Merge pull request #123 from pachterlab/dev

Fix Windows issue with gget setup elm

Author: lauraluebbert

gget/__init__.py

@@ -25,6 +25,6 @@
 # Mute numexpr threads info
 logging.getLogger("numexpr").setLevel(logging.WARNING)
 
-__version__ = "0.28.3"
+__version__ = "0.28.4"
 __author__ = "Laura Luebbert"
 __email__ = "[email protected]"

gget/gget_setup.py

@@ -25,10 +25,10 @@
 
 ## Variables for elm module
 ELM_FILES = os.path.join(PACKAGE_PATH, "elm_files")
-ELM_INSTANCES_FASTA = f"{ELM_FILES}/elm_instances.fasta"
-ELM_CLASSES_TSV = f"{ELM_FILES}/elms_classes.tsv"
-ELM_INSTANCES_TSV = f"{ELM_FILES}/elm_instances.tsv"
-ELM_INTDOMAINS_TSV = f"{ELM_FILES}/elm_interaction_domains.tsv"
+ELM_INSTANCES_FASTA = os.path.join(ELM_FILES, "elm_instances.fasta")
+ELM_CLASSES_TSV = os.path.join(ELM_FILES, "elms_classes.tsv")
+ELM_INSTANCES_TSV = os.path.join(ELM_FILES, "elm_instances.tsv")
+ELM_INTDOMAINS_TSV = os.path.join(ELM_FILES, "elm_interaction_domains.tsv")
 
 ## Variables for alphafold module
 ALPHAFOLD_GIT_REPO = "https://github.com/deepmind/alphafold"
@@ -132,10 +132,10 @@ def setup(module, verbose=True, out=None):
 
         if out is not None:
             elm_files_out = os.path.abspath(out)
-            elm_instances_fasta = f"{elm_files_out}/elm_instances.fasta"
-            elm_classes_tsv = f"{elm_files_out}/elms_classes.tsv"
-            elm_instances_tsv = f"{elm_files_out}/elm_instances.tsv"
-            elm_intdomains_tsv = f"{elm_files_out}/elm_interaction_domains.tsv"
+            elm_instances_fasta = os.path.join(elm_files_out, "elm_instances.fasta")
+            elm_classes_tsv = os.path.join(elm_files_out, "elms_classes.tsv")
+            elm_instances_tsv = os.path.join(elm_files_out, "elm_instances.tsv")
+            elm_intdomains_tsv = os.path.join(elm_files_out, "elm_interaction_domains.tsv")
 
             # Create folder for ELM files (if it does not exist)
             if not os.path.exists(elm_files_out):
@@ -151,14 +151,17 @@ def setup(module, verbose=True, out=None):
             if not os.path.exists(ELM_FILES):
                 os.makedirs(ELM_FILES)
 
+        print(platform.system())
         if platform.system() == "Windows":
             # The double-quotation marks allow white spaces in the path, but this does not work for Windows
             command = f"""
-                curl -o {elm_instances_fasta} {ELM_INSTANCES_FASTA_DOWNLOAD} \
-                &&  curl -o {elm_classes_tsv} {ELM_CLASSES_TSV_DOWNLOAD} \
-                &&  curl -o {elm_instances_tsv} {ELM_INSTANCES_TSV_DOWNLOAD} \
-                &&  curl -o {elm_intdomains_tsv} {ELM_INTDOMAINS_TSV_DOWNLOAD}
+                curl -o {elm_instances_fasta} \"{ELM_INSTANCES_FASTA_DOWNLOAD}\" \
+                &&  curl -o {elm_classes_tsv} \"{ELM_CLASSES_TSV_DOWNLOAD}\" \
+                &&  curl -o {elm_instances_tsv} \"{ELM_INSTANCES_TSV_DOWNLOAD}\" \
+                &&  curl -o {elm_intdomains_tsv} \"{ELM_INTDOMAINS_TSV_DOWNLOAD}\"
                 """
+            print(command)
+        
         else:
             command = f"""
                 curl -o '{elm_instances_fasta}' {ELM_INSTANCES_FASTA_DOWNLOAD} \