gt bioss notebooks

clreda · May 16, 2024 · dae3868 · dae3868
1 parent 8bc3729
commit dae3868
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Showing 5 changed files with 8 additions and 3 deletions.
diff --git a/GTBioss2024/README.md → Application_GTBioss2024/README.md b/GTBioss2024/README.md → Application_GTBioss2024/README.md
@@ -9,6 +9,7 @@ Note that NORDic relies on [BoneSiS](https://github.com/bioasp/bonesis) for the
 conda create -n nordic_env python=3.8 -y
 conda activate nordic_env
 
+conda install -c colomoto -y -q maboss
 python3 -m pip install nordic jupyter
 
 ## clean up (if needed)

diff --git a/GTBioss2024/synthetic_random_diff3-1.ipynb → ...TBioss2024/synthetic_random_diff3-1.ipynb b/GTBioss2024/synthetic_random_diff3-1.ipynb → ...TBioss2024/synthetic_random_diff3-1.ipynb
diff --git a/GTBioss2024/toy_reprogramming_1.ipynb → ...ion_GTBioss2024/toy_reprogramming_1.ipynb b/GTBioss2024/toy_reprogramming_1.ipynb → ...ion_GTBioss2024/toy_reprogramming_1.ipynb
diff --git a/GTBioss2024/toy_star_1.ipynb → Application_GTBioss2024/toy_star_1.ipynb b/GTBioss2024/toy_star_1.ipynb → Application_GTBioss2024/toy_star_1.ipynb
diff --git a/src/NORDic/UTILS/STRING_utils.py b/src/NORDic/UTILS/STRING_utils.py
@@ -8,7 +8,7 @@
 from io import StringIO
 from copy import deepcopy
 from subprocess import check_output as sbcheck_output
-from subprocess import call as sbcall
+from subprocess import Popen
 
 string_api_url = lambda v : "https://version-"+"-".join(v.split("."))+".string-db.org/api"
 
@@ -78,6 +78,9 @@ def get_protein_names_from_STRING(gene_list, taxon_id, app_name=None, version="1
     if ("Error" in res_df.columns):
         print("<STRING_utils> Error from STRING: %s" % str(res_df["ErrorMessage"]))
         return None
+    print(gene_list[:5])
+    print(len(gene_list))
+    print(res_df.columns)
     return res_df[["queryItem", "stringId", "preferredName", "annotation"]]
 
 def get_image_from_STRING(my_genes, taxon_id, file_name="network.png", min_score=0, network_flavor="evidence", network_type="functional", app_name=None, version="11.5", quiet=False):
@@ -318,7 +321,8 @@ def get_interactions_from_STRING(gene_list, taxon_id, min_score=0, app_name=None
     if (not quiet):
         print("<STRING> Retrieving the file from STRING", end="... ")
     if (file_folder is not None and not os.path.exists(protein_action_fname)):
-        sbcall("wget -qO- \""+STRING_url+"\" | gzip -d -c > "+protein_action_fname, shell=True)
+        proc = Popen(("wget -qO- \""+STRING_url+"\" | gzip -d -c > "+protein_action_fname).split(" "), shell=True)
+        proc.wait()
     if (file_folder is not None):
         if (not quiet):
             print("Saved at %s" % protein_action_fname)
@@ -412,4 +416,4 @@ def get_interactions_from_STRING(gene_list, taxon_id, min_score=0, app_name=None
         print("... Aggregate info once again")
     network.index = range(network.shape[0])
     network.sort_values(by="score", ascending=False)
-    return network
+    return network