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 --seq_file input1.fasta --seq_file_2 input2.fasta --out_file output1.fasta --out_file_2 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 --seq_file input.fasta --in_gff input.gff --out_file output.fasta --out_gff 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

GFF region directives

Output ##sequence-region directives are filtered to the retained FASTA records. ### group delimiters stay after retained feature groups; delimiters for groups with no retained features are omitted. With coordinate repair enabled, directive intervals are intersected with the sequence bounds, empty intervals are omitted, and both directives and features are checked against the output sequences before writing. With repair disabled, bounds of retained directives are preserved.

Citation

No separate method paper is designated for this utility. Report the CDSKIT version, command and options; see citing CDSKIT.