[Tutor] map one file and print it out following the sequence

[lina]

<snip>

> I think your final version of sortfile() might look something like:
>
> def sortfile(infilename=**INFILENAME, outfilename=OUTFILENAME):
>    infile = open(infilename, "r")
>    intext = infile.readlines()
>    outfile = open(OUTFILENAME, "w")
>    for chainid in CHAINID:
>        print("chain id = ",chainid)
>         sortoneblock(chainid, intext, outfile)
>    infile.close()
>    outfile.close()
>

$ python3 map-to-itp.py
{'O4': '2', 'C19': '3', 'C21': '1'}
C
Traceback (most recent call last):
  File "map-to-itp.py", line 55, in <module>
    sortfile()
  File "map-to-itp.py", line 17, in sortfile
    sortoneblock(chainid,intext,OUTFILENAME)
  File "map-to-itp.py", line 29, in sortoneblock
    f.write(line[1].strip() for line in temp)
TypeError: must be str, not generator


I don't know how to fix the writing issue.

can I write the different chainID one into the same OUTFILE?

Thanks, I attached the code I used below:

 #!/usr/bin/python3

import os.path

LINESTOSKIP=0
CHAINID="CDEFGHI"
INFILENAME="pdbone.pdb"
OUTFILENAME="sortedone.pdb"
DICTIONARYFILE="itpone.itp"
mapping={}
valuefromdict={}

def sortfile():
    intext=fetchonefiledata(INFILENAME)
    for chainid in CHAINID:
        print(chainid)
        sortoneblock(chainid,intext,OUTFILENAME)



def sortoneblock(cID,TEXT,OUTFILE):
    temp = []
    for line in TEXT:
        blocks=line.strip().split()
        if len(blocks)== 11 and  blocks[3] == "CUR" and blocks[4] == cID and
blocks[2] in mapping.keys():
            temp.append((mapping[blocks[2]],line))
    temp.sort()
    with open(OUTFILE,"w") as f:
        f.write(line[1].strip() for line in temp)




def generatedictionary(dictfilename):
    text=fetchonefiledata(DICTIONARYFILE)
    for line in text:
        parts=line.strip().split()
        if len(parts)==8:
            mapping[parts[4]]=parts[0]
    print(mapping)



def fetchonefiledata(infilename):
    text=open(infilename).readlines()
    if os.path.splitext(infilename)[1]==".itp":
        return text
    if os.path.splitext(infilename)[1]==".pdb":
        return text[LINESTOSKIP:]
    infilename.close()


if __name__=="__main__":
    generatedictionary(DICTIONARYFILE)
    sortfile()



>
>
> --
>
> DaveA
>
>
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