fixup

meta_data_analysis/surface_res3.py

@@ -0,0 +1,55 @@
+#!/usr/bin/python
+# Surface calculation
+#
+from pylab import *
+from Bio.SeqUtils import ProtParamData
+from Bio.SeqUtils.ProtParam import ProteinAnalysis
+from Bio import SeqIO
+from Bio.Alphabet.IUPAC import IUPACProtein
+import pprint as pp
+import pandas as pd
+import numpy as np
+
+
+infile='/home/tanu/git/Data/pyrazinamide/input/original/3pl1.fasta.txt'
+
+window=9
+offset=round((window/2)-0.5)
+
+fh = open(infile)
+
+for record in SeqIO.parse(fh, "fasta"):
+    id = record.id
+    seq = record.seq
+    num_residues = len(seq)
+fh.close()
+
+sequence = str(seq)
+
+X = ProteinAnalysis(sequence)
+
+values=(X.protein_scale(ProtParamData.kd,window))
+
+print('Sequence Length:', num_residues)
+print('Post-Analysis Length:',len(values))
+print('Window Length:',window)
+print('Window Offset:',offset)
+
+dfSeq=pd.DataFrame({'seq':list(sequence)})
+dfVals=pd.DataFrame({'values':values})
+
+# FIXME:
+# These need to be offset by 'offset' from the start and finish
+# so that the sequence letters line up with the value calculated
+df=pd.concat([dfSeq,dfVals], ignore_index=True, axis=1)
+
+print(df)
+#df=pd.DataFrame(list(sequence), values)
+
+#plot(185, values, linewidth=1.0)
+#axis(xmin = 1, xmax = num_residues)
+#xlabel("Residue Number")
+#ylabel("Hydrophobicity")
+#title("K&D Hydrophobicity for " + id)
+#show()
+