Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Add the phenotype module #755

Closed
wants to merge 89 commits into from
Closed

Add the phenotype module #755

wants to merge 89 commits into from

Commits on Jan 20, 2016

  1. Bio.Phenomics: read/write Phenotype Microarray data 

    Provides access to PlateRecord and WellRecord objects
PM data can be read from csv or JSON files
PM data can be written to JSON files
    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    f76954f View commit details
    Browse the repository at this point in the history

  2. Bio.Phenomics: tests

    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    4e71a9c View commit details
    Browse the repository at this point in the history

  3. Tests: use biopython StringIO

    @mgalardini
    Marco Galardini authored and mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    e3a2da4 View commit details
    Browse the repository at this point in the history

  4. Bio.Phenomics -> Bio.Phenotype

    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    6ddfd40 View commit details
    Browse the repository at this point in the history

  5. tests: Bio.Phenomics -> Bio.Phenotype

    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    79940c3 View commit details
    Browse the repository at this point in the history

  6. Phenotype: docstring style update

    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    414bf46 View commit details
    Browse the repository at this point in the history

  7. Bio.Phenotype: access PlateRecord rows and columns like in ALignIO

    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    b7a55cf View commit details
    Browse the repository at this point in the history

  8. Tests: Bio.Phenotype PlateRecord new __getitem__ access

    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    6b3fe40 View commit details
    Browse the repository at this point in the history

  9. Tests: Bio.Phenotype doesn't have doctests

    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    7598669 View commit details
    Browse the repository at this point in the history

  10. Bio.Phenotype: no more camel cases

    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    240f4b2 View commit details
    Browse the repository at this point in the history

  11. Tests: Bio.Phenotype no more camel cases

    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    4677c62 View commit details
    Browse the repository at this point in the history

  12. Bio.Phenotype: PM plates have no alphabet

    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    a194934 View commit details
    Browse the repository at this point in the history

  13. Bio.Phenotype: calculate curve parameters 

    Three sigmoid functions are used
This approach needs scipy, a warning is raised if it's missing
    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    eb9bd28 View commit details
    Browse the repository at this point in the history

  14. Bio.Phenotype: forgot some docstrings

    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    43bce10 View commit details
    Browse the repository at this point in the history

  15. Bio.Phenotype: some more missing docstrings

    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    370e2ab View commit details
    Browse the repository at this point in the history

  16. Bio.Phenotype: better handling of sigmoid functions in fit()

    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    c4bc86f View commit details
    Browse the repository at this point in the history

  17. Tests: test sigmoid fitting

    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    056fe71 View commit details
    Browse the repository at this point in the history

  18. Bio.Phenotype: fix the WellRecord slicing

    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    6889eec View commit details
    Browse the repository at this point in the history

  19. Bio.Phenotype: improve sigmoid fitting 

    An initial guess of the curve parameters are added: without
this, the sigmoid function fitting was incorrect in most
of the cases.
    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    92a3e56 View commit details
    Browse the repository at this point in the history

  20. Bio.Phenotype: slightly better guess for y0 parameter

    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    b992bbc View commit details
    Browse the repository at this point in the history

  21. Bio.Phenotype: consistent exception when importing pm_fitting

    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    4485152 View commit details
    Browse the repository at this point in the history

  22. Revert "Tests: Bio.Phenotype doesn't have doctests" 

    This reverts commit 28a0c3f.

The wrong file has been modified in the previous commit
    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    0562535 View commit details
    Browse the repository at this point in the history

  23. Bio.Phenotype -> Bio.phenotype

    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    a661993 View commit details
    Browse the repository at this point in the history

  24. Styling improvements for Bio.phenotype

    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    d45fc21 View commit details
    Browse the repository at this point in the history

  25. Bio.phenotype: no mutable defaults

    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    edb489e View commit details
    Browse the repository at this point in the history

  26. Bio.phenotype: better imports for logistic fitting

    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    408a5db View commit details
    Browse the repository at this point in the history

  27. Bio.phenotype: fix tests

    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    4a6f87e View commit details
    Browse the repository at this point in the history

  28. Bio.phenotype: PEP8 fixes

    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    a6b644a View commit details
    Browse the repository at this point in the history

  29. Scar files removed

    @mgalardini
    Marco Galardini authored and mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    8be948c View commit details
    Browse the repository at this point in the history

  30. No dictionary comprehension in python2.6 

    Including more PEP8 changes
    @mgalardini
    Marco Galardini authored and mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    0015597 View commit details
    Browse the repository at this point in the history

