Moderator: Peter

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Peter5.8k
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Scotland, UK
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http://blastedbio.blog...
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Last seen:
9 months ago
Joined:
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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: 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 9 months ago by Peter5.8k
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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 9 months ago by Peter5.8k
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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 9 months ago by Peter5.8k
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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 9 months ago by Peter5.8k
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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 9 months ago by Peter5.8k
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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 9 months ago by Peter5.8k
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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 13 months ago by Peter5.8k
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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 13 months ago by Peter5.8k
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Comment: C: Using STDIN with BioPython's PDB methods
... I can see from the code you care about the peptide fragments as inferred from the structural data (breaking at discontinuities), otherwise it would be one line to get the PDB sequence out as FASTA format: $ python -c "import sys; from Bio import SeqIO; SeqIO.convert(sys.stdin, 'pdb-atom', sys.s ...
written 13 months ago by Peter5.8k
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Comment: C: Using STDIN with BioPython's PDB methods
... You have forgotten to say what version of Biopython, Python, etc you are using. Also could you simplify your example? Does this work for you - I was using Python 2.7.10 or Python 3.7.0rc1 with Biopython 1.73dev0 (i.e. a prerelease of 1.73 from git) and things seem fine? $ python -c "import sy ...
written 13 months ago by Peter5.8k

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Teacher 12 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 13 months ago, created a post with more than 5 votes. For A: Speed Of Efetch In Biopython
Teacher 13 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?
Teacher 24 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 2.2 years 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 2.5 years ago, created an answer that has been accepted. For A: The Longest Chromosome > Sizeof(Int32)
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Teacher 3.4 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
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Epic Question 3.6 years ago, created a question with more than 10,000 views. For Bash $@ (Dollar At Variable) Loses Quote Characters
Scholar 3.8 years ago, created an answer that has been accepted. For A: The Longest Chromosome > Sizeof(Int32)
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Teacher 4.0 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 4.0 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 4.0 years ago, created an answer that has been accepted. For A: The Longest Chromosome > Sizeof(Int32)
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Appreciated 4.6 years ago, created a post with more than 5 votes. For A: Biopython Embl Parser Only Reads One Entry
Scholar 4.6 years ago, created an answer that has been accepted. For A: The Longest Chromosome > Sizeof(Int32)
Scholar 4.6 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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