# HG changeset patch
# User jay
# Date 1612059421 0
# Node ID 6822d43a5f84b11bc1210e8d580faa83ba79dcc6
# Parent 48eedcb9bfa7050608c46dd247561d6edc0caba7
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit e8c8198105af7eab636fb2405e5ff335539ca14b"
diff -r 48eedcb9bfa7 -r 6822d43a5f84 PDAUG_AA_Property_Based_Peptide_Generation/PDAUG_AA_Property_Based_Peptide_Generation.py
--- 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: ")
+
+
diff -r 48eedcb9bfa7 -r 6822d43a5f84 PDAUG_Peptide_Core_Functions/PDAUG_Peptide_Core_Functions.xml
--- 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 @@
-
-
-
+
+
+
@@ -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.
-----