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Getting non unique lines from concatenated files

 
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Top Forums UNIX for Dummies Questions & Answers Getting non unique lines from concatenated files
# 1  
Old 03-18-2011
Lightbulb Getting non unique lines from concatenated files
Hi All,

Is there a way to get NON unique lines from 2 or more concatenated files?
Basically I have several files which are very similar with the exception of few lines and I want to find out which lines are different in each file. Very simple example is

Code:
file1 contains:
1
2
3
4
5

Code:
file2 contains
1
3
4
5
6
8

How can I get an output to say 2 was unique in file1 and 3,6 and 8 were unique in file2?

I'll aprreciate your suggestions and input.
PS:I'm new to unix so your comments on the code will be of great help.
This User Gave Thanks to pawannoel For This Post:
coolcalin812
# 2  
Old 03-18-2011
Try:
Code:
comm -3 <(sort file1) <(sort file2)

BTW... 3 is not unique to file2, it is present in file1 as well.
This User Gave Thanks to bartus11 For This Post:
pawannoel
# 3  
Old 03-18-2011
Yeah infact you are right, I made a mistake about 3 being unique to file2, was meant to be 2.

Thanks a lot for the useful input, however my original .gff files to be analysed have huge/long lines and thus the output of your code is not recognisable as tab delimited file specific entires. Is there a way to arrange them in long format where file spepcific entries are separated by multiple new lines / hashes / dots / undescores for the sake of easy reading ?

Thanks Smilie
# 4  
Old 03-19-2011
You have to provide us with sample files contents, and desired output.
# 5  
Old 03-19-2011
Lightbulb
OK here is an example

file1 looks like:

Code:
chr01   levure5 SNP     12745   12745   0.000000        .        .        genotype=S;reference=C;coverage=91;refAlleleCounts=44;refAlleleStarts=28;refAlleleMeanQV=19;novelAlleleCounts=40;novelAlleleStarts=25;novelAlleleMeanQV=18;diColor1=22;diColor2=11;het=1;flag=
chr01   levure6 SNP     12745   12745   0.000000        .       .        genotype=S;reference=C;coverage=62;refAlleleCounts=29;refAlleleStarts=19;refAlleleMeanQV=19;novelAlleleCounts=32;novelAlleleStarts=20;novelAlleleMeanQV=20;diColor1=11;diColor2=22;het=1;flag=
chr01   levure7 SNP     12745   12745   0.000000        .       .        genotype=S;reference=C;coverage=24;refAlleleCounts=9;refAlleleStarts=8;refAlleleMeanQV=23;novelAlleleCounts=13;novelAlleleStarts=12;novelAlleleMeanQV=20;diColor1=11;diColor2=22;het=1;flag=
chr01   levure8 SNP     12745   12745   0.000000        .       .        genotype=S;reference=C;coverage=37;refAlleleCounts=18;refAlleleStarts=17;refAlleleMeanQV=18;novelAlleleCounts=18;novelAlleleStarts=13;novelAlleleMeanQV=20;diColor1=11;diColor2=22;het=1;flag=
chr01   levure5 SNP     16254   16254   0.000000        .       .        genotype=R;reference=G;coverage=111;refAlleleCounts=82;refAlleleStarts=41;refAlleleMeanQV=18;novelAlleleCounts=28;novelAlleleStarts=9;novelAlleleMeanQV=18;diColor1=10;diColor2=32;het=1;flag=
chr01   levure6 SNP     16254   16254   0.000000        .       .        genotype=R;reference=G;coverage=96;refAlleleCounts=72;refAlleleStarts=38;refAlleleMeanQV=17;novelAlleleCounts=24;novelAlleleStarts=6;novelAlleleMeanQV=15;diColor1=10;diColor2=32;het=1;flag=
chr01   levure7 SNP     16254   16254   0.000000        .       .        genotype=R;reference=G;coverage=32;refAlleleCounts=20;refAlleleStarts=18;refAlleleMeanQV=19;novelAlleleCounts=12;novelAlleleStarts=5;novelAlleleMeanQV=17;diColor1=10;diColor2=32;het=1;flag=
chr01   levure8 SNP     16254   16254   0.000000        .       .        genotype=R;reference=G;coverage=45;refAlleleCounts=33;refAlleleStarts=25;refAlleleMeanQV=20;novelAlleleCounts=10;novelAlleleStarts=6;novelAlleleMeanQV=19;diColor1=10;diColor2=32;het=1;flag=
chr01   levure5 SNP     16511   16511   0.000000        .       .        genotype=A;reference=G;coverage=42;refAlleleCounts=0;refAlleleStarts=0;refAlleleMeanQV=0;novelAlleleCounts=35;novelAlleleStarts=16;novelAlleleMeanQV=19;diColor1=12;diColor2=12;het=0;flag=h4,h10,h9,
chr01   levure6 SNP     16511   16511   0.000000        .       .        genotype=A;reference=G;coverage=32;refAlleleCounts=0;refAlleleStarts=0;refAlleleMeanQV=0;novelAlleleCounts=23;novelAlleleStarts=11;novelAlleleMeanQV=17;diColor1=12;diColor2=12;het=0;flag=h4,h10,h9,

file2 looks like:

Code:
chr01   levure5 SNP     12745   12745   0.000000        .        .        genotype=S;reference=C;coverage=91;refAlleleCounts=44;refAlleleStarts=28;refAlleleMeanQV=19;novelAlleleCounts=40;novelAlleleStarts=25;novelAlleleMeanQV=18;diColor1=22;diColor2=11;het=1;flag=
chr01   levure6 SNP     12745   12745   0.000000        .       .        genotype=S;reference=C;coverage=62;refAlleleCounts=29;refAlleleStarts=19;refAlleleMeanQV=19;novelAlleleCounts=32;novelAlleleStarts=20;novelAlleleMeanQV=20;diColor1=11;diColor2=22;het=1;flag=
chr01   levure7 SNP     12745   12745   0.000000        .       .        genotype=S;reference=C;coverage=24;refAlleleCounts=9;refAlleleStarts=8;refAlleleMeanQV=23;novelAlleleCounts=13;novelAlleleStarts=12;novelAlleleMeanQV=20;diColor1=11;diColor2=22;het=1;flag=
chr01   levure5 SNP     16254   16254   0.000000        .       .        genotype=R;reference=G;coverage=111;refAlleleCounts=82;refAlleleStarts=41;refAlleleMeanQV=18;novelAlleleCounts=28;novelAlleleStarts=9;novelAlleleMeanQV=18;diColor1=10;diColor2=32;het=1;flag=
chr01   levure6 SNP     16254   16254   0.000000        .       .        genotype=R;reference=G;coverage=96;refAlleleCounts=72;refAlleleStarts=38;refAlleleMeanQV=17;novelAlleleCounts=24;novelAlleleStarts=6;novelAlleleMeanQV=15;diColor1=10;diColor2=32;het=1;flag=
chr01   levure7 SNP     16254   16254   0.000000        .       .        genotype=R;reference=G;coverage=32;refAlleleCounts=20;refAlleleStarts=18;refAlleleMeanQV=19;novelAlleleCounts=12;novelAlleleStarts=5;novelAlleleMeanQV=17;diColor1=10;diColor2=32;het=1;flag=
chr01   levure5 SNP     16511   16511   0.000000        .       .        genotype=A;reference=G;coverage=42;refAlleleCounts=0;refAlleleStarts=0;refAlleleMeanQV=0;novelAlleleCounts=35;novelAlleleStarts=16;novelAlleleMeanQV=19;diColor1=12;diColor2=12;het=0;flag=h4,h10,h9,
chr01   levure6 SNP     16511   16511   0.000000        .       .        genotype=A;reference=G;coverage=32;refAlleleCounts=0;refAlleleStarts=0;refAlleleMeanQV=0;novelAlleleCounts=23;novelAlleleStarts=11;novelAlleleMeanQV=17;diColor1=12;diColor2=12;het=0;flag=h4,h10,h9,
chr01   levure7 SNP     16511   16511   0.000000        .       .        genotype=A;reference=G;coverage=17;refAlleleCounts=0;refAlleleStarts=0;refAlleleMeanQV=0;novelAlleleCounts=14;novelAlleleStarts=11;novelAlleleMeanQV=20;diColor1=12;diColor2=12;het=0;flag=h4,h10,h9,
chr01   levure5 SNP     189778  189778  0.000000        .       .        genotype=G;reference=A;coverage=16;refAlleleCounts=0;refAlleleStarts=0;refAlleleMeanQV=0;novelAlleleCounts=16;novelAlleleStarts=12;novelAlleleMeanQV=24;diColor1=10;diColor2=10;het=0;flag=h4,h10,;transposable_element;ID=COPY_YORCTy2-1;Name=COPY_YORCTy2-1

Expected output should be like :

Code:
file1_unique

chr01   levure8 SNP     12745   12745   0.000000        .       .        genotype=S;reference=C;coverage=37;refAlleleCounts=18;refAlleleStarts=17;refAlleleMeanQV=18;novelAlleleCounts=18;novelAlleleStarts=13;novelAlleleMeanQV=20;diColor1=11;diColor2=22;het=1;flag=
chr01   levure8 SNP     16254   16254   0.000000        .       .        genotype=R;reference=G;coverage=45;refAlleleCounts=33;refAlleleStarts=25;refAlleleMeanQV=20;novelAlleleCounts=10;novelAlleleStarts=6;novelAlleleMeanQV=19;diColor1=10;diColor2=32;het=1;flag=  

###################################################

file2-unique

chr01   levure5 SNP     189778  189778  0.000000        .       .        genotype=G;reference=A;coverage=16;refAlleleCounts=0;refAlleleStarts=0;refAlleleMeanQV=0;novelAlleleCounts=16;novelAlleleStarts=12;novelAlleleMeanQV=24;diColor1=10;diColor2=10;het=0;flag=h4,h10,;transposable_element;ID=COPY_YORCTy2-1;Name=COPY_YORCTy2-1

So basically the output needs to be in long format or preferably even as output files named file1_unique and file2_unique.

Here unique might seem confusing because the unix 'uniq' command keeps only one line if more than one copy of the same line exists, but here we need all lines which occur once and exclusively in a particular file.

Hope its much clear ... will be waiting for your reply Smilie

Thank you.
# 6  
Old 03-19-2011
Try:
Code:
 comm -3 <(sort file_1) <(sort file_2) | perl -pe 'BEGIN{print "file_2 unique\n\n";$x=1}{if(/^\w/ && $x){print "\n#################\n\nfile_1 unique\n\n"; $x=0}s/^\s+//}'

This User Gave Thanks to bartus11 For This Post:
pawannoel
# 7  
Old 03-19-2011
I dont get any output with this command Smilie

i get

Code:
noel$ comm -3 <(sort file_1) <(sort file_2) | perl -pe 'BEGIN{print "file_2 unique\n\n";$x=1}{if(/^\w/ && $x){print "\n#################\n\nfile_1 unique\n\n"; $x=0}s/^\s+//}'
noel$


Did it work for you?

Let me know
 
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