Hi,
The following code (luckily) partial achieved what I wanted, but I
still have few questions:
#!/usr/bin/python3
import os.path
INFILEEXT=".txt"
OUTFILEEXT=".new"
DICTIONARYFILE="dictionary.pdb"
orig_dictionary={}
new_dictionary={}
abetaABresidues={}
def processonefiledata(infilename):
with open(infilename,"r") as f:
for line in f:
parts=line.strip().split()
orig_dictionary[parts[0]]=parts[1]
def build_abetadictionary(infilename,olddict):
with open(infilename,"r") as f:
for line in f:
parts=line.strip().split()
if parts[0] != "85CUR" and (parts[0] not in abetaABresidues.keys()):
abetaABresidues[parts[0]]=0
for residues, numbers in abetaABresidues.items():
if residues in olddict.keys():
new_dictionary[residues]=olddict[residues]
else:
new_dictionary[residues]=0
with open(base+OUTFILEEXT,"w") as f:
for residues, numbers in new_dictionary.items():
print(residues,numbers,file=f)
## Q1: How can I sort the results, like the effect of | sort -g
from something like:
84ALA 12
:
:
83ILE 28
:
:
to
:
83ILE 28
84ALA 12
:
if __name__=="__main__":
for filename in os.listdir("."):
base, ext =os.path.splitext(filename)
if ext == INFILEEXT:
print(filename)
processonefiledata(filename)
build_abetadictionary(DICTIONARYFILE,orig_dictionary)
Thanks for any comments or suggestions you may give.
The relevant testing file are attached below links:
https://docs.google.com/open?id=0B93SVRfpVVg3YjdhNjlmYTAtMTdkYy00ZTNjLThkOWEtOGMyNTM1YTBiMmU4
https://docs.google.com/open?id=0B93SVRfpVVg3OWNiZmUwODktMDU4Ny00ZDUyLWExYzQtM2E2ZmY5NGJhNzgz
https://docs.google.com/open?id=0B93SVRfpVVg3MTBmNTM3M2UtYjdiMC00N2UwLWE1YTQtNmU3OGQzOGYwNDc3
Best regards,
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