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Hi.
I have loaded sequences to my BioSQL schema (using ruby 2.0.0, rails 3.2.15, postgresql 9.1).
I fetch sequence so:
seq = Bio::SQL.fetch_accession(entry.accession)
and export selected sequence to…
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Periodically sweep through the DbEntry objects and place gis that are not available from SLLBioSQL to its fetch queue.
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Fetch from biosql json object in 'calculate' when creating Taxon objects.
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The load_database model holds a reference to a sequence_database object and a taxonset. The taxonset is either a URL to a RESTful web service that returns a set of NCBI taxon ids (as json) or the stri…
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Replace the current hierarchical implementation with domain, kingdom, ..., species, strain.
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You guys are borrowing from a lot of previous work - Genbank feature location syntax, BioPerl location model, etc just to name a few. So I'm not really sure what you want to genuinely claim copyright,…
hlapp updated
10 years ago
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Hi Brad, AnnotationSketch is complaining about the parsed file again:
GenomeTools error: CDS feature on line 27 in file "../../mirna-django/src/scripts/tp53.gff3" has the wrong phase 0 (should be 1)
…
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I tried following http://biopython.org/wiki/GFF_Parsing to parse UCSC-generated GTF file.
After executing
```
pprint.pprint(examiner.parent_child_map(handle))
```
the output was
```
{}
```
Simila…
spock updated
13 years ago
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Biopython 1.49 beta was released November 7th, 2008. Its a bigger release than the number indicates - one nice thing was a change from requiring Numeric for some things to using numpy consistently,…
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On March 22, 2008, the biopython devs released version 1.45. I have put an updated sage package at:
http://www.d.umn.edu/~mhampton/biopython-1.45.spkg
Component: **packages: optional**
Keywords:…