cdskit intersection

cdskit intersection drops non-overlapping sequence labels between two sequences files or between a sequence file and a gff file.

Example 1: Sequence vs sequence intersection

Command

cdskit intersection --seqfile input1.fasta --seqfile2 input2.fasta --outfile output1.fasta --outfile2 output2.fasta

input1.fasta

>seq1
AAAAAAAAAA
>seq2
TTTTTTTTTT
>seq3
GGGGGGGGGG
>seq4
CCCCCCCCCC

input2.fasta

>seq3
GGGGGGGGGGCCCCCCCCCC
>seq4
CCCCCCCCCCATATATATAT
>seq5
ATATATATATAGAGAGAGAG
>seq6
AGAGAGAGAGGGGGGGGGGG

output1.fasta

>seq3
GGGGGGGGGG
>seq4
CCCCCCCCCC

output2.fasta

>seq3
GGGGGGGGGGCCCCCCCCCC
>seq4
CCCCCCCCCCATATATATAT

Example 2: Sequence vs gff intersection

Command

cdskit intersection --seqfile input.fasta --ingff input.gff --outfile output.fasta --outgff output.gff

input.fasta

>seq1
AAAAAAAAAA
>seq2
TTTTTTTTTT
>seq3
GGGGGGGGGG
>seq4
CCCCCCCCCC

input.gff

seq1	cdskit	gene	1	10	.	+	.	ID=gene1;Name=gene1
seq1	cdskit	mRNA	1	10	.	+	.	ID=gene1-mRNA1;Parent=gene1;Name=gene1-mRNA1
seq1	cdskit	exon	1	3	.	+	.	ID=gene1-mRNA1:exon1;Parent=gene1-mRNA1
seq1	cdskit	exon	5	10	.	+	.	ID=gene1-mRNA1:exon2;Parent=gene1-mRNA1
seq1	cdskit	CDS	1	3	.	+	0	ID=gene1-mRNA1-cds1;Parent=gene1-mRNA1
seq1	cdskit	CDS	5	10	.	+	2	ID=gene1-mRNA1-cds2;Parent=gene1-mRNA1
seq2	cdskit	gene	1	10	.	+	.	ID=gene2;Name=gene2
seq2	cdskit	mRNA	1	10	.	+	.	ID=gene2-mRNA1;Parent=gene2;Name=gene2-mRNA1
seq2	cdskit	exon	1	3	.	+	.	ID=gene2-mRNA1:exon1;Parent=gene2-mRNA1
seq2	cdskit	exon	5	10	.	+	.	ID=gene2-mRNA1:exon2;Parent=gene2-mRNA1
seq2	cdskit	CDS	1	3	.	+	0	ID=gene2-mRNA1-cds1;Parent=gene2-mRNA1
seq2	cdskit	CDS	5	10	.	+	2	ID=gene2-mRNA1-cds2;Parent=gene2-mRNA1
seq5	cdskit	gene	1	10	.	+	.	ID=gene5;Name=gene5
seq5	cdskit	mRNA	1	10	.	+	.	ID=gene5-mRNA1;Parent=gene5;Name=gene5-mRNA1
seq5	cdskit	exon	1	3	.	+	.	ID=gene5-mRNA1:exon1;Parent=gene5-mRNA1
seq5	cdskit	exon	5	10	.	+	.	ID=gene5-mRNA1:exon2;Parent=gene5-mRNA1
seq5	cdskit	CDS	1	3	.	+	0	ID=gene5-mRNA1-cds1;Parent=gene5-mRNA1
seq5	cdskit	CDS	5	10	.	+	2	ID=gene5-mRNA1-cds2;Parent=gene5-mRNA1
seq6	cdskit	gene	1	10	.	+	.	ID=gene6;Name=gene6
seq6	cdskit	mRNA	1	10	.	+	.	ID=gene6-mRNA1;Parent=gene6;Name=gene6-mRNA1
seq6	cdskit	exon	1	3	.	+	.	ID=gene6-mRNA1:exon1;Parent=gene6-mRNA1
seq6	cdskit	exon	5	10	.	+	.	ID=gene6-mRNA1:exon2;Parent=gene6-mRNA1
seq6	cdskit	CDS	1	3	.	+	0	ID=gene6-mRNA1-cds1;Parent=gene6-mRNA1
seq6	cdskit	CDS	5	10	.	+	2	ID=gene6-mRNA1-cds2;Parent=gene6-mRNA1

output.fasta

>seq1
AAAAAAAAAA
>seq2
TTTTTTTTTT

output.gff

seq1	cdskit	gene	1	10	.	+	.	ID=gene1;Name=gene1
seq1	cdskit	mRNA	1	10	.	+	.	ID=gene1-mRNA1;Parent=gene1;Name=gene1-mRNA1
seq1	cdskit	exon	1	3	.	+	.	ID=gene1-mRNA1:exon1;Parent=gene1-mRNA1
seq1	cdskit	exon	5	10	.	+	.	ID=gene1-mRNA1:exon2;Parent=gene1-mRNA1
seq1	cdskit	CDS	1	3	.	+	0	ID=gene1-mRNA1-cds1;Parent=gene1-mRNA1
seq1	cdskit	CDS	5	10	.	+	2	ID=gene1-mRNA1-cds2;Parent=gene1-mRNA1
seq2	cdskit	gene	1	10	.	+	.	ID=gene2;Name=gene2
seq2	cdskit	mRNA	1	10	.	+	.	ID=gene2-mRNA1;Parent=gene2;Name=gene2-mRNA1
seq2	cdskit	exon	1	3	.	+	.	ID=gene2-mRNA1:exon1;Parent=gene2-mRNA1
seq2	cdskit	exon	5	10	.	+	.	ID=gene2-mRNA1:exon2;Parent=gene2-mRNA1
seq2	cdskit	CDS	1	3	.	+	0	ID=gene2-mRNA1-cds1;Parent=gene2-mRNA1
seq2	cdskit	CDS	5	10	.	+	2	ID=gene2-mRNA1-cds2;Parent=gene2-mRNA1