cdskit split

cdskit split writes the first, second, and third codon positions of an aligned CDS to three separate sequence files.

Example

Command

cdskit split --seq_file input.fasta --prefix output

input.fasta

>Drosophila_melanogaster_AE014298.5_cds_AAF48408.2_3478
ATGAACCCAGCCGCTCAACTGCTGCGCATGCGCAGCGCT
>Drosophila_melanogaster_AE014298.5_cds_ADV37672.1_3479
ATGAACCCAGCCGCTCAACTGCTGCGCATGCGCAGCGCT
>Drosophila_melanogaster_AE014298.5_cds_AFH07387.1_3480
ATGAACCCAGCCGCTCAACTGCTGCGCATGCGCAGCGCT
>Drosophila_melanogaster_AE014298.5_cds_AHN59727.1_3481
ATGAACCCAGCCGCTCAACTGCTGCGCATGCGCAGCGCT
>Drosophila_melanogaster_AE014134.6_cds_AAF52246.1_6873
---------------------------ATGAACAGCAAG
>Drosophila_melanogaster_AE013599.5_cds_AAF58513.1_13350
---------------------------ATGGCCATGATA
>Drosophila_melanogaster_AE013599.5_cds_AAF46628.2_15780
---------------------------ATGAGCTGTGAG
>Drosophila_melanogaster_AE013599.5_cds_AAF46629.1_15781
---------------------------ATGGCGTCCACC
>Drosophila_melanogaster_AE013599.5_cds_AAF47206.1_16961
---------------------------ATGCCGACAAAG
>Drosophila_melanogaster_AE014296.5_cds_AAF50738.3_18793
---------------------------ATGGGTGAATTG
>Drosophila_melanogaster_AE014296.5_cds_AAF50737.2_18794
---------------------------ATGGCTGAAATG
>Drosophila_melanogaster_AE014296.5_cds_AGB94148.1_18795
---------------------------ATGGCTGAAATG
>Drosophila_melanogaster_AE014297.3_cds_AAF54758.1_25318
---------------------------ATGTCCAAGTTA
>Drosophila_melanogaster_AE014297.3_cds_AAF55696.2_27167
---------------------------------------
>Drosophila_melanogaster_AE014297.3_cds_AAF55697.2_27168
---------------------------------------
>Drosophila_melanogaster_AE014297.3_cds_AAF55698.1_27169
---------------------------ATGTTGGACCTC
>Drosophila_melanogaster_AE014297.3_cds_AAF55699.1_27170
---------------------------------------
>Drosophila_melanogaster_AE014297.3_cds_AAF55700.2_27171
---------------------------ATGAATCGCTCG
>Drosophila_melanogaster_AE014297.3_cds_AAF56245.1_28374
------------------ATGACTTCAAAGCTACTGCCC

output_1st_codon_positions.fasta

>Drosophila_melanogaster_AE014298.5_cds_AAF48408.2_3478
AACGGCCCCACAG
>Drosophila_melanogaster_AE014298.5_cds_ADV37672.1_3479
AACGGCCCCACAG
>Drosophila_melanogaster_AE014298.5_cds_AFH07387.1_3480
AACGGCCCCACAG
>Drosophila_melanogaster_AE014298.5_cds_AHN59727.1_3481
AACGGCCCCACAG
>Drosophila_melanogaster_AE014134.6_cds_AAF52246.1_6873
---------AAAA
>Drosophila_melanogaster_AE013599.5_cds_AAF58513.1_13350
---------AGAA
>Drosophila_melanogaster_AE013599.5_cds_AAF46628.2_15780
---------AATG
>Drosophila_melanogaster_AE013599.5_cds_AAF46629.1_15781
---------AGTA
>Drosophila_melanogaster_AE013599.5_cds_AAF47206.1_16961
---------ACAA
>Drosophila_melanogaster_AE014296.5_cds_AAF50738.3_18793
---------AGGT
>Drosophila_melanogaster_AE014296.5_cds_AAF50737.2_18794
---------AGGA
>Drosophila_melanogaster_AE014296.5_cds_AGB94148.1_18795
---------AGGA
>Drosophila_melanogaster_AE014297.3_cds_AAF54758.1_25318
---------ATAT
>Drosophila_melanogaster_AE014297.3_cds_AAF55696.2_27167
-------------
>Drosophila_melanogaster_AE014297.3_cds_AAF55697.2_27168
-------------
>Drosophila_melanogaster_AE014297.3_cds_AAF55698.1_27169
---------ATGC
>Drosophila_melanogaster_AE014297.3_cds_AAF55699.1_27170
-------------
>Drosophila_melanogaster_AE014297.3_cds_AAF55700.2_27171
---------AACT
>Drosophila_melanogaster_AE014297.3_cds_AAF56245.1_28374
------AATACCC

