how two join and arrange two files together

amrita at iisermohali.ac.in amrita at iisermohali.ac.in
Thu Jul 23 09:22:15 CEST 2009


Hi,

I have two large files:

FileA
15 ALA H = 8.05	N = 119.31 CA = 52.18 HA = 4.52	C =
21 ALA H = 7.66	N = 123.58 CA = 54.33 HA = C = 179.35
23 ALA H = 8.78	N =  CA =  HA = C = 179.93.................

and

FileB
21 ALA  helix (helix_alpha, helix2)
23 ALA  helix (helix_alpha, helix3)
38 ALA  helix (helix_alpha, helix3)...........

now what i want that i will make another file in which i will join the two
file in such a way that only matching entries will come like here 21 and
23 ALA is in both files, so the output will be something like:-

21 ALA H = 7.66	N = 123.58 CA = 54.33 HA = C = 179.35| 21 ALA  helix
(helix_alpha, helix2)
23 ALA H = 8.78	N =  CA =  HA = C = 179.93|23 ALA  helix (helix_alpha,
helix3)

and further i will make another file in which i will be able to put those
lines form this file based on the missing atom value, like for 21 ALA HA
is not defined so i will put it another file based on its HA missing value
similarly i will put 23 ALA on another file based on its missing N,CA and
HA value.

I tried to join the two file based on their matching entries by:---
>>>from collections import defaultdict
>>>
>>> if __name__ == "__main__":
...      a = open("/home/amrita/alachems/chem100.txt")
...      c = open("/home/amrita/secstr/secstr100.txt")
...
>>> def source(stream):
...     return (line.strip() for line in stream)
...
...
>>> def merge(sources):
...     for m in merge([source(a),source(c)]):
...         print "|".join(c.ljust(10) for c in m)
...

but it is not giving any value.






Thanks,
Amrita Kumari
Research Fellow
IISER Mohali
Chandigarh
INDIA




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