Where communities thrive


  • Join over 1.5M+ people
  • Join over 100K+ communities
  • Free without limits
  • Create your own community
People
Repo info
Activity
  • Sep 12 23:48

    harmsm on n_mutations

    (compare)

  • Sep 08 02:30

    dependabot[bot] on pip

    (compare)

  • Sep 08 02:30
    dependabot[bot] closed #29
  • Sep 08 02:30
    dependabot[bot] commented #29
  • Sep 08 02:30
    dependabot[bot] labeled #32
  • Sep 08 02:30
    dependabot[bot] opened #32
  • Sep 08 02:30

    dependabot[bot] on pip

    Bump pillow from 7.2.0 to 8.3.2… (compare)

  • Sep 07 22:01
    harmsm closed #15
  • Sep 07 22:01
    harmsm closed #16
  • Aug 27 01:43
    dependabot[bot] edited #28
  • Aug 27 01:37
    dependabot[bot] edited #28
  • Aug 27 01:37
    dependabot[bot] synchronize #28
  • Aug 27 01:37

    dependabot[bot] on pip

    Bump py from 1.9.0 to 1.10.0 B… (compare)

  • Aug 27 01:37
    dependabot[bot] edited #28
  • Aug 27 01:30
    dependabot[bot] edited #28
  • Aug 27 01:29

    harmsm on main

    updated/upgraded tests; now pas… update to require python3.7+ Merge pull request #31 from har… (compare)

  • Aug 27 01:29
    harmsm closed #31
  • Aug 27 01:29
    harmsm opened #31
  • Aug 26 23:10

    harmsm on main

    Create python-app.yml (compare)

  • Aug 26 22:47

    harmsm on master

    (compare)

Julia Domingo
@JuliaDiumenge_twitter
Hi, my name is Julia Domingo. I am a PhD student in Ben Lehner's Lab in CRG, Barcelona. I would like to use your epistasis code (found in your published paper in Genetics 2017) to look for higher order interactions (Very cool paper by the way!).
I am having trouble installing the package gpmap
following your installation suggestions I run the follwing:

DGKQN00ZGG7F:seqspace julia$ cd ..
DGKQN00ZGG7F:Python julia$ cd gpmap/
DGKQN00ZGG7F:gpmap julia$ pip install -e .
Obtaining file:///Users/julia/Develop/Python/gpmap
Complete output from command python setup.py egg_info:
running egg_info
writing requirements to gpmap.egg-info/requires.txt
writing gpmap.egg-info/PKG-INFO
writing top-level names to gpmap.egg-info/top_level.txt
writing dependency_links to gpmap.egg-info/dependency_links.txt
error: package directory 'gpmap/evolve' does not exist

----------------------------------------

Command "python setup.py egg_info" failed with error code 1 in /Users/julia/Develop/Python/gpmap/

I always get the last error
should the folder gpmap/evolve be in the repository or should be created during installation. Due to this I cannot run the gpmap funcion GenotypePhenotypeMap.from_json
Julia Domingo
@JuliaDiumenge_twitter
I get the following error when running the example in the tutorial/docs.io

In [14]: gpm = GenotypePhenotypeMap(wildtype, genotypes, phenotypes)

AttributeError Traceback (most recent call last)

<ipython-input-14-bc69f2bd6a49> in <module>()
----> 1 gpm = GenotypePhenotypeMap(wildtype, genotypes, phenotypes)

//anaconda/lib/python2.7/site-packages/gpmap/gpm.pyc in init(self, wildtype, genotypes, phenotypes, stdeviations, log_transform, mutations, n_replicates, logbase, **kwargs)
128 # Constructs a complete sequence space and stores genotypes missing in the
129 # data as an attribute, missing_genotypes.
--> 130 self.binary = BinaryMap(self)
131
132 # Construct the error maps

//anaconda/lib/python2.7/site-packages/gpmap/binary.pyc in init(self, GPM)
49 def init(self, GPM):
50 self._GPM = GPM
---> 51 self._build()
52 self.std = StandardDeviationMap(self)
53 self.err = StandardErrorMap(self)

//anaconda/lib/python2.7/site-packages/gpmap/binary.pyc in _build(self)
121
122 # Sort binary representation to match genotypes
--> 123 mapping = self._GPM.map("genotypes", "indices")
124 binary = np.empty(self._GPM.n, dtype="U" + str(self._length))
125

//anaconda/lib/python2.7/site-packages/gpmap/base.pyc in map(self, attr1, attr2)
64
65 obj, attr = nested_attr(self, attr2)
---> 66 values = getattr(obj, attr)
67
68 # Construct map

//anaconda/lib/python2.7/site-packages/gpmap/gpm.pyc in indices(self)
321 def indices(self):
322 """Return numpy array of genotypes position. """
--> 323 return self._indices
324
325 # ----------------------------------------------------------

AttributeError: GenotypePhenotypeMap instance has no attribute '_indices'

Zachary Sailer
@Zsailer
The install problem should be fixed.
I'm trying to recreate the second problem, but I'm not getting the error you're seeing...
Try the fresh install, and let me know if it works.