0.6.9 create_dataset improved with pandarallel

docs/source/installation.rst

@@ -33,4 +33,5 @@ Additionally, required packages include:
 - pytorch-lightning==1.9.0
 - torchmetrics
 - biopython
-- fair-esm
+- fair-esm
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+- pandarallel
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requirements.txt

@@ -11,4 +11,5 @@ scikit-learn
 pytorch-lightning==1.9.0
 torchmetrics
 biopython
-fair-esm
+fair-esm
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+pandarallel
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senseppi/commands/create_dataset.py

@@ -11,7 +11,7 @@ import gzip
 import shutil
 import random
 from ..network_utils import get_string_url, DOWNLOAD_LINK_STRING
-
+from pandarallel import pandarallel
 
 def _count_generator(reader):
     b = reader(1024 * 1024)
@@ -182,7 +182,7 @@ class STRINGDatasetCreation:
         interactions = pd.read_csv("protein.pairs_{}.tsv.tmp".format(self.species), sep='\t')
 
         logging.info('Generating negative pairs.')
-        tqdm.pandas()
+        pandarallel.initialize(progress_bar=True)
 
         proteins1 = random.choices(proteins, k=len(interactions) * 12)
         proteins2 = random.choices(proteins, k=len(interactions) * 12)
@@ -191,7 +191,7 @@ class STRINGDatasetCreation:
         logging.info('Negative pairs generated. Filtering out duplicates.')
 
         # Make protein1 and protein2 in alphabetical order
-        negative_pairs['protein1'], negative_pairs['protein2'] = zip(*negative_pairs.progress_apply(
+        negative_pairs['protein1'], negative_pairs['protein2'] = zip(*negative_pairs.parallel_apply(
             lambda x: (x['protein1'], x['protein2']) if x['protein1'] < x['protein2'] else (
                 x['protein2'], x['protein1']), axis=1))
         negative_pairs = negative_pairs.drop_duplicates()
@@ -199,17 +199,17 @@ class STRINGDatasetCreation:
         logging.info('Duplicates filtered out. Filtering out pairs that are already in the positive interactions file.')
 
         negative_pairs = negative_pairs[
-            ~negative_pairs.progress_apply(lambda x: len(interactions[(interactions['protein1'] == x[
+            ~negative_pairs.parallel_apply(lambda x: len(interactions[(interactions['protein1'] == x[
                 'protein1']) & (interactions['protein2'] == x['protein2'])]) > 0, axis=1)]
         negative_pairs = negative_pairs[
-            ~negative_pairs.progress_apply(lambda x: len(interactions[(interactions['protein1'] == x[
+            ~negative_pairs.parallel_apply(lambda x: len(interactions[(interactions['protein1'] == x[
                 'protein2']) & (interactions['protein2'] == x['protein1'])]) > 0, axis=1)]
 
         logging.info(
             'Pairs that are already in the positive interactions file filtered out. Filtering out pairs that are in '
             'the same cluster with proteins interacting with a given one already.')
 
-        negative_pairs = negative_pairs[~negative_pairs.progress_apply(
+        negative_pairs = negative_pairs[~negative_pairs.parallel_apply(
             lambda x: clusters_preprocessed[x['protein2']] in [clusters_preprocessed[i] for i in
                                                                interactions[interactions['protein1'] == x['protein1']][
                                                                    'protein2'].unique()], axis=1)]
@@ -253,10 +253,10 @@ def add_args(parser):
                         help="The Taxon identifier of the organism of interest.")
     parser.add_argument("--interactions", type=str, default=None,
                         help="The physical links (full) file from STRING for the "
-                             "organism of interest.")
+                             "organism of interest. If not provided, the file will be downloaded from STRING.")
     parser.add_argument("--sequences", type=str, default=None,
-                        help="The sequences file downloaded from the same page of STRING. "
-                             "For both files see https://string-db.org/cgi/download")
+                        help="The fasta file with sequences. If not provided, it will be downloaded from "
+                             "STRING. For both files see https://string-db.org/cgi/download")
     parser.add_argument("--not_remove_long_short_proteins", action='store_true',
                         help="If specified, does not remove proteins "
                              "shorter than --min_length and longer than --max_length. "

setup.py

@@ -42,6 +42,7 @@ setup(
         "pytorch-lightning==1.9.0",
         "torchmetrics",
         "biopython",
-        "fair-esm"
+        "fair-esm",
+        "pandarallel",
     ],
 )
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