Is it possible to pipe a list of numbers into sed?
The pipeline I currently have looks something like:
grep -nP 'foo' file_full.txt | sort | awk -F'[:;\t]' '{print $1,$3,$9,$13}'
The output of this:
2374 213 MID=212 GO=1
2462 213 MID=477 GO=137
2394 233 MID=232 GO=1
2464 233 MID=668 GO=1070
2185 24 MID=23 GO=1
2465 24 MID=752 GO=1083
2146 48 MID=354 GO=1010
1893 48 MID=47 GO=1
2219 58 MID=57 GO=1
2463 58 MID=595 GO=1057
My main goal here is to look at $2 for identical values then compare their $4 or GO values. The line with the larger GO value needs to be deleted.
When I add: sed 's/GO=/& /' | sort -k2,2 -k5n | awk 'a[$2]++ {sub(/GO= /,"GO="); print $1}'
to the previous pipeline I get:
2462
2464
2465
2146
2463
Which is a list of line numbers I wish to remove from file_full.txt
I know sed -i '2462d;2464d;2465d;2146d;2463d' file_full.txt
would work but I am unsure how to pipe each of those numbers from above into one sed command.
Am I missing something?
Raw data:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT i0 i1 i2 i3 i4 i5 i6 i7 i8 i9 i10 i11 i12 i13 i14
1 1 . A T 1000 PASS MID=0;S=0.0324764;DOM=0.5;PO=1;GO=1;MT=0;AC=200;DP=1000 GT 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1
1 2 . A T 1000 PASS MID=1;S=0.0125739;DOM=0.5;PO=1;GO=1;MT=5;AC=200;DP=1000 GT 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1
1 3 . A T 1000 PASS MID=2;S=-0.0693919;DOM=0.5;PO=1;GO=1;MT=9;AC=200;DP=1000 GT 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1
1 4 . A T 1000 PASS MID=3;S=0.0611535;DOM=0.5;PO=1;GO=1;MT=12;AC=200;DP=1000 GT 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1
1 5 . A T 1000 PASS MID=4;S=-0.0791182;DOM=0.5;PO=1;GO=1;MT=16;AC=200;DP=1000 GT 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1
1 6 . A T 1000 PASS MID=5;S=0.0463103;DOM=0.5;PO=1;GO=1;MT=21;AC=200;DP=1000 GT 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1
1 7 . A T 1000 PASS MID=6;S=0.0509527;DOM=0.5;PO=1;GO=1;MT=25;AC=200;DP=1000 GT 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1
1 8 . A T 1000 PASS MID=7;S=-0.0134404;DOM=0.5;PO=1;GO=1;MT=28;AC=200;DP=1000 GT 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1
1 9 . A T 1000 PASS MID=8;S=-0.00478324;DOM=0.5;PO=1;GO=1;MT=32;AC=200;DP=1000 GT 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1
1 10 . A T 1000 PASS MID=9;S=0.03588;DOM=0.5;PO=1;GO=1;MT=36;AC=200;DP=1000 GT 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1
1 11 . A T 1000 PASS MID=10;S=-0.028843;DOM=0.5;PO=1;GO=1;MT=41;AC=200;DP=1000 GT 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1
1 12 . A T 1000 PASS MID=11;S=-0.0832497;DOM=0.5;PO=1;GO=1;MT=45;AC=200;DP=1000 GT 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1
1 13 . A T 1000 PASS MID=12;S=0.0389281;DOM=0.5;PO=1;GO=1;MT=48;AC=200;DP=1000 GT 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1
1 14 . A T 1000 PASS MID=13;S=0.0362106;DOM=0.5;PO=1;GO=1;MT=53;AC=200;DP=1000 GT 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1
1 15 . A T 1000 PASS MID=14;S=0.0375309;DOM=0.5;PO=1;GO=1;MT=57;AC=200;DP=1000 GT 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1
1 16 . A T 1000 PASS MID=15;S=0.0112808;DOM=0.5;PO=1;GO=1;MT=60;AC=200;DP=1000 GT 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1
1 17 . A T 1000 PASS MID=16;S=0.0243286;DOM=0.5;PO=1;GO=1;MT=65;AC=200;DP=1000 GT 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1
1 18 . A T 1000 PASS MID=17;S=0.0596463;DOM=0.5;PO=1;GO=1;MT=69;AC=200;DP=1000 GT 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1
1 24 . A T 1000 PASS MID=23;S=-0.0086571;DOM=0.5;PO=1;GO=1;MT=92;AC=199;DP=1000;MULTIALLELIC GT 1|1 1|1 1|1 1|1 1|1 1|1 1|1
1 58 . A T 1000 PASS MID=57;S=-0.0926969;DOM=0.5;PO=1;GO=1;MT=229;AC=198;DP=1000;MULTIALLELIC GT 1|1 0|1 1|1 1|1 0|1 1|1
1 213 . A T 1000 PASS MID=212;S=-0.0925562;DOM=0.5;PO=1;GO=1;MT=848;AC=196;DP=1000;MULTIALLELIC GT 1|1 1|1 1|1 1|1 1|1 1|1
1 233 . A T 1000 PASS MID=232;S=-0.0868037;DOM=0.5;PO=1;GO=1;MT=929;AC=199;DP=1000;MULTIALLELIC GT 1|1 1|1 1|1 1|1 1|1 1|1
1 213 . A T 1000 PASS MID=477;S=0.0600971;DOM=0.5;PO=1;GO=1037;MT=849;AC=4;DP=1000;MULTIALLELIC GT 0|0 0|0 0|0 0|0 0|0 0|0
1 58 . A T 1000 PASS MID=595;S=0.0450203;DOM=0.5;PO=1;GO=1057;MT=228;AC=2;DP=1000;MULTIALLELIC GT 0|0 1|0 0|0 0|0 1|0 0|0
1 233 . A T 1000 PASS MID=668;S=-0.0447337;DOM=0.5;PO=1;GO=1070;MT=928;AC=1;DP=1000;MULTIALLELIC GT 0|0 0|0 0|0 0|0 0|0 0|0
1 24 . A T 1000 PASS MID=752;S=-0.104791;DOM=0.5;PO=1;GO=1083;MT=93;AC=1;DP=1000;MULTIALLELIC GT 0|0 0|0 0|0 0|0 0|0 0|0
bcftools
etc. Also, do you want the entire line of the vcf file? What output are you expecting?