Aaryan Lokwani
A Bioinformatician
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Perl script to count number of Ns in a multifasta file !
By Aaryan Lokwani 2138 days ago Comments (1)
#!/usr/bin/perl
my ($h, $n, $l);
open(I,$ARGV[0]) or die($!);
while(<I>){
chomp;
next if /^$/;
if(/^>/){
$h=substr($_,1);
}else{
$n=($_=~tr/nN/nN/);
$l=length($_);
print $h,"\t",$l,"\t",$n,"\t",$n/($l-$n),"\n";
}
}
close(I);
__END__
Note: Convert sequences in oneline first
perl -pe '/^>/ ? print "\n" : chomp' scaffolds_backup.fasta > out.fasta
perl countN.pl scaff.fa
Result
➜ SSPACED_P2 perl countN.pl out.fasta
scaffold1_size15575755 15575755 71824 0.00463263155647429
scaffold2_size10632363 10632363 64900 0.00614149299600103
scaffold3_size10490233 10490233 14872 0.0014197124089566
scaffold4_size8615068 8615068 28079 0.00326994712582024
scaffold5_size7253348 7253348 0 0
scaffold6_size5859599 5859599 51144 0.00880509533085821
scaffold7_size5312044 5312044 144 2.71089440689772e-05
scaffold8_size4790259 4790259 167678 0.0362736748150005
scaffold9_size2901530 2901530 4652 0.001605866729631
scaffold10_size2523421 2523421 142217 0.0597248282801474
scaffold11_size2396892 2396892 6066 0.00253719844104088
scaffold12_size2309371 2309371 240122 0.11604306683246
scaffold13_size2240539 2240539 48209 0.0219898464191066
scaffold14_size2236206 2236206 132012 0.0627375612704912
scaffold15_size2184218 2184218 29144 0.0135234335340689
scaffold16_size2020193 2020193 11868 0.00590940211370172
scaffold17_size1776796 1776796 132882 0.0808326956276302
scaffold18_size1445477 1445477 50836 0.0364509576299564
scaffold19_size1287487 1287487 102593 0.0865841163850944
scaffold20_size1287226 1287226 23771 0.0188142830571726
scaffold21_size1176376 1176376 18339 0.0158362815695872
scaffold22_size1164766 1164766 82205 0.075935674756434
scaffold23_size1108643 1108643 36256 0.0338086903328742
scaffold24_size1010466 1010466 93216 0.10162551103843
scaffold25_size1009266 1009266 51939 0.0542541890075178
scaffold26_size990651 990651 75286 0.082246972519159
scaffold27_size971184 971184 55725 0.0608711040035654
scaffold28_size898523 898523 92917 0.115338018833028
scaffold29_size889417 889417 33420 0.0390421929048817
scaffold30_size864014 864014 80076 0.10214583296128
scaffold31_size790135 790135 0 0
scaffold32_size767454 767454 42932 0.0592556195671077
scaffold33_size711456 711456 0 0
scaffold34_size672622 672622 0 0
scaffold35_size649832 649832 0 0
scaffold36_size583465 583465 10815 0.0188858814284467
scaffold37_size532901 532901 19453 0.0378869914772285
scaffold38_size462550 462550 16583 0.0371843656593425
scaffold39_size413010 413010 29289 0.0763288952129281
scaffold40_size395146 395146 72775 0.225749214414448
scaffold41_size385263 385263 0 0
scaffold42_size378415 378415 0 0
scaffold43_size374696 374696 0 0
scaffold44_size369872 369872 0 0
scaffold45_size357218 357218 0 0
scaffold46_size308025 308025 25709 0.0910646226214596
scaffold47_size306566 306566 16299 0.056151749940572
scaffold48_size288610 288610 59285 0.258519568298267
scaffold49_size269035 269035 0 0
scaffold50_size267296 267296 0 0
scaffold51_size239237 239237 0 0
scaffold52_size229546 229546 81 0.000352995010132264
scaffold53_size228017 228017 3283 0.0146083814643089
scaffold54_size218690 218690 9299 0.0444097406287758
scaffold55_size205658 205658 0 0
scaffold56_size203300 203300 0 0
scaffold57_size189523 189523 54248 0.401020144150804
scaffold58_size164988 164988 0 0
scaffold59_size158628 158628 0 0
scaffold60_size158343 158343 29807 0.231896122487085
scaffold61_size148599 148599 0 0
scaffold62_size137911 137911 19923 0.168856154863206
scaffold63_size129836 129836 0 0
scaffold64_size127140 127140 2695 0.0216561533207441
scaffold65_size121401 121401 0 0
scaffold66_size119540 119540 7247 0.0645365249837479
scaffold67_size114479 114479 11483 0.111489766592877
scaffold68_size111283 111283 0 0
scaffold69_size106201 106201 0 0
scaffold70_size102444 102444 7907 0.0836392100447444
scaffold71_size97059 97059 9770 0.11192704693604
scaffold72_size94628 94628 14575 0.182066880691542
scaffold73_size86984 86984 0 0
scaffold74_size80782 80782 0 0
scaffold75_size68265 68265 0 0
scaffold76_size67964 67964 0 0
scaffold77_size56495 56495 0 0
scaffold78_size51859 51859 0 0
scaffold79_size46742 46742 0 0
scaffold80_size44222 44222 0 0
scaffold81_size39139 39139 0 0
scaffold82_size36951 36951 0 0
scaffold83_size35745 35745 0 0
scaffold84_size34131 34131 0 0
scaffold85_size33753 33753 0 0
scaffold86_size33604 33604 0 0
scaffold87_size32653 32653 0 0
scaffold88_size32281 32281 0 0
scaffold89_size32217 32217 0 0
scaffold90_size29934 29934 0 0
scaffold91_size29230 29230 0 0
scaffold92_size22007 22007 0 0
scaffold93_size20584 20584 0 0
Comments
If you want to count all 'N' in miltifasta file.