output_2nd_codon_positions.fasta

>Drosophila_melanogaster_AE014298.5_cds_AAF48408.2_3478
TACCCATTGTGGC
>Drosophila_melanogaster_AE014298.5_cds_ADV37672.1_3479
TACCCATTGTGGC
>Drosophila_melanogaster_AE014298.5_cds_AFH07387.1_3480
TACCCATTGTGGC
>Drosophila_melanogaster_AE014298.5_cds_AHN59727.1_3481
TACCCATTGTGGC
>Drosophila_melanogaster_AE014134.6_cds_AAF52246.1_6873
---------TAGA
>Drosophila_melanogaster_AE013599.5_cds_AAF58513.1_13350
---------TCTT
>Drosophila_melanogaster_AE013599.5_cds_AAF46628.2_15780
---------TGGA
>Drosophila_melanogaster_AE013599.5_cds_AAF46629.1_15781
---------TCCC
>Drosophila_melanogaster_AE013599.5_cds_AAF47206.1_16961
---------TCCA
>Drosophila_melanogaster_AE014296.5_cds_AAF50738.3_18793
---------TGAT
>Drosophila_melanogaster_AE014296.5_cds_AAF50737.2_18794
---------TCAT
>Drosophila_melanogaster_AE014296.5_cds_AGB94148.1_18795
---------TCAT
>Drosophila_melanogaster_AE014297.3_cds_AAF54758.1_25318
---------TCAT
>Drosophila_melanogaster_AE014297.3_cds_AAF55696.2_27167
-------------
>Drosophila_melanogaster_AE014297.3_cds_AAF55697.2_27168
-------------
>Drosophila_melanogaster_AE014297.3_cds_AAF55698.1_27169
---------TTAT
>Drosophila_melanogaster_AE014297.3_cds_AAF55699.1_27170
-------------
>Drosophila_melanogaster_AE014297.3_cds_AAF55700.2_27171
---------TAGC
>Drosophila_melanogaster_AE014297.3_cds_AAF56245.1_28374
------TCCATTC

output_3rd_codon_positions.fasta

>Drosophila_melanogaster_AE014298.5_cds_AAF48408.2_3478
GCACTAGGCGCCT
>Drosophila_melanogaster_AE014298.5_cds_ADV37672.1_3479
GCACTAGGCGCCT
>Drosophila_melanogaster_AE014298.5_cds_AFH07387.1_3480
GCACTAGGCGCCT
>Drosophila_melanogaster_AE014298.5_cds_AHN59727.1_3481
GCACTAGGCGCCT
>Drosophila_melanogaster_AE014134.6_cds_AAF52246.1_6873
---------GCCG
>Drosophila_melanogaster_AE013599.5_cds_AAF58513.1_13350
---------GCGA
>Drosophila_melanogaster_AE013599.5_cds_AAF46628.2_15780
---------GCTG
>Drosophila_melanogaster_AE013599.5_cds_AAF46629.1_15781
---------GGCC
>Drosophila_melanogaster_AE013599.5_cds_AAF47206.1_16961
---------GGAG
>Drosophila_melanogaster_AE014296.5_cds_AAF50738.3_18793
---------GTAG
>Drosophila_melanogaster_AE014296.5_cds_AAF50737.2_18794
---------GTAG
>Drosophila_melanogaster_AE014296.5_cds_AGB94148.1_18795
---------GTAG
>Drosophila_melanogaster_AE014297.3_cds_AAF54758.1_25318
---------GCGA
>Drosophila_melanogaster_AE014297.3_cds_AAF55696.2_27167
-------------
>Drosophila_melanogaster_AE014297.3_cds_AAF55697.2_27168
-------------
>Drosophila_melanogaster_AE014297.3_cds_AAF55698.1_27169
---------GGCC
>Drosophila_melanogaster_AE014297.3_cds_AAF55699.1_27170
-------------
>Drosophila_melanogaster_AE014297.3_cds_AAF55700.2_27171
---------GTCG
>Drosophila_melanogaster_AE014297.3_cds_AAF56245.1_28374
------GTAGAGC

Output naming

--prefix PREFIX produces PREFIX_1st_codon_positions.FORMAT, PREFIX_2nd_codon_positions.FORMAT, and PREFIX_3rd_codon_positions.FORMAT. If no prefix is supplied, the input path is used; standard input uses stdin. Input sequences must be nucleotide data with lengths divisible by three.

Citation

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