kamhung.soh at gmail
May 17, 2008, 6:08 PM
Post #2 of 2
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Re: comparison of files using set function
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On Sun, 18 May 2008 00:47:55 +1000, Beema shafreen
<beema.shafreen [at] gmail> wrote:
> I have files with two column, column 1 is with id and column 2 is with
> data(sequence)
> My goal is to create a table in such a way, the column one of the table
> should have all the id from the files and next column will be have the
> respective seq of the file1 with correlation to the id and the third
> column
> will be sequence information of the next file with respective to the id
> original files look like this
>
> 45 ytut
> 46 erete
> 37 dfasf
> 45 dassdsd
>
>
> and so on for all the 10 files that is it has two column as mentioned
> above.
>
> The output should look like this:
>
> Id file1 file2 file3 file4 file5
> 43 ytuh ytuh ytuh ytuh ytuh
> 46 erteee rty ryyy ertyu
> 47 yutio rrr eeerr
>
>
>
> The goal is if the pick all the common id in the files and with their
> respective information in the adjacent rows.
> the various conditons ca also prevails
> 1) common id present in all the files, which have same information
> 2)common id present in all the files, which donot have same information
> 3) common id may not be present in all the files
>
> But the goal is exactly find the common id in all the files and add their
> corresponding information in the file to the table as per the view
> my script :
> def file1_search(*files1):
> for file1 in files1:
> gi1_lis = []
> fh = open(file1,'r')
> for line in fh.readlines():
> data1 = line.strip().split('\t')
> gi1 = data1[0].strip()
> seq1 = data1[1].strip()
> gi1_lis.append(gi1)
> return gi1_lis
> def file2_search(**files2):
> for file2 in files2:
> for file in files2[file2]:
> gi2_lis = []
> fh1 = open(file,'r')
> for line1 in fh1.readlines():
> data2 = line1.strip().split('\t')
> gi2 = data2[0].strip()
> seq2 = data2[1].strip()
> gi2_lis.append(gi2)
>
> return gi2_lis
> def set_compare(data1,data2,*files1,**files2):
> A = set(data1)
> B = set(data2)
> I = A&B # common between thesetwo sets
>
> D = A-B #57 is the len of D
> C = B-A #176 is the len of c
> # print len(C)
> # print len(D)
> for file1 in files1:
> for gi in D:
> fh = open(file1,'r')
> for line in fh.readlines():
> data1 = line.strip().split('\t')
> gi1 = data1[0].strip()
> seq1 = data1[1].strip()
> if gi == gi1:
> # print line.strip()
> pass
>
> for file2 in files2:
> for file in files2[file2]:
> for gi in C:
> fh1 = open(file,'r')
> for line1 in fh1.readlines():
> data2 = line1.strip().split('\t')
> gi2 = data2[0].strip()
> seq2 = data2[1].strip()
> if gi == gi2:
> # print line1.strip()
> pass
> if __name__ == "__main__":
> files1 = ["Fr20.txt",\
> "Fr22.txt",\
> "Fr24.txt",\
> "Fr60.txt",\
> "Fr62.txt"]
> files2 = {"data":["Fr64.txt",\
> "Fr66.txt",\
> "Fr68.txt",\
> "Fr70.txt",\
> "Fr72.txt"]}
> data1 = file1_search(*files1)
>
> """113 is the total number of gi"""
> data2 = file2_search(**files2)
> #for j in data2:
> # print j
> """232 is the total number of gi found"""
> result = set_compare(data1,data2,*files1,**files2)
>
> It doesnot work fine... some body please suggest me the way i can
> proceed .
> Thanks a lot
>
1. Test with a small number of short files with a clear idea of the
expected result.
2. Use better variable names. Names such as file1_search, file2_search,
gi, gi2, A, B, C and D make it nearly impossible to understand your code.
--
Kam-Hung Soh <a href="http://kamhungsoh.com/blog">Software Salariman</a>
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