Merge pull request #45 from kipoi/hotfix_string_format

hotfix string formatting

Author: Avsecz

.circleci/config.yml

@@ -10,6 +10,11 @@ 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
@@ -105,6 +110,23 @@ 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:
@@ -145,6 +167,7 @@ workflows:
   test:
     jobs:
       - test-py36
+      - test-py35
       - build-deploy-docs:
           requires:
             - test-py36

kipoiseq/dataclasses.py

@@ -18,9 +18,9 @@ def __init__(self,
                  ref: str,
                  alt: str,
                  id: str = '',
-                 qual: float=0,
-                 filter: str='PASS',
-                 info: dict=None,
+                 qual: float = 0,
+                 filter: str = 'PASS',
+                 info: dict = None,
                  source=None):
         """Variant container.
 
@@ -109,7 +109,7 @@ def __hash__(self):
         return hash((self.chrom, self.pos, self.ref, self.alt))
 
     def __str__(self):
-        return f"{self.chrom}:{self.pos}:{self.ref}>{self.alt}"
+        return "{}:{}:{}>{}".format(self.chrom, self.pos, self.ref, self.alt)
 
     @classmethod
     def from_str(cls, s):
@@ -118,7 +118,8 @@ def from_str(cls, s):
         return cls(chrom=chrom, pos=int(pos), ref=ref, alt=alt)
 
     def __repr__(self):
-        return f"Variant(chrom='{self.chrom}', pos={self.pos}, ref='{self.ref}', alt='{self.alt}', id='{self.id}',...)"
+        return ("Variant(chrom='{}', pos={}, ref='{}', alt='{}', id='{}',...)"
+                .format(self.chrom, self.pos, self.ref, self.alt, self.id))
 
 
 class Interval:
@@ -141,10 +142,10 @@ def __init__(self,
                  chrom: str,
                  start: int,  # 0-based
                  end: int,  # 0-based
-                 name: str='',
-                 score: float=0,
-                 strand: str='.',
-                 attrs: dict=None):
+                 name: str = '',
+                 score: float = 0,
+                 strand: str = '.',
+                 attrs: dict = None):
         self._chrom = chrom
         self._start = start
         self._end = end
@@ -218,7 +219,7 @@ def center(self, use_strand=True):
         center = (self.end + self.start) // 2
         return center + add_offset * delta
 
-    def shift(self, x: int, use_strand: bool=True):
+    def shift(self, x: int, use_strand: bool = True):
         """Shift the interval by x.
 
         Args:
@@ -257,10 +258,11 @@ def __hash__(self):
         return hash((self.chrom, self.start, self.end, self.strand))
 
     def __str__(self):
-        return (f"{self.chrom}:{self.start}-{self.end}:{self.strand}")
+        return ("{}:{}-{}:{}".format(self.chrom, self.start, self.end, self.strand))
 
     def __repr__(self):
-        return (f"Interval(chrom='{self.chrom}', start={self.start}, end={self.end}, name='{self.name}', strand='{self.strand}', ...)")
+        return ("Interval(chrom='{}', start={}, end={}, name='{}', strand='{}', ...)"
+                .format(self.chrom, self.start, self.end, self.name, self.strand))
 
     @classmethod
     def from_str(cls, s):