Getting non unique lines from concatenated files Post: 302506259

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Top Forums UNIX for Dummies Questions & Answers Getting non unique lines from concatenated files Post 302506259 by bartus11 on Saturday 19th of March 2011 03:18:15 PM

03-19-2011

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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=

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