On 6/13/2010 5:45 PM, Hs Hs wrote:
hi:
I have a very large file 15Gb. Starting from 15th line this file shows
the following lines:
HWUSI-EAS1211_0001:1:1:977:20764#0
HWUSI-EAS1211_0001:1:1:977:20764#0
HWUSI-EAS1521_0001:1:1:978:13435#0
HWUSI-EAS1521_0001:1:1:978:13435#0
Every two lines are part of one readgroup. I want to add two variables
to every line. First variable goes to all lines with odd numbers.
Second variable should be appended to all even number lines. like the
following:
HWUSI-EAS1211_0001:1:1:977:20764#0 RG:Z:2301
HWUSI-EAS1211_0001:1:1:977:20764#0 RG:Z:2302
HWUSI-EAS1521_0001:1:1:978:13435#0 RG:Z:2301
HWUSI-EAS1521_0001:1:1:978:13435#0 RG:Z:2302
Since I cannot read the entire file, I wanted to cat the file
something like this:
cat myfile | python myscript.py > myfile.sam
I do not know how to execute my logic after I read the line, althought
I tried:
myscript.py:
while True:
second = raw_input()
x = second.split('\t')
# do something with first 14 lines?
while True:
line = raw_input().rstrip()
if not line: break
print line + " RG:Z:2301"
line = raw_input().rstrip()
if not line: break
print line + " RG:Z:2302"
--
Bob Gailer
919-636-4239
Chapel Hill NC
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