Merge pull request #80 from Hoeze/utr_dl

UTR data loader and cleanup of protein dataloader

Author: Hoeze

.circleci/config.yml

@@ -10,11 +10,6 @@ variables:
       name: create env
       command: |
         conda create -n kipoi-dev python=3.6
-  create_env_py35: &create_env_py35
-    run:
-      name: create env
-      command: |
-        conda create -n kipoi-dev python=3.5
   install_git_lfs: &install_git_lfs
     run:
       name: Install git-lfs
@@ -43,7 +38,7 @@ variables:
         apt-get update -y
         apt-get install build-essential -y
         conda install -y cython
-        conda install -y -c bioconda cyvcf2 pybedtools genomelake pyfaidx
+        conda install -y -c bioconda cyvcf2 pybedtools genomelake pyfaidx biopython
   install_kipoi: &install_kipoi
     run:
       name: Install Kipoi
@@ -82,8 +77,8 @@ variables:
     run:
       name: run coveralls
       command: |
-          source activate kipoi-dev
-          coveralls || true
+        source activate kipoi-dev
+        coveralls || true
   store_test_results: &store_test_results
     store_test_results:
       path: test-reports
@@ -113,23 +108,6 @@ jobs:
       - *store_test_results
       - *store_test_artifacts
 
-  test-py35:
-    docker:
-      - image: continuumio/miniconda3:4.5.12
-    working_directory: ~/repo
-    steps:
-      - checkout
-      - *update_conda
-      - *create_env_py35
-      - *update_pytorch
-      - *install_conda_deps
-      - *install_kipoi
-      - *install_kipoiseq
-      - *kipoi_ls
-      - *run_tests
-      - *run_coveralls
-      - *store_test_results
-      - *store_test_artifacts
 
 
   build-deploy-docs:
@@ -170,7 +148,6 @@ workflows:
   test:
     jobs:
       - test-py36
-      - test-py35
       - build-deploy-docs:
           requires:
             - test-py36

kipoiseq/__init__.py

@@ -10,5 +10,3 @@
 from . import dataloaders
 from . import extractors
 from . import transforms
-
-

kipoiseq/dataclasses.py

@@ -6,6 +6,8 @@
 from copy import deepcopy
 # from kipoi_utils.data_utils import numpy_collate, numpy_collate_concat
 import math
+
+
 # import numpy as np
 # -------------------------------------------
 # basepair implementation
@@ -91,9 +93,8 @@ def from_cyvcf(cls, obj):
         # if there is a deletion
         # empty string
         if len(obj.ALT) == 0:
-            obj.ALT = [''] 
-        
-            
+            obj.ALT = ['']
+
         return cls(chrom=obj.CHROM,
                    pos=obj.POS,
                    ref=obj.REF,
@@ -104,10 +105,10 @@ def from_cyvcf(cls, obj):
                    info=dict(obj.INFO),
                    source=obj,
                    )
-    
+
     @classmethod
     def from_cyvcf_and_given_alt(cls, obj, alt):
-            
+
         return cls(chrom=obj.CHROM,
                    pos=obj.POS,
                    ref=obj.REF,