0.5.6 documentation and parser updates

senseppi/__init__.py

-__version__ = "0.5.5"
+__version__ = "0.5.6"
 __author__ = "Konstantin Volzhenin"
 
 from . import model, commands, esm2_model, dataset, utils, network_utils

senseppi/__main__.py

 import argparse
 import logging
+import os
 import torch
 from .commands import *
 from senseppi import __version__
@@ -44,8 +45,12 @@ def main():
 
         logging.info('Device used: {}'.format(params.device))
 
+    if hasattr(params, 'model_path'):
+        if params.model_path is None:
+            params.model_path = os.path.join(os.path.dirname(__file__), "default_model", "senseppi.ckpt")
+
     params.func(params)
 
 
 if __name__ == "__main__":
-    main()
+    main()
\ No newline at end of file

senseppi/commands/create_dataset.py

@@ -258,8 +258,9 @@ def add_args(parser):
                         help="The sequences file downloaded from the same page of STRING. "
                              "For both files see https://string-db.org/cgi/download")
     parser.add_argument("--not_remove_long_short_proteins", action='store_true',
-                        help="Whether to remove proteins that are too short or too long. "
-                             "Normally, the long and short proteins are removed.")
+                        help="If specified, does not remove proteins "
+                             "shorter than --min_length and longer than --max_length. "
+                             "By default, long and short proteins are removed.")
     parser.add_argument("--min_length", type=int, default=50,
                         help="The minimum length of a protein to be included in the dataset.")
     parser.add_argument("--max_length", type=int, default=800,
@@ -290,27 +291,30 @@ def main(params):
         logging.info('STRING version: {}'.format(version))
 
         try:
-            url = "{0}protein.physical.links.full.v{1}/{2}.protein.physical.links.full.v{1}.txt.gz".format(DOWNLOAD_LINK_STRING, version, params.species)
+            url = "{0}protein.physical.links.full.v{1}/{2}.protein.physical.links.full.v{1}.txt.gz".format(
+                DOWNLOAD_LINK_STRING, version, params.species)
             string_file_name_links = "{1}.protein.physical.links.full.v{0}.txt".format(version, params.species)
-            wget.download(url, out=string_file_name_links+'.gz')
-            with gzip.open(string_file_name_links+'.gz', 'rb') as f_in:
+            wget.download(url, out=string_file_name_links + '.gz')
+            with gzip.open(string_file_name_links + '.gz', 'rb') as f_in:
                 with open(string_file_name_links, 'wb') as f_out:
                     shutil.copyfileobj(f_in, f_out)
 
-            url = "{0}protein.sequences.v{1}/{2}.protein.sequences.v{1}.fa.gz".format(DOWNLOAD_LINK_STRING, version, params.species)
+            url = "{0}protein.sequences.v{1}/{2}.protein.sequences.v{1}.fa.gz".format(DOWNLOAD_LINK_STRING, version,
+                                                                                      params.species)
             string_file_name_seqs = "{1}.protein.sequences.v{0}.fa".format(version, params.species)
-            wget.download(url, out=string_file_name_seqs+'.gz')
-            with gzip.open(string_file_name_seqs+'.gz', 'rb') as f_in:
+            wget.download(url, out=string_file_name_seqs + '.gz')
+            with gzip.open(string_file_name_seqs + '.gz', 'rb') as f_in:
                 with open(string_file_name_seqs, 'wb') as f_out:
                     shutil.copyfileobj(f_in, f_out)
         except HTTPError:
             raise Exception('The files are not available for the specified species. '
-                         'There might be two reasons for that: \n '
-                         '1) the species is not available in STRING. Please check the STRING species list to verify. \n'
-                         '2) the download link has changed. Please raise an issue in the repository. ')
+                            'There might be two reasons for that: \n '
+                            '1) the species is not available in STRING. Please check the STRING species list to '
+                            'verify. \n '
+                            '2) the download link has changed. Please raise an issue in the repository. ')
 
