changeset 6:6822d43a5f84 draft

"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit e8c8198105af7eab636fb2405e5ff335539ca14b"

--- a/PDAUG_AA_Property_Based_Peptide_Generation/PDAUG_AA_Property_Based_Peptide_Generation.py	Thu Jan 28 04:02:31 2021 +0000
+++ b/PDAUG_AA_Property_Based_Peptide_Generation/PDAUG_AA_Property_Based_Peptide_Generation.py	Sun Jan 31 02:17:01 2021 +0000
@@ -129,6 +129,21 @@
             OutFasta.write(">sequence_"+str(i)+'\n')
             OutFasta.write(O+'\n')
 
+
+def MixedLibrary_seq(seqnum, centrosymmetric, centroasymmetric, helix, kinked, oblique, rand, randAMP, randAMPnoCM, OutFasta):
+
+    lib = MixedLibrary(int(seqnum), int(centrosymmetric), int(centroasymmetric), int(helix), int(kinked), int(oblique), int(rand), int(randAMP), int(randAMPnoCM))
+    lib.generate_sequences()
+    OutFasta = open(OutFasta, 'w')
+
+    OutPep = lib.sequences
+        
+    for i,O in enumerate(OutPep):
+        OutFasta.write(">sequence_"+str(i)+'\n')
+        OutFasta.write(O+'\n')
+
+
+
 if __name__=='__main__':
 
     parser = argparse.ArgumentParser(description='Deployment tool')
@@ -192,6 +207,19 @@
     Arc.add_argument("-y","--hyd_gra", default='False', help="Method to mutate the generated sequences to have a hydrophobic gradient by substituting the last third of the sequence amino acids to hydrophobic.")
     Arc.add_argument("-O", "--OutFasta", required=True, default=None, help="Output Fasta")
 
+    Mix = subparsers.add_parser('MixedLibrary')
+    Mix.add_argument("-s","--seq_num", required=True, default=None, help="number of sequences to be generated")
+    Mix.add_argument("-c","--centrosymmetric", required=False, default=1, help="ratio of symmetric centrosymmetric sequences in the library")
+    Mix.add_argument("-ca","--centroasymmetric", required=False, default=1, help="ratio of asymmetric centrosymmetric sequences in the library")
+    Mix.add_argument("-hl","--helix", required=False, default=1, help="ratio of asymmetric centrosymmetric sequences in the library")
+    Mix.add_argument("-k","--kinked", required=False, default=1,   help="ratio of asymmetric centrosymmetric sequences in the library")
+    Mix.add_argument("-o", "--oblique", required=False, default=1,  help=" ratio of oblique oriented amphipathic helical sequences in the library")
+    Mix.add_argument("-r", "--rand", required=False, default=1,  help="ratio of random sequneces in the library")
+    Mix.add_argument("-ra", "--randAMP", required=False, default=1,  help="ratio of random sequences with APD2 amino acid distribution in the library")
+    Mix.add_argument("-rp", "--randAMPnoCM", required=False, default=1, help="ratio of random sequences with APD2 amino acid distribution without Cys and Met in the library")
+    Mix.add_argument("-O", "--OutFasta", required=True, default=None, help="Output Fasta")
+
+
     args = parser.parse_args()
 
     if sys.argv[1] == 'Random':
@@ -212,5 +240,9 @@
         AMPngrams_seq(args.seq_num, args.n_min, args.n_max, args.OutFasta)
     elif sys.argv[1] == 'AmphipathicArc':
         AmphipathicArc_seq(int(args.seq_num), int(args.lenmin_s), int(args.lenmax_s), int(args.arcsize), args.hyd_gra, args.OutFasta)
+    elif sys.argv[1] == 'MixedLibrary':
+        MixedLibrary_seq(args.seq_num, args.centrosymmetric, args.centroasymmetric, args.helix, args.kinked, args.oblique, args.rand, args.randAMP, args.randAMPnoCM, args.OutFasta)
     else:
-        print("You entered Wrong Values: ")
\ No newline at end of file
+        print("You entered Wrong Values: ")
+
+

--- a/PDAUG_Peptide_Core_Functions/PDAUG_Peptide_Core_Functions.xml	Thu Jan 28 04:02:31 2021 +0000
+++ b/PDAUG_Peptide_Core_Functions/PDAUG_Peptide_Core_Functions.xml	Sun Jan 31 02:17:01 2021 +0000
@@ -36,9 +36,9 @@
 
         <param name="CoreFunction" type="select" label="Analysis options" argument="">
           <option value="mutateAA">Mutate Amino Acid</option>
-          <option value="filterduplicates">Filter Duplicates</option>
-          <option value="keepnaturalaa">Keep Naturalaa</option>
-          <option value="filteraa">Filter Amino Acid</option>
+          <option value="filterduplicates">Filter Duplicates Peptides</option>
+          <option value="keepnaturalaa">Remove Peptides With Unatural Amino Acids</option>
+          <option value="filteraa">Filter Peptides With Specific Amino Acid</option>
         </param>
 
         <when value="mutateAA">
@@ -94,8 +94,8 @@
 
 This tool performs some core functions on the peptide sequences and equipped with various options
 
-  * **Mutated Amino Acid** Method to mutate with prob probability an nr of positions per sequence randomly.
-  * **Filter Duplicates** Method to filter duplicates in the sequences from the class attribute sequences.
+  * **Mutate Amino Acid** Method to mutate with prob probability an nr of positions per sequence randomly.
+  * **Filter Duplicates Peptides** Method to filter duplicates in the sequences from the class attribute sequences.
   * **Keep Naturalaa** Method to filter out sequences that do not contain natural amino acids. If the sequence contains a character.
   * **Filter Amino Acid** Method to filter out corresponding names and descriptor values of sequences with given amino acids in the argument list aminoacids.
 
@@ -108,13 +108,13 @@
         * **--nr**  Number of mutations. 
         * **--probability** Probability of mutating a sequence.
 
-    2 **Filter Duplicates***
+    2 **Filter Duplicates Peptides***
         * **--InFile** takes Fasta file with peptide sequences. 
 
-    3 **Keep Naturalaa**
+    3 **Remove Peptides With Unatural Amino Acids**
         * **--InFile** takes Fasta file with peptide sequences. 
 
-    4 **Filter Amino Acid**
+    4 **Filter Peptides With Specific Amino Acid**
         * **--InFile** takes Fasta file with peptide sequences. 
 
 -----