Mercurial > repos > jay > pdaug_sequence_based_peptide_generation
changeset 6:dd21da1ac55c draft
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit e8c8198105af7eab636fb2405e5ff335539ca14b"
| author | jay |
|---|---|
| date | Sun, 31 Jan 2021 02:26:52 +0000 |
| parents | 4a58c72769df |
| children | c3d4800f6573 |
| files | PDAUG_AA_Property_Based_Peptide_Generation/PDAUG_AA_Property_Based_Peptide_Generation.py PDAUG_Sequence_Based_Peptide_Generation/PDAUG_Sequence_Based_Peptide_Generation.xml |
| diffstat | 2 files changed, 36 insertions(+), 4 deletions(-) [+] |
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--- a/PDAUG_AA_Property_Based_Peptide_Generation/PDAUG_AA_Property_Based_Peptide_Generation.py Thu Jan 28 04:13:09 2021 +0000 +++ b/PDAUG_AA_Property_Based_Peptide_Generation/PDAUG_AA_Property_Based_Peptide_Generation.py Sun Jan 31 02:26:52 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_Sequence_Based_Peptide_Generation/PDAUG_Sequence_Based_Peptide_Generation.xml Thu Jan 28 04:13:09 2021 +0000 +++ b/PDAUG_Sequence_Based_Peptide_Generation/PDAUG_Sequence_Based_Peptide_Generation.xml Sun Jan 31 02:26:52 2021 +0000 @@ -38,9 +38,9 @@ <conditional name='SelMethod' > <param name="Method" type="select" label="Methods to generate peptides " argument=""> - <option value="MutatedPeptides">MutatedPeptides</option> - <option value="RandomPeptides">RandomPeptides</option> - <option value="SlidingWindowPeptide">SlidingWindowPeptide</option> + <option value="MutatedPeptides">Mutated Peptides</option> + <option value="RandomPeptides">Random Peptides</option> + <option value="SlidingWindowPeptide">Sliding Window Peptide</option> </param> <when value="MutatedPeptides">