Moderator: Peter

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Peter5.9k
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Scotland, UK
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http://blastedbio.blog...
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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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Comment: C: Which Alphabet Type Should I Use With Fasta Files In Biopython?
... And as of Biopython 1.78, you can't specify the alphabet - Bio.Alphabet was removed. ...
written 2 days ago by Peter5.9k
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Answer: A: SeqIO error: local variable 'qual' referenced before assignment
... Bug should have already been fixed in Biopython 1.77 ...
written 3 months ago by Peter5.9k
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Comment: C: Code for splitting long string into Genbank record gives error
... It seems you must have been using an older version of Biopython, the code I shared needed Biopython 1.73 onwards (which I didn't realise at the time). It is always a good idea to state the version of a tool you are using in your question - and also the version of Python as that can be very important ...
written 21 months ago by Peter5.9k
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Comment: C: Code for splitting long string into Genbank record gives error
... You need Biopython 1.73 for this to work: qualifier = Qualifier("/translation=", '"%s"' % row['Seq']) As you worked out, on older versions you must use: qualifier = Qualifier() qualifier.key = "/translation=" qualifier.value = '"%s"' % row['Seq'] ...
written 21 months ago by Peter5.9k
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Comment: C: Creating Genbank files with Python using BioGenBankRecord
... You can specify the organism the ``SeqRecord`` for output in GenBank format via ``Bio.SeqIO.write(...)`` as the ``SOURCE`` and `` ORGANISM`` lines. You would need to populate ``seq_record.annotations['source']``, and this is the approach I would recommend here. Relevant code: https://github.com/bio ...
written 21 months ago by Peter5.9k
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Answer: A: Code for splitting long string into Genbank record gives error
... The ``SeqRecord`` approach is intended to be more 'high level' with less of the file format details exposed directly. The GenBank specific ``Record`` object approach is quite 'low level' with lots of details you have to do yourself. But the immediate problem is you need to use as list of ``Qualifier ...
written 21 months ago by Peter5.9k
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Comment: C: Creating Genbank files with Python using BioGenBankRecord
... You should be able to use ``Record(...)`` with arguments, but may of the terms in your first attempt are not available as arguments to the class initialiser: https://github.com/biopython/biopython/blob/biopython-173/Bio/GenBank/Record.py#L164 ...
written 21 months ago by Peter5.9k
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Comment: C: Creating Genbank files with Python using BioGenBankRecord
... No, the ``SeqFeature`` class goes with the ``SeqRecord`` class and these are intended to be file format neutral as used in ``Bio.SeqIO``, but the design was heavily influenced by GenBank files. The GenBank ``Record`` class uses its own GenBank specific ``Feature`` objects etc all defined in https:// ...
written 21 months ago by Peter5.9k
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Comment: C: (solved) I couldn't reproduce the problem of max_target_seqs
... I checked too, before simply asking - the reason there is a cache on archive.org from 2 November is because I requested the snapshot ;) ...
written 2.1 years ago by Peter5.9k
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Comment: C: Using STDIN with BioPython's PDB methods
... Strange but perhaps you are right and something happens inside argparse? I would suggest setting the defaults to the string ``"-"`` (minus sign) in the command line API, and when you come to call ``get_structure`` use: if args.input == "-": structure = PDB.get_structure("File from stdi ...
written 2.1 years ago by Peter5.9k

Latest awards to Peter

Scholar 21 months ago, created an answer that has been accepted. For A: Error importing Biopython module
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?
Scholar 21 months ago, created an answer that has been accepted. For A: Can't access individual attributes of tabular outfmt 6 blast output while parsin
Scholar 21 months ago, created an answer that has been accepted. For A: How detect complement reverse sequence in a EMBL/Genbank file with biopython?
Scholar 21 months ago, created an answer that has been accepted. For A: Mapping blast xml report elements to their variable names in biopython
Scholar 21 months ago, created an answer that has been accepted. For A: Filter out specific reads from FASTQ files
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?
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: Is There A Way To Sort A Biopython Alignment By A Feature Other Then Id?
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Scholar 3.4 years ago, created an answer that has been accepted. For A: The Longest Chromosome > Sizeof(Int32)
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Appreciated 3.7 years ago, created a post with more than 5 votes. For A: Speed Of Efetch In Biopython
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Epic Question 4.6 years ago, created a question with more than 10,000 views. For Bash $@ (Dollar At Variable) Loses Quote Characters
Scholar 4.7 years ago, created an answer that has been accepted. For A: The Longest Chromosome > Sizeof(Int32)
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