Entering edit mode
7.9 years ago
lakhujanivijay
5.9k
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?
PS: I am loving this tool (all thanks to Wei Shen)and trying to exploit the utilities to make a new tool!
You might have better luck posting a bug report on the github repo.
Oh my dear friend, it's shenwei, or Wei Shen. In Chinese, the last name (Shen) is in front of the first name (Wei), so my social media ID is shenwei*
Oh my dearest friend!, thanks for the information but I just wanted to highlight your username.
Many thanks for your prompt attention!!
PS: I just edited my post :)