hello, the doubt I have because according to the main classes of mobile elements according to the context of the question are the DNA, LTR, LINES, SINES
EXAMPLE
scaffold_1 RepeatMasker . 33 148 663 - . snRNA:U5
scaffold_1 RepeatMasker . 605 720 663 - . snRNA:U5
scaffold_1 RepeatMasker . 969 1132 831 - . DNA/TcMar-Tc2:Mariner-2N2_XT
scaffold_1 RepeatMasker . 1496 1730 1279 - . DNA/TcMar-Tc2:Mariner-2N2_XT
scaffold_1 RepeatMasker . 1645 1810 342 - . DNA/hAT-Charlie:hAT-N5_XT
scaffold_1 RepeatMasker . 1946 2097 876 + . DNA/Kolobok-T2:XBR_Xt
scaffold_1 RepeatMasker . 2474 2917 3699 - . DNA/Kolobok-T2:Kolobok-1N2_XT
scaffold_1 RepeatMasker . 3306 3322 16 + . Simple_repeat:(A)n
scaffold_1 RepeatMasker . 3689 3989 1732 - . DNA/hAT-Charlie:POR-1_Xt
scaffold_1 RepeatMasker . 4876 5605 5823 + . LINE/L1:L1-42A_XT
scaffold_1 RepeatMasker . 5600 6436 23824 + . LINE/L1:L1-42A_XT
So I guess I should take each one and do a count ... but the problem is that each name that appears with DNA, LTR, etc. is different so I can not do a count because the names are different .. How can I solve this through a command in the terminal, I also use the bedtools tool
2 answers
Maybe these is not the best solution, but appear that you have several patterns of names, like DNA/TcMar, DNA/Kolobok, LINE/L1... You can create a list of those names:
DNA/TcMar
DNA/Kolobok
LINE/L1
And, for example, if you named that list as TE.lst; you can use a for with grep:
for i in `cat TEs.lst`;do grep -c "$i";done
Where -c count lines with pattern.
I make a test with this TE.lst example using your information:
the ouput:
2
2
2
A little bit laborious but worked, I hope.
In the end, what I did was make a count by changing the words of each one to DNA, LINE, LTR, SINE ... so I could group them easily with the following command ... a bit repetitive but it serves
awk 'BEGIN {FS = OFS = "\ t"} ($ 9 ~ "DNA") {$ 9 = "DNA"; print $ 0}' xentr4_repeatmasker_annotation_first200000.gff3> countingDNA.txt
awk 'BEGIN {FS = OFS = "\ t"} ($ 9 ~ "LINE") {$ 9 = "LINE"; print $ 0}' xentr4_repeatmasker_annotation_first200000.gff3> countingLINE.txt
awk 'BEGIN {FS = OFS = "\ t"} ($ 9 ~ "SINE") {$ 9 = "SINE"; print $ 0}' xentr4_repeatmasker_annotation_first200000.gff3> countingDNA.txt
awk 'BEGIN {FS = OFS = "\ t"} ($ 9 ~ "LTR") {$ 9 = "LTR"; print $ 0}' xentr4_repeatmasker_annotation_first200000.gff3> countingLTR.txt
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