Possible bug seqkit stats?

[lakhujanivijay]

Tool used: seqkit

Dummy fasta file (fasta.fa):

>test1
GCATCGATCAGCTACGATCATCACTA
GNNNNNNTACATCAGCACTACATCACTNNNNN
>test2
GTACGCTACGANNNGCTACGACTACGATATATATATATATATATATATATATATATATATATAT
GCTACGATCACNTACATCGACTA
>test3
GTGTGCTACATCATCACTACGTACTACAT
>test4
AA

Command:

./seqkit stat fasta.fa

Output:

file      format  type  num_seqs  sum_len  min_len  avg_len  max_len
fasta.fa  FASTA   DNA          4      176        0       44       87

Problem:
min_len =0 (however, minimum length should be 2; sequence id "test4")

Validation using seqkit:

Command:

./seqkit fx2tab -l fasta.fa

Output:

test1	GCATCGATCAGCTACGATCATCACTAGNNNNNNTACATCAGCACTACATCACTNNNNN		58
test2	GTACGCTACGANNNGCTACGACTACGATATATATATATATATATATATATATATATATATATATGCTACGATCACNTACATCGACTA		87
test3	GTGTGCTACATCATCACTACGTACTACAT		29
test4	AA		2

Notice: length of sequence test4 is "2"

Is it a bug or I misunderstood something?

[shenwei356]

Sorry for that, it's fixed in the latest version (v0.4.3), please update.

Affected verions: v0.4.0, v0.4.1, v0.4.2

[lakhujanivijay]

Thanks! Perfect!

One more question please - How can I get contigs from scaffolds (use seqkit). Please see below

input scaffolds file

>test1
GCATCGATCAGCTACGATCATCACTA
GNNNNNNTACATCAGCACTACATCACTNNNNN
>test2
GTACGCTACGANNNGCTACGACTACGATATATATATATATATATATATATATATATATATATAT
GCTACGATCACNTACATCGACTA
>test3
GTGTGCTACATCATCACTACGTACTACAT
>test4
AA

output contigs file

>test1
GCATCGATCAGCTACGATCATCACTA
G
>test1_2
ACATCAGCACTACATCACT
>test2
GTACGCTACGA
>test2_1
GCTACGACTACGATATATATATATATATATATATATATATATATATATAT
GCTACGATCACNTACATCGACTA
>test3
GTGTGCTACATCATCACTACGTACTACAT
>test4
AA

i.e. essentially splitting the sequences by n/N.

[shenwei356]

We talked about this: https://www.biostars.org/p/211400/