  31. Tests: fix Bio.phenotype

    @mgalardini
    Marco Galardini authored and mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    8116eae View commit details
    Browse the repository at this point in the history

  32. Bio.phenotype: python2.6 compatibility fix

    @mgalardini
    Marco Galardini authored and mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    acb2e05 View commit details
    Browse the repository at this point in the history

  33. Tests: another python2.6 fix

    @mgalardini
    Marco Galardini authored and mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    a752cb0 View commit details
    Browse the repository at this point in the history

  34. Bio.phenotype: more code improvements and tests

    @mgalardini
    Marco Galardini authored and mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    0d1cff4 View commit details
    Browse the repository at this point in the history

  35. Avoid parsing errors when csv files end with empty spaces

    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    0941a99 View commit details
    Browse the repository at this point in the history

  36. Correctly check for last plate presence for csv files

    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    0bc7a66 View commit details
    Browse the repository at this point in the history

  37. Final correction for the last plate parsing

    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    4e335f6 View commit details
    Browse the repository at this point in the history

  38. bio.phenotype: more standard plates to be considered

    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    da87963 View commit details
    Browse the repository at this point in the history

  39. Bio.phenotype: warning -> warnings

    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    20f9f6d View commit details
    Browse the repository at this point in the history

  40. Example plate file added

    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    854b93e View commit details
    Browse the repository at this point in the history

  41. Bio.phenotype: docs syntax typo

    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    04b7c18 View commit details
    Browse the repository at this point in the history

  42. Bio.Phenomics: read/write Phenotype Microarray data 

    Provides access to PlateRecord and WellRecord objects
PM data can be read from csv or JSON files
PM data can be written to JSON files
    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    4c9a4f6 View commit details
    Browse the repository at this point in the history

  43. Bio.Phenomics: tests

    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    1c3144d View commit details
    Browse the repository at this point in the history

  44. Tests: use biopython StringIO

    @mgalardini
    Marco Galardini authored and mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    0aa5973 View commit details
    Browse the repository at this point in the history

  45. Bio.Phenomics -> Bio.Phenotype

    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    02d0734 View commit details
    Browse the repository at this point in the history

  46. tests: Bio.Phenomics -> Bio.Phenotype

    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    bfb20b0 View commit details
    Browse the repository at this point in the history

  47. Phenotype: docstring style update

    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    3a59c5f View commit details
    Browse the repository at this point in the history

  48. Bio.Phenotype: access PlateRecord rows and columns like in ALignIO

    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    c54aa95 View commit details
    Browse the repository at this point in the history

  49. Tests: Bio.Phenotype PlateRecord new __getitem__ access

    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    61ed24e View commit details
    Browse the repository at this point in the history

  50. Tests: Bio.Phenotype doesn't have doctests

    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    e62dc42 View commit details
    Browse the repository at this point in the history

  51. Bio.Phenotype: no more camel cases

    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    02e90ed View commit details
    Browse the repository at this point in the history

  52. Tests: Bio.Phenotype no more camel cases

    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    964c63f View commit details
    Browse the repository at this point in the history

  53. Bio.Phenotype: PM plates have no alphabet

    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    7ce42ce View commit details
    Browse the repository at this point in the history

  54. Bio.Phenotype: calculate curve parameters 

    Three sigmoid functions are used
This approach needs scipy, a warning is raised if it's missing
    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    d8d65f0 View commit details
    Browse the repository at this point in the history

  55. Bio.Phenotype: forgot some docstrings

    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    1b7845d View commit details
    Browse the repository at this point in the history

  56. Bio.Phenotype: some more missing docstrings

    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    4100ce6 View commit details
    Browse the repository at this point in the history

  57. Bio.Phenotype: better handling of sigmoid functions in fit()

    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    d8f7a92 View commit details
    Browse the repository at this point in the history

  58. Tests: test sigmoid fitting

    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    5c10fcd View commit details
    Browse the repository at this point in the history

  59. Bio.Phenotype: fix the WellRecord slicing

    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    9d72c28 View commit details
    Browse the repository at this point in the history

  60. Bio.Phenotype: improve sigmoid fitting 

    An initial guess of the curve parameters are added: without
this, the sigmoid function fitting was incorrect in most
of the cases.
    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    85d52d0 View commit details
    Browse the repository at this point in the history

  61. Bio.Phenotype: slightly better guess for y0 parameter

    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    7869e44 View commit details
    Browse the repository at this point in the history

  62. Bio.Phenotype: consistent exception when importing pm_fitting

    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    90f827d View commit details
    Browse the repository at this point in the history

  63. Revert "Tests: Bio.Phenotype doesn't have doctests" 

    This reverts commit 28a0c3f.

