duplicate in master db

[thsyd]

Hi,
>IS1004_IS200/IS605_IS200
and the associated sequence
is duplicate in https://raw.githubusercontent.com/thanhleviet/ISfinder-sequences/master/IS.fna
lines 13 and 15 (and 14 and 16 respectively)
Probably the same for the fsa and csv versions?

>IS1004_IS200/IS605_IS200
TGTCATCCCTAAACCACCGCTTTTAGCGGTGGTGATTGTCCCTAGGGGCTTTTGCCCGAAAATGCGCCCATGTTAGAAGACAAACTCTTATTCACCATAAGTAAGAGGATTCAAATAACATGGGCGACTACAGAAGTTCATCACACGTCTATTGGCGTTGCAAATATCATATCGTTTGGACACCAAAATTTCGTTTTAAGATCTTAAAAGGTAATGTTGCCAAAGAGCTAAATCGTTCGATCTACATTCTTTGTAATATGAAAGATTGTGAAGTTTTGGAACTCAATGTTCAGCCAGATCATGTCCACTTAGTTGCGATAATTCCGCCCAAAGTATCGATTTCGACGTTGATGGGAGTTTTAAAGGGTAGGAGTGCAATTAGGCTATTCAACAAGTTTCCACATATCAGGAAAAAGTTATGGGