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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
# 8  
Old 03-19-2011
Code:
[root@linux ~]# cat file_1
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,
[root@linux ~]# cat file_2
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
[root@linux ~]#
[root@linux ~]# 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+//}'
file_2 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
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,

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

file_1 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=

This User Gave Thanks to bartus11 For This Post:
pawannoel
# 9  
Old 03-19-2011
I dont know why but when I do the same thing as above it doesnt work !! Really strange

I even tried to recreate file_1 and file_2 but still didnt work ....

Any idea why it might be ? I'm using OSX 10.4.11

thanks anyway

---------- Post updated at 03:34 PM ---------- Previous update was at 03:27 PM ----------

the part which works is
Code:
comm -3 <(sort file_1) <(sort file_2)

and gives me the 4 lines which are different, but then I cant differentiate the origin of those lines as to which file they belonged to

using the entire code just prompts me to a new command input
# 10  
Old 03-19-2011
Hmm, I have zero experience with Perl on Macs. Do you have access to some Linux or Unix machine?
This User Gave Thanks to bartus11 For This Post:
pawannoel
# 11  
Old 03-19-2011
Hi Bartus11,

I figured it out .... had a small problem in my /usr/bin directory ..... sorted that out and your code works great now ....

Thanks very much for your help Smilie

Hv a nice weekend !!

PS: By the way if you hv any suggestions about learning awk from scratch, i'll appreciate a lot .... I need to start from basics ... cheers
# 12  
Old 03-19-2011
I learned it from tutorials on the Web Smilie And from studying AWK solutions posted on this forum Smilie
This User Gave Thanks to bartus11 For This Post:
pawannoel
# 13  
Old 03-19-2011
Your code is helping me with doing the comprision for 2 files but what if I had multiple files ?? .... how could I include more files and infact more lines of code ?? ..Indeed I have 10 such files and I need to know which lines are unique in each file

Can you help again ?

Thanks Smilie
# 14  
Old 03-19-2011
Assuming your files are named "file_1, file_2, file_3..." (if not, then rename them Smilie)
Code:
N=10;perl -0e 'BEGIN{$N=10;}for $i (1..$N){for $j (1..$i-1,$i+1..$N){open I,"<file_$j";$a.=<I>}open O,">file_${i}.tmp";print O $a;$a=""}'; 
for i in `seq 1 $N`; do echo "file_$i unique"; echo; comm -23 <(sort file_$i) <(sort file_$i.tmp); 
rm -f file_$i.tmp; echo;echo "##############";echo; done

If you want to increase number of files, change red parts of the code. Those files should be named file_11, file_12 etc.
This User Gave Thanks to bartus11 For This Post:
pawannoel
 
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