The wrong file has been modified in the previous commit
    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    36a880d View commit details
    Browse the repository at this point in the history

  64. Bio.Phenotype -> Bio.phenotype

    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    d90a48d View commit details
    Browse the repository at this point in the history

  65. Styling improvements for Bio.phenotype

    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    7e8f3cd View commit details
    Browse the repository at this point in the history

  66. Bio.phenotype: no mutable defaults

    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    e96c235 View commit details
    Browse the repository at this point in the history

  67. Bio.phenotype: better imports for logistic fitting

    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    ea819dc View commit details
    Browse the repository at this point in the history

  68. Bio.phenotype: fix tests

    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    69d7ab8 View commit details
    Browse the repository at this point in the history

  69. Bio.phenotype: PEP8 fixes

    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    acc193e View commit details
    Browse the repository at this point in the history

  70. Scar files removed

    @mgalardini
    Marco Galardini authored and mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    c2a7cf2 View commit details
    Browse the repository at this point in the history

  71. No dictionary comprehension in python2.6 

    Including more PEP8 changes
    @mgalardini
    Marco Galardini authored and mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    33cb862 View commit details
    Browse the repository at this point in the history

  72. Tests: fix Bio.phenotype

    @mgalardini
    Marco Galardini authored and mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    1dee94d View commit details
    Browse the repository at this point in the history

  73. Bio.phenotype: python2.6 compatibility fix

    @mgalardini
    Marco Galardini authored and mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    d4f865d View commit details
    Browse the repository at this point in the history

  74. Tests: another python2.6 fix

    @mgalardini
    Marco Galardini authored and mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    7768cbf View commit details
    Browse the repository at this point in the history

  75. Bio.phenotype: more code improvements and tests

    @mgalardini
    Marco Galardini authored and mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    1f3b51b View commit details
    Browse the repository at this point in the history

  76. Avoid parsing errors when csv files end with empty spaces

    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    1e0138c View commit details
    Browse the repository at this point in the history

  77. Correctly check for last plate presence for csv files

    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    e2d2c18 View commit details
    Browse the repository at this point in the history

  78. Final correction for the last plate parsing

    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    c94c241 View commit details
    Browse the repository at this point in the history

  79. bio.phenotype: more standard plates to be considered

    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    aa6af82 View commit details
    Browse the repository at this point in the history

  80. Bio.phenotype: warning -> warnings

    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    519b00c View commit details
    Browse the repository at this point in the history

  81. Documentation update with the Bio.phenotype module

    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    69c0608 View commit details
    Browse the repository at this point in the history

  82. Typo in Bio.phenotype tests

    @mgalardini
    mgalardini committed Jan 20, 2016
    Configuration menu
    Copy the full SHA
    9dc8d13 View commit details
    Browse the repository at this point in the history

Commits on Jan 21, 2016

  1. Add trailing comma in modules list

    @mgalardini
    mgalardini committed Jan 21, 2016
    Configuration menu
    Copy the full SHA
    94e8625 View commit details
    Browse the repository at this point in the history

  2. Docstrings multiline style fix

    @mgalardini
    mgalardini committed Jan 21, 2016
    Configuration menu
    Copy the full SHA
    bd42ff9 View commit details
    Browse the repository at this point in the history

  3. Docs multiline code style fix

    @mgalardini
    mgalardini committed Jan 21, 2016
    Configuration menu
    Copy the full SHA
    22eb5a8 View commit details
    Browse the repository at this point in the history

  4. PlateRecord and WellRecord repr style fix

    @mgalardini
    mgalardini committed Jan 21, 2016
    Configuration menu
    Copy the full SHA
    6a244cd View commit details
    Browse the repository at this point in the history

  5. No mutable objects as function keyword arguments

    @mgalardini
    mgalardini committed Jan 21, 2016
    Configuration menu
    Copy the full SHA
    fbeb252 View commit details
    Browse the repository at this point in the history

  6. Test the repr changes for PlateRecord and WellRecord

    @mgalardini
    mgalardini committed Jan 21, 2016
    Configuration menu
    Copy the full SHA
    d51574d View commit details
    Browse the repository at this point in the history

Commits on Apr 18, 2016

  1. Add a BiopythonExperimentalWarning to the phenotype module

    @mgalardini
    mgalardini committed Apr 18, 2016
    Configuration menu
    Copy the full SHA
    0944f92 View commit details
    Browse the repository at this point in the history