-        os.remove(string_file_name_seqs+'.gz')
-        os.remove(string_file_name_links+'.gz')
+        os.remove(string_file_name_seqs + '.gz')
+        os.remove(string_file_name_links + '.gz')
 
         params.interactions = string_file_name_links
         params.sequences = string_file_name_seqs
@@ -330,4 +334,3 @@ if __name__ == '__main__':
     parser = add_args(parser)
     params = parser.parse_args()
     main(params)
-

senseppi/commands/predict.py

@@ -68,9 +68,10 @@ def add_args(parser):
     parser._action_groups[0].add_argument("fasta_file", type=pathlib.Path,
                                           help="FASTA file on which to extract the ESM2 representations and then test.",
                                           )
-    predict_args.add_argument("--model_path", type=str, default=os.path.join(os.path.dirname(__file__), "..", "default_model", "senseppi.ckpt"),
-                                          help="A path to .ckpt file that contains weights to a pretrained model. If "
-                                               "None, the senseppi trained version is used.")
+    predict_args.add_argument("--model_path", type=str, default=None,
+                              help="A path to .ckpt file that contains weights to a pretrained model. If "
+                                   "None, the preinstalled senseppi.ckpt trained version is used. "
+                                   "(Trained on human PPIs)")
     predict_args.add_argument("--pairs_file", type=str, default=None,
                               help="A path to a .tsv file with pairs of proteins to test (Optional). If not provided, "
                                    "all-to-all pairs will be generated.")
@@ -79,7 +80,7 @@ def add_args(parser):
                                    "(.tsv format will be added automatically)")
     predict_args.add_argument("--with_self", action='store_true',
                               help="Include self-interactions in the predictions."
-                                   "By default they are not included since they were not part of training but"
+                                   "By default they are not included since they were not part of training but "
                                    "they can be included by setting this flag to True.")
     predict_args.add_argument("-p", "--pred_threshold", type=float, default=0.5,
                               help="Prediction threshold to determine interacting pairs that "

senseppi/commands/predict_string.py

@@ -109,7 +109,7 @@ def main(params):
 
         sns.heatmap(labels_heatmap, cmap=cmap, vmin=0, vmax=1,
                     ax=ax1, mask=labels_heatmap == -1,
-                    cbar=False, square=True)  # , linewidths=0.5, linecolor='white')
+                    cbar=False, square=True)
 
         cbar = ax1.figure.colorbar(ax1.collections[0], ax=ax1, location='right', pad=0.15)
         cbar.ax.yaxis.set_ticks_position('right')
@@ -172,26 +172,28 @@ def add_args(parser):
     parser._action_groups[0].add_argument("genes", type=str, nargs="+",
                                           help="Name of gene to fetch from STRING database. Several names can be "
                                                "typed (separated by whitespaces).")
-    string_pred_args.add_argument("--model_path", type=str, default=os.path.join(os.path.dirname(__file__), "..", "default_model", "senseppi.ckpt"),
+    string_pred_args.add_argument("--model_path", type=str, default=None,
                                   help="A path to .ckpt file that contains weights to a pretrained model. If "
-                                       "None, the senseppi trained version is used.")
+                                       "None, the preinstalled senseppi.ckpt trained version is used. "
+                                       "(Trained on human PPIs)")
     string_pred_args.add_argument("-s", "--species", type=int, default=9606,
-                                  help="Species from STRING database. Default: 9606 (H. Sapiens)")
+                                  help="Species from STRING database. Default: H. Sapiens")
     string_pred_args.add_argument("-n", "--nodes", type=int, default=10,
-                                  help="Number of nodes to fetch from STRING database. Default: 10")
+                                  help="Number of nodes to fetch from STRING database. ")
     string_pred_args.add_argument("-r", "--score", type=int, default=0,
-                                  help="Score threshold for STRING connections. Range: (0, 1000). Default: 0")
+                                  help="Score threshold for STRING connections. Range: (0, 1000). ")
     string_pred_args.add_argument("-p", "--pred_threshold", type=int, default=500,
-                                  help="Prediction threshold. Range: (0, 1000). Default: 500")
+                                  help="Prediction threshold. Range: (0, 1000). ")
     string_pred_args.add_argument("--graphs", action='store_true',
                                   help="Enables plotting the heatmap and a network graph.")
     string_pred_args.add_argument("-o", "--output", type=str, default="preds_from_string",
                                   help="A path to a file where the predictions will be saved. "
                                        "(.tsv format will be added automatically)")
-    string_pred_args.add_argument("--network_type", type=str, default="physical",
-                                  help="Network type: \"physical\" or \"functional\". Default: \"physical\"")
+    string_pred_args.add_argument("--network_type", type=str, default="physical", choices=['physical', 'functional'],
+                                  help="Network type to fetch from STRING database. ")
     string_pred_args.add_argument("--delete_proteins", type=str, nargs="+", default=None,
-                                  help="List of proteins to delete from the graph. Default: None")
+                                  help="List of proteins to delete from the graph. "
+                                       "Several names can be specified separated by whitespaces. ")
 
