First fully assembled version 0.1.0

Comments, arguments and outdated code have to be cleaned, the version still needs some testing

senseppi/commands/test.py

@@ -37,7 +37,7 @@ def test(params):
 def add_args(parser):
     parser = add_general_args(parser)
 
-    predict_args = parser.add_argument_group(title="Predict args")
+    test_args = parser.add_argument_group(title="Predict args")
     parser._action_groups[0].add_argument("model_path", type=str,
                                           help="A path to .ckpt file that contains weights to a pretrained model.")
     parser._action_groups[0].add_argument("pairs_file", type=str, default=None,
@@ -47,10 +47,10 @@ def add_args(parser):
                                           help="FASTA file on which to extract the ESM2 "
                                                "representations and then evaluate.",
                                           )
-    predict_args.add_argument("-o", "--output", type=str, default="test_metrics",
+    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)")
-    predict_args.add_argument("--crop_data_to_model_lims", action="store_true",
+    test_args.add_argument("--crop_data_to_model_lims", action="store_true",
                               help="If set, the data will be cropped to the limits of the model: "
                                    "evaluations will be done only for proteins >50aa and <800aa.")
 

senseppi/commands/train.py

 import pytorch_lightning as pl
 from pytorch_lightning.callbacks import ModelCheckpoint
 import pathlib
+import argparse
 from ..utils import add_general_args
 from ..model import SensePPIModel
 from ..dataset import PairSequenceData

senseppi/network_utils.py

@@ -13,12 +13,11 @@ import gzip
 import shutil
 
 
-def generate_pairs(fasta_file, mode='all_to_all', with_self=False, delete_proteins=None):
+def generate_pairs_string(fasta_file, output_file, with_self=False, delete_proteins=None):
     ids = []
     for record in SeqIO.parse(fasta_file, "fasta"):
         ids.append(record.id)
 
-    if mode == 'all_to_all':
     if with_self:
         all_pairs = [p for p in product(ids, repeat=2)]
     else:
@@ -51,7 +50,7 @@ def generate_pairs(fasta_file, mode='all_to_all', with_self=False, delete_protei
         pairs = pairs[~pairs['seq1'].isin(string_ids_to_delete)]
         pairs = pairs[~pairs['seq2'].isin(string_ids_to_delete)]
 
-        pairs.to_csv('protein.actions.tsv', sep='\t', index=False, header=False)
+    pairs.to_csv(output_file, sep='\t', index=False, header=False)
 
 
 def generate_dscript_gene_names(file_path,