hi I have a file and it is in chunks:
I want to be able to select the number that follows 'Elution: ' where the line
startswith (TITLE)(say
72.958) and check if it is larger than my choice of number (say
71.4). If it is then I want to print chunk from BEGIN LINE to END
LINE separated by one empty line.
I wrote the following script, when executed in IDEL or python mode, it works.
however I use python test_script_test.py , I get name error:
could you please help me whats wrong here.
thanks
Command line mode:
$ python test_script_test.py
Traceback (most recent call last):
File "test_script_test.py", line 14, in <module>
newk = dat[mystartl:myfinish]
NameError: name 'myfinish' is not defined
In python mode:
>>> f1 = open('test','r')
>>> da = f1.read().split('\n')
>>> dat = da[:-1]
>>> mytimep = 71.4
>>> for i in range(len(dat)):
... if dat[i].startswith('BEGIN LINE'):
... mystartl = i
... if dat[i].startswith('END LINE'):
... myfinish = i
... if dat[i].startswith('Title'):
... col = dat[i].split(',')
... x= float(col[2].split()[1])
... if x > mytimep:
... newk = dat[mystartl:myfinish]
... for x in newk:
... print x
...
BEGIN LINE
MYMASS=643.973587067287
CHARGE=2+
Title=File:xyx, sample= Cyst 7 band 7 (sample number 8), Elution: 72.958 to
73.198 min, Period: 1
132.4082 0.0323
133.0418 0.2596
136.0618 0.3276
138.0482 0.546
140.4848 0.0499
140.7096 0.0333
END LINE
BEGIN LINE
MYMASS=643.973587067287
CHARGE=2+
Title=File:xyx, sample= Cyst 7 band 7 (sample number 8), Elution: 72.958 to
73.198 min, Period: 1
132.4082 0.0323
133.0418 0.2596
136.0618 0.3276
138.0482 0.546
140.4848 0.0499
140.7096 0.0333
my file:
BEGIN LINE
MYMASS=643.973587067287
CHARGE=2+
Title=File:xyx, sample= Cyst 7 band 7 (sample number 8), Elution: 72.958 to
73.198 min, Period: 1
132.4082 0.0323
133.0418 0.2596
136.0618 0.3276
138.0482 0.546
140.4848 0.0499
140.7096 0.0333
END LINE
BEGIN LINE
MYMASS=643.973587067287
CHARGE=2+
Title=File:xyx, sample= Cyst 7 band 7 (sample number 8), Elution: 72.958 to
73.198 min, Period: 1
132.4082 0.0323
133.0418 0.2596
136.0618 0.3276
138.0482 0.546
140.4848 0.0499
140.7096 0.0333
END LINE
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