minor fixes

geneontology · Mar 11, 2020 · 6b0ff9c · 6b0ff9c
1 parent 5969dcb
commit 6b0ff9c
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Showing 3 changed files with 1 addition and 6 deletions.
diff --git a/pathway_connections.py b/pathway_connections.py
@@ -38,8 +38,8 @@
     "stabilization" : "GO:0003674",
     "sumoylation" : "GO:0061665",
     "s-nitrosylation" : "GO:0035605", # peptidyl-cysteine S-nitrosylase activity
-    "transcriptional regulation" : "GO:0140110",
     "transcriptional activation": "GO:0140110",
+    "transcriptional regulation": "GO:0140110",
     "transcriptional repression": "GO:0140110",
     "translation regulation": "GO:0045182",
     "trimethylation" : "GO:0008276",
@@ -205,13 +205,11 @@ def __init__(self, filename=None):
 
                     # If up-regulates (including any variants of this), use RO:0002629 if DIRECT, and use RO:0002213 if not DIRECT or UNKNOWN
                     relation = None
-
                     if line["EFFECT"].startswith("up-regulates"):
                         if line["DIRECT"] == "YES":
                             relation = "RO:0002629"
                         elif line["DIRECT"] == "NO":
                             relation = "RO:0002213"
-
                     # If down-regulates (including any variants of this), use RO:0002630 if DIRECT, and use RO:0002212 if not DIRECT or UNKNOWN
                     elif line["EFFECT"].startswith("down-regulates"):
                         if line["DIRECT"] == "YES":
@@ -225,7 +223,6 @@ def __init__(self, filename=None):
                     elif line["EFFECT"] == "form complex":
                         continue
 
-
                     pc = PathwayConnection(
                         line["IDA"],
                         line["IDB"],

diff --git a/pathway_importer.py b/pathway_importer.py
@@ -5,7 +5,6 @@
 from prefixcommons.curie_util import expand_uri
 from pathway_connections import PathwayConnectionSet
 import argparse
-import os
 
 ro = OboRO()
 ENABLED_BY = URIRef(expand_uri(ro.enabled_by))

diff --git a/requirements.txt b/requirements.txt
@@ -6,7 +6,6 @@ chardet==3.0.4
 click==6.7
 decorator==4.2.1
 gocamgen==0.0.4
-
 idna==2.6
 isodate==0.6.0
 isort==4.3.4