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Refactor / rewrite / remove convert.py #24

Merged
merged 68 commits into from
Mar 19, 2015
Merged

Refactor / rewrite / remove convert.py #24

merged 68 commits into from
Mar 19, 2015

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bewt85
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@bewt85 bewt85 commented Mar 17, 2015

As suggested, I've mostly focused on convert.py and made minimal changes elsewhere.

I've gone for something a like a Factory without going too class mad. I could probably have added something like FeatureFactory or Attributes or an AttributeFactory but I don't think it would make things any readable yet.

There is probably a little bit more that could be done in EMBLWriter. I'd consider little changes like passing around file handles rather than filenames which means that you could use a StringIO in the tests (rather than writing to disk).

Comments / suggested changes are welcome though :)

bewt85 added 30 commits March 11, 2015 10:55
@bewt85
Change variables names in EMBLConverter
041eff2
@bewt85
Remove code from visit region which doesn't do anything, probably
3f7b307
@bewt85
Refactor out function to check if a feature is seen
d4773f3
@bewt85
Rename old EMBLWriter for refactor
09ed237
@bewt85
Update .gitignore to vim
8483ddd
@bewt85
WIP refactor header writing code
e65a761
@bewt85
WIP add init for Header object
d4e5f50 
as part of refactor
@bewt85
WIP refactor EMBLHeader to take sequence length
e3f008d
@bewt85
WIP Add EMBLFeature object
e814823
@bewt85
WIP add coordinate formatter to EMBLFeature
72cdc81
@bewt85
WIP Ignore ID and protein features
65b9d26
@bewt85
WIP reformat eC_number feature_type
602b8e1
@bewt85
WIP Lookup which attribute creator for feature
59b938d
@bewt85
WIP create features for products
8c7e9e3
@bewt85
WIP create locus_tag attributes for features
6fb8f3d
@bewt85
WIP create EC_number attributes for features
4ea94f7
@bewt85
WIP moved EC_number reformatting
9eebb17
@bewt85
WIP create inference attribute for feature
8c8f3a7
@bewt85
WIP add inference attribute to features
2ee0124
@bewt85
WIP default attribute for features
a32fc83
@bewt85
WIP: wrap multiline attributes for features
c07a7da
@bewt85
WIP pick feature builder for feature_type
13e7bea
@bewt85
WIP create most features
91fbc1a
@bewt85
WIP create translation_table attribute for feature
7812d91
@bewt85
WIP create CDS features
a6bbc06
@bewt85
WIP create uninitialized feature objects
f85cf20 
These help test the EMBLFeature methods without involving the
__init__ method
@bewt85
WIP setup initializer for EMBLFeature objects
9f38317
@bewt85
WIP don't create features for ID or protein_id types
dcdbfc9
@bewt85
WIP add test for initializing ID and protein_id features
463478d
@bewt85
WIP update whitespace
1ccaf45
bewt85 added 20 commits March 16, 2015 16:32
@bewt85
WIP format a sequence body
d276559
@bewt85
WIP format a sequence object
79d9b92
@bewt85
WIP initialize sequences
af68549
@bewt85
WIP add contig formatter
022ec55
@bewt85
WIP add add_feature to EMBLContig
d06293d
@bewt85
WIP contig can add sequence data
529d198
@bewt85
WIP add_header to contig
12cd240
@bewt85
Fix bug in tests
55a4223 
Don't compare dicitonaries with assertItemEquals, it only looks at keys
@bewt85
WIP don't add a feature to a contig if it should be ignored
297449f
@bewt85
Fix Bug: contif features are a dictionary
ff8ba99
@bewt85
WIP add sequence length to EMBLSequence
df407fd
@bewt85
Almost replaced all convert.py code
7947e81 
TODO:
- tests are failing because the features / contigs are in a different order
- remove duplication in Writer
- delete some code
- rename Writer
@bewt85
Fix bug in test case
804a899 
I'm not sure how this slipped through but the format of the features was wrong
@bewt85
Sort output, seems to work like the old version
8ebbec8
@bewt85
Removed description, not being used anyway
3d32d4f
@bewt85
Remove parameters from EMBLConverter which it doesn't need
5e8f8d7
@bewt85
Remove all uses of convert.py
fea2bc4
@bewt85
Clean up imports
23c4d69
@bewt85
Rename OldEMBLWriter back to EMBLWriter
8737fc7 
fix some whitespace
@bewt85
Add some helpful comments to EMBLContig
fb8b369
@bewt85
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bewt85 commented Mar 17, 2015

As discussed

  • I'm going to make the organism in the header wrap if it is too long
  • In fact I'll get it to error if any of the lines is more than 80 characters long
  • I'll also bump the version number

@bewt85 bewt85 closed this Mar 17, 2015
bewt85 added 4 commits March 17, 2015 13:22
@bewt85
Remove last traces of convert.py
ba2cb47 
For some reason, despite deleting convert.py, the tests kept passing
until I did a git clean.  Must be a *.pyc thing.
@bewt85
Treat source feature in header as a feature
908dabe 
The source feature within the EMBLHeader is now an actual EMBLFeature.
This is so that it wraps nicely onto the next line just like other features
@bewt85
Raise ValueError if an output line is more than 80 characters long
9d81a42
@bewt85
Update version number
cab93e7
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bewt85 commented Mar 17, 2015

Made updates as discussed above

@bewt85 bewt85 reopened this Mar 17, 2015
andrewjpage added a commit that referenced this pull request Mar 19, 2015
@andrewjpage
Merge pull request #24 from bewt85/BT5_refactoring
446df52 
Refactor / rewrite / remove convert.py
@andrewjpage andrewjpage merged commit 446df52 into sanger-pathogens:master Mar 19, 2015
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@bewt85 @andrewjpage