diff PDAUG_Peptide_Core_Functions/PDAUG_Peptide_Core_Functions.py @ 0:7557b48b2872 draft

"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PDAUG_Peptide_Core_Functions/PDAUG_Peptide_Core_Functions.py	Wed Oct 28 02:10:12 2020 +0000
@@ -0,0 +1,168 @@
+from modlamp.core import BaseSequence
+import pandas as pd
+import os, sys
+import argparse
+
+
+parser = argparse.ArgumentParser(description='Deployment tool')
+subparsers = parser.add_subparsers()
+
+mutateAA = subparsers.add_parser('mutateAA')
+mutateAA.add_argument("-I","--InFile", required=True, default=None, help="Input fasta sequence")
+mutateAA.add_argument("-N","--nr", required=True, default=None, help="Number of mutations to perform per sequence")
+mutateAA.add_argument("-P","--Prob", required=True, default=None, help="Probability of mutating a sequence")
+mutateAA.add_argument("-F","--FastOut", required=False, default='Out.fasta', help="Mutated output fasta")
+
+filterduplicates = subparsers.add_parser('filterduplicates')
+filterduplicates.add_argument("-I","--InFile", required=True, default=None, help="Input file")
+filterduplicates.add_argument("-F","--FastOut", required=False, default='Out.fasta', help="Output file")
+
+
+keepnaturalaa = subparsers.add_parser('keepnaturalaa')
+keepnaturalaa.add_argument("-I","--InFile", required=True, default=None, help="Inputt file")
+keepnaturalaa.add_argument("-F","--FastOut", required=False, default='Out.fasta', help="Output file")
+
+
+filteraa = subparsers.add_parser('filteraa')
+filteraa.add_argument("-I","--InFile", required=True, default=None, help="Input file")
+filteraa.add_argument("-F","--FastOut", required=False, default='Out.fasta', help="Output file")
+filteraa.add_argument("-A","--FilterAA", required=True, default=None, help="Filter amino acide")
+
+args = parser.parse_args()
+
+if sys.argv[1] == 'mutateAA':
+
+    Pep = []
+    Index = []
+
+    f = open(args.InFile)
+    lines = f.readlines()
+
+    for line in lines:
+        if '>' in line:
+            line = line.strip('\n')
+            line = line.strip('\r')
+            Index.append(line)
+        else:
+            line = line.strip('\n')
+            line = line.strip('\r')
+            Pep.append(line)
+
+    b = BaseSequence(len(Pep))
+    b.sequences = Pep
+    b.mutate_AA(int(args.nr), float(args.Prob))
+    OutPep = b.sequences
+
+    OutFasta = open(args.FastOut, 'w')
+
+    for i,O in enumerate(OutPep):
+
+        OutFasta.write(Index[i]+'\n')
+        OutFasta.write(O+'\n')
+
+
+elif sys.argv[1] == 'filterduplicates':
+
+    Pep = []
+    Index = []
+
+    f = open(args.InFile)
+    lines = f.readlines()
+
+    for line in lines:
+        if '>' in line:
+            line = line.strip('\n')
+            line = line.strip('\r')
+            Index.append(line)
+        else:
+            line = line.strip('\n')
+            line = line.strip('\r')
+            Pep.append(line)
+
+    b = BaseSequence(len(Pep))
+
+    b.sequences = Pep
+
+    b.filter_duplicates()
+
+    OutPep = b.sequences
+
+    OutFasta = open(args.FastOut, 'w')
+
+    for i,O in enumerate(OutPep):
+
+        OutFasta.write(Index[i]+'\n')
+        OutFasta.write(O+'\n')
+
+
+elif sys.argv[1] == 'keepnaturalaa':
+
+    Pep = []
+    Index = []
+
+    f = open(args.InFile)
+    lines = f.readlines()
+
+    for line in lines:
+        if '>' in line:
+            line = line.strip('\n')
+            line = line.strip('\r')
+            Index.append(line)
+        else:
+            line = line.strip('\n')
+            line = line.strip('\r')
+            Pep.append(line)
+
+    b = BaseSequence(len(Pep))
+    b.sequences = Pep
+    b.keep_natural_aa()
+
+    OutFasta = open(args.FastOut, 'w')
+
+    OutPep = b.sequences
+
+    for i,O in enumerate(OutPep):
+
+        OutFasta.write(Index[i]+'\n')
+        OutFasta.write(O+'\n')
+
+
+elif sys.argv[1] == 'filteraa':
+
+    Pep = []
+    Index = []
+
+    f = open(args.InFile)
+    lines = f.readlines()
+
+    for line in lines:
+        if '>' in line:
+            line = line.strip('\n')
+            line = line.strip('\r')
+            Index.append(line)
+        else:
+            line = line.strip('\n')
+            line = line.strip('\r')
+            Pep.append(line)
+
+
+    b = BaseSequence(len(Pep))
+    b.sequences = Pep
+
+    FilterAA = args.FilterAA.split(',')
+
+    b.filter_aa(FilterAA)
+
+    OutPep = b.sequences
+
+    OutFasta = open(args.FastOut, 'w')
+
+    for i,O in enumerate(OutPep):
+
+        OutFasta.write(Index[i]+'\n')
+        OutFasta.write(O+'\n')
+    
+
+
+
+