Moderator: Peter
Peter ♦ 5.9k
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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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... And as of Biopython 1.78, you can't specify the alphabet - Bio.Alphabet was removed. ...
written 2 days ago by
Peter ♦ 5.9k
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... Bug should have already been fixed in Biopython 1.77 ...
written 3 months ago by
Peter ♦ 5.9k
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... 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
Peter ♦ 5.9k
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... 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
Peter ♦ 5.9k
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... 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
Peter ♦ 5.9k
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... 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
Peter ♦ 5.9k
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... 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
Peter ♦ 5.9k
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... 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
Peter ♦ 5.9k
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... 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
Peter ♦ 5.9k
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... 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
Peter ♦ 5.9k
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