diff PDAUG_Peptide_Core_Descriptors/PDAUG_Peptide_Core_Descriptors.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_Descriptors/PDAUG_Peptide_Core_Descriptors.py	Wed Oct 28 02:10:12 2020 +0000
@@ -0,0 +1,43 @@
+from modlamp.core import BaseDescriptor
+from modlamp.descriptors import PeptideDescriptor
+import pandas as pd
+import argparse, os
+
+parser = argparse.ArgumentParser()
+
+parser.add_argument("-I", "--InFile", required=True, default=None, help="Input file")
+parser.add_argument("-O", "--OutFile", required=True, default=None, help="Output file")
+parser.add_argument("-N", "--Ngrams", required=True, default=None, help="ngrams")
+
+args = parser.parse_args()
+
+file = open(args.InFile)
+lines = file.readlines()
+
+Index = []
+Pep = []
+
+
+for line in lines:
+    if '>' in line:
+        Index.append(line.strip('\n'))
+    else:
+        line = line.strip('\n')
+        line = line.strip('\r')
+        Pep.append(line)
+
+df =    pd.DataFrame()
+
+for i, l in enumerate(Pep):
+
+    D = PeptideDescriptor(l)
+    D.count_ngrams([int(args.Ngrams)])
+
+    df1 = pd.DataFrame(D.descriptor, index=["sequence"+str(i),])
+    df = pd.concat([df, df1], axis=0)
+
+df =  df.fillna(0)
+df.to_csv(args.OutFile, sep='\t', index=None)
+
+
+