yes.. i want to add program 2 to program one.. i want to know what difference will
readlines() from an o/p file(containing this masterList) and directly refering to for item in masterList make..
The error can be corrected if i understand this difference...
aboxylica
Last Activity: Dec 28 '07, 08:12 AM
Joined: Jul 5 '07
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you mean it will have a "\n" that will make the diffrence. so what should i do ? add a "\n" to my list? it doesnt really make sense to me!...Leave a comment:
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basic!
i have a basic doubt.. i have a program that does a particular task..this prg(2) actually works with the o/p from another program(1). The program 1 gives the o/p in the form of a list that is written to a file.. now my program 2 works fine when i take its input as the o/p file but now i want to string in the prg2 to the prg1.
the program one works on a list called masterList.this is written to a file and taken as i/p
my program... -
i am getting an error and still many sequence headers whose values are less than 2 are printed!
but i want the headers only for those value is more than 2
Traceback (most recent call last):
File "C:\Python25\th is_final_1.py", line 165, in <module>
calcdata=compil eData(fnArray,f nSeq,arraySet,s eqSet)
File "C:\Python25\th is_final_1.py", line 137, in compileD
seqList1.ap...Leave a comment:
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i want to print the header only if it satifies the following condition:
how do i do it??
Code:return 'Sequence Header: %s\n%s' % (dataSeq[0], outStr)if (log10(num/denList[i]))>=2
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I want to know if i should write a seperate function to compute average or can i do it in the main part??Leave a comment:
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I have done this average calculation to a part of my output_file.. but i should be doing this on resultlist directly. i dont now how to exactly do that.here is the code for calculating average for a small part of my o/p file
...Code:# Open the file. File is in the same directory as source code f=file("result.txt") # Put the Contents os the testfile in list a a=f.readlines()Leave a comment:
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okay.. i dont want to do that because this is not the final result of my task so.. i am not going to write it to a file.
what i should be doing is that..
i get the results which have log values of ones with four headers...like
>skud
>scer
>smik
>spar
if my result list has something like this
Array set # = 1
Sequence set # = 3
Sequence Header:...Leave a comment:
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yup.. I got the o/p file for the last sequence file.. its about 87 KB. if i want all the values for all the 5000 files in my folder.. it will take 440MB..is it possible to write such a huge file?? because i need the entire output.Leave a comment:
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i want the entire result..i.e; all the log values greater than two(I am taking these values as one..the values lesser than this.. i dont care about). i want the entire thing written in a file.. will that be possible or will their be memory error??Leave a comment:
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but when i change
while not calcdata is None:
to while calcdata:
the array set is not iterating at all.. the set is one through out.why is this happening??
and what exactly is the difference between the two lines??
and also
if any log value is greater than two then am taking that value as one.. only for these sequences.. i want to print the seqset,arrayset and calculated value.
...Leave a comment:
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I have changed the indendation of this part so that only whatever is >1 is only printed is it correct?.. dont know if it is checking for the entire file!
...Code:for i, num in enumerate(numList): if (log10(num/denList[i]))>=2: outStr = '\n'.join(['Sequence = %s Calculation = %d' % (seqList[i], res) for i, res in enumerate(resultList)]) return 'Array set # = %d\nSequence set # = %d\nSequenceLeave a comment:
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And i also think that this program should not take such a longtime to run..though my sequence folder is 18MB and array file is 69KB. though it is pretty huge the calculation is simple only.. can i compute how long it will typically take to calculate??
I think there is some serious error
waiting for ur reply,
cheers!!Leave a comment:
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my code is running successffully.. my code ran for five hours.results were ok
but when its writing to a file it said.
We have reached the end of the file! sequence file
We have reached the end of the file! matrix file
Traceback (most recent call last):
File "C:\Python25\th is_final_1.py", line 174, in <module>
f.write('\n'.jo in(masterList))...Leave a comment:
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this is what am doing and it doesnt seem to solve the problem.
...Code:numList = [] denList = [] seqList = [] for i in xrange(len(seq) - len(subKeys)): subseq = seq[0:len(subKeys)] seqList.append(subseq) num, den = 1, 1 for j, s in enumerate(subseq): if s=="N": value[s]=0Leave a comment:
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okay.. i have to say that if it encounters "N" the value of this alphabet should be taken as "0"... I am able to do this for denominator.. but for the numerator being calculated.. i want to specify that the log value of "N" is zero .. and if many "NNNNN" come together.. this part of "NNNN" can be omitted.. how do i do this??Leave a comment:
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reading a file a printing a list of values
I have a file like this!Sequence Header: >Sbay YOR009W c606:3651..4650
Sequence = CCTAATCTTGAAAAA A Calculation = 1
Sequence = CTAATCTTGAAAAAA A Calculation = 1
Sequence = TAATCTTGAAAAAAA A Calculation = 1
Sequence = AATCTTGAAAAAAAA A Calculation = 1
Sequence = ATCTTGAAAAAAAAA A Calculation = 1
Sequence = TCTTGAAAAAAAAAA A Calculation = 1
Sequence = CTTGAAAAAAAAAAA A Calculation = 1
Sequence... -
i am encountering a problem when i run my code for a huge folder containing many sequence files.. this is what it says
Traceback (most recent call last):
File "this_final_11. py", line 163, in <module>
calcdata=compil eData(fnArray,f nSeq,arraySet,s eqSet)
File "this_final_11. py", line 121, in compileData
num *= dataArray[s][subKeys[j]]
KeyError: 'N'
...Code:def compileData(fnArray,
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oh........ i got the problem! ThanksLeave a comment:
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and here is the code with spaces removed!
...Code:from math import * print "hellllllllo" def parseArray(fn, dataset=1, key='PO', term='/'): ''' Read a formatted data file in matrix format and compile data into a dictionary ''' f = open(fn) # skip to required data set for _ in range(dataset):Leave a comment:
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