biopython
Teacher 14 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 21 months ago, created a post with more than 5 votes. For A: Speed Of Efetch In Biopython
Teacher 21 months 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 21 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?
Epic Question 2.0 years ago, created a question with more than 10,000 views. For Bash $@ (Dollar At Variable) Loses Quote Characters
Teacher 2.0 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?
Scholar 2.2 years ago, created an answer that has been accepted. For A: The Longest Chromosome > Sizeof(Int32)
Good Answer 2.4 years ago, created an answer that was upvoted at least 5 times. For A: Biopython Embl Parser Only Reads One Entry
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?
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 2.4 years ago, created an answer that has been accepted. For A: The Longest Chromosome > Sizeof(Int32)
Teacher 2.7 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 2.9 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 3.0 years ago, created a post with more than 5 votes. For A: Biopython Embl Parser Only Reads One Entry
Scholar 3.0 years ago, created an answer that has been accepted. For A: The Longest Chromosome > Sizeof(Int32)
Teacher 3.1 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?
Scholar 3.1 years ago, created an answer that has been accepted. For A: BioPython: convert fasta to fastq without quality score input file
Scholar 3.1 years ago, created an answer that has been accepted. For A: BioPython: convert fasta to fastq without quality score input file
Scholar 3.2 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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