Update to version 1.1

Author: Jan Ludwiczak

pipred.py

@@ -1,19 +1,20 @@
 import argparse
 from Bio import SeqIO
 import os
+os.environ['TF_CPP_MIN_LOG_LEVEL'] = '3'
+
 import sys
 import random
 import numpy as np
 from utils import enc_seq_onehot, enc_pssm, is_fasta, get_pssm_sequence, PiPred_Model, decode,exit
-import keras.backend as K
+import tensorflow as tf
+tf.compat.v1.logging.set_verbosity(tf.compat.v1.logging.ERROR)
+import tensorflow.keras.backend as K
+
+
 
-# cx_freeze specific
-if getattr(sys, 'frozen', False):
-    my_loc = os.path.dirname(os.path.abspath(sys.executable))
-else:
-    my_loc = os.path.dirname(os.path.realpath(__file__))
+my_loc = os.path.dirname(os.path.abspath(__file__))
 
-#my_loc = os.path.dirname(os.path.abspath(__file__))
 parser = argparse.ArgumentParser(description='PiPred')
 parser.add_argument('-i',
                     help='Input file with sequence in fasta format.',
@@ -60,7 +61,7 @@
     print("ERROR: Sequence identifiers in the fasta file are not unique!")
     exit()
 # Check sequence length and presence of non standard residues
-aa1 = "ACDEFGHIKLMNPQRSTVWY"
+aa1 = "ACDEFGHIKLMNPQRSTVWYX"
 for entry, seq in zip(entries, sequences):
     if not (len(seq) >= 25 and len(seq) <= 700):
         print('ERROR: Not accepted sequence length (ID %s - %s). Only sequences between 30 and 700 residues are accepted!' % (
@@ -104,11 +105,10 @@
     enc_sequences.append(np.concatenate((enc_seq_onehot(seq, pad_length=700),
                                          enc_pssm(pssm_fn, pad_length=700)), axis=1))
 
-# Create model (supress warnings).
-stderr = sys.stderr
-sys.stderr = open(os.devnull, 'w')
+# Create model 
 model = PiPred_Model()
-sys.stderr = stderr
+
+
 enc_sequences = np.asarray(enc_sequences)
 
 

requirements.txt

@@ -1,16 +1,30 @@
-biopython==1.70
-bleach==1.5.0
-enum34==1.1.6
-h5py==2.7.1
-html5lib==0.9999999
-Keras==2.2.0
-Markdown==2.6.11
-numpy==1.14.3
-protobuf==3.6.0
-PyYAML==3.12
-scipy==1.1.0
-six==1.11.0
-setuptools==39.1.0
-tensorflow==1.10.0
-tensorflow-tensorboard==0.4.0
-Werkzeug==0.14.1
+absl-py==0.11.0
+astor==0.8.1
+biopython==1.78
+cached-property==1.5.2
+gast==0.2.2
+google-pasta==0.2.0
+grpcio==1.33.2
+h5py==2.10.0
+importlib-metadata==3.1.0
+joblib==0.17.0
+Keras-Applications==1.0.8
+Keras-Preprocessing==1.1.2
+Markdown==3.3.3
+numpy==1.18.5
+opt-einsum==3.3.0
+pandas==1.1.4
+protobuf==3.14.0
+python-dateutil==2.8.1
+pytz==2020.4
+scikit-learn==0.23.2
+scipy==1.5.4
+six==1.15.0
+tensorboard==1.15.0
+tensorflow-estimator==1.15.1
+tensorflow-gpu==1.15.4
+termcolor==1.1.0
+threadpoolctl==2.1.0
+Werkzeug==1.0.1
+wrapt==1.12.1
+zipp==3.4.0