     parser = SensePPIModel.add_model_specific_args(parser)
     remove_argument(parser, "--lr")

senseppi/commands/test.py

@@ -37,16 +37,17 @@ def add_args(parser):
     parser = add_general_args(parser)
 
     test_args = parser.add_argument_group(title="Predict args")
-    parser._action_groups[0].add_argument("pairs_file", type=str, default=None,
+    parser._action_groups[0].add_argument("pairs_file", type=str,
                                           help="A path to a .tsv file with pairs of proteins to test.")
     parser._action_groups[0].add_argument("fasta_file",
                                           type=pathlib.Path,
                                           help="FASTA file on which to extract the ESM2 "
                                                "representations and then evaluate.",
                                           )
-    test_args.add_argument("--model_path", type=str, default=os.path.join(os.path.dirname(__file__), "..", "default_model", "senseppi.ckpt"),
+    test_args.add_argument("--model_path", type=str, default=None,
                            help="A path to .ckpt file that contains weights to a pretrained model. If "
-                                "None, the senseppi trained version is used.")
+                                "None, the preinstalled senseppi.ckpt trained version is used. "
+                                "(Trained on human PPIs)")
     test_args.add_argument("-o", "--output", type=str, default="test_metrics",
                            help="A path to a file where the test metrics will be saved. "
                                 "(.tsv format will be added automatically)")

senseppi/esm2_model.py

@@ -16,8 +16,10 @@ def add_esm_args(parent_parser):
     parser = parent_parser.add_argument_group(title="ESM2 model args",
                                               description="ESM2: Extract per-token representations and model "
                                                           "outputs for sequences in a FASTA file. "
-                                                          "If you would like to use the basic version of SENSE-PPI "
-                                                          "do no edit the default values of the arguments below. ")
+                                                          "The representations are saved in --output_dir_esm folder so "
+                                                          "they can be reused in multiple runs. In order to reuse the "
+                                                          "embeddings, make sure that --output_dir_esm is set to the "
+                                                          "correct folder.")
     parser.add_argument(
         "--model_location_esm",
         type=str, default="esm2_t36_3B_UR50D",

senseppi/network_utils.py

@@ -107,7 +107,9 @@ def get_interactions_from_string(gene_names, species=9606, add_nodes=10, require
     string_interactions = pd.DataFrame([line.split('\t') for line in lines[1:]], columns=lines[0].split('\t'))
 
     if 'Error' in string_interactions.columns:
-        raise Exception(string_interactions['ErrorMessage'].values[0])
+        err_msg = string_interactions['ErrorMessage'].values[0]
+        err_msg = err_msg.replace('<br>', '\n').replace('<br/>', '\n').replace('<p>', '\n').replace('</p>', '\n')
+        raise Exception(err_msg)
     if len(string_interactions) == 0:
         raise Exception('No interactions found. Please revise your input parameters.')
 

senseppi/utils.py

@@ -7,15 +7,28 @@ import argparse
 
 
 class ArgumentParserWithDefaults(argparse.ArgumentParser):
-    def add_argument(self, *args, help=None, default=None, **kwargs):
-        if help is not None:
-            kwargs['help'] = help
-        if default is not None and args[0] != '-h':
-            kwargs['default'] = default
-            if help is not None:
-                kwargs['help'] += ' Default: {}'.format(default)
+    def add_argument(self, *args, **kwargs):
+        if 'help' in kwargs and kwargs['help'] is not argparse.SUPPRESS and 'default' in kwargs and args[0] != '-h':
+            kwargs['help'] += ' (Default: {})'.format(kwargs['default'])
         super().add_argument(*args, **kwargs)
 
+    def add_argument_group(self, *args, **kwargs):
+        group = ArgumentGroupWithDefaults(self, *args, **kwargs)
+        self._action_groups.append(group)
+        return group
+
+
+class ArgumentGroupWithDefaults(argparse._ArgumentGroup):
+    def add_argument(self, *args, **kwargs):
+        if 'help' in kwargs and kwargs['help'] is not argparse.SUPPRESS and 'default' in kwargs and args[0] != '-h':
+            kwargs['help'] += ' (Default: {})'.format(kwargs['default'])
+        super().add_argument(*args, **kwargs)
+
+    def add_argument_group(self, *args, **kwargs):
+        group = self._ArgumentGroup(self, *args, **kwargs)
+        self._action_groups.append(group)
+        return group
+
 
 def add_general_args(parser):
     parser.add_argument("-v", "--version", action="version", version="SENSE_PPI v{}".format(__version__))