Moderator: Peter
Peter ♦ 5.8k
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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).
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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 15 months ago by
Peter ♦ 5.8k
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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 15 months ago by
Peter ♦ 5.8k
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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 15 months ago by
Peter ♦ 5.8k
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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 15 months ago by
Peter ♦ 5.8k
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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 15 months ago by
Peter ♦ 5.8k
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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 15 months ago by
Peter ♦ 5.8k
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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 19 months ago by
Peter ♦ 5.8k
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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 19 months ago by
Peter ♦ 5.8k
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... 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 19 months ago by
Peter ♦ 5.8k
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... 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 19 months ago by
Peter ♦ 5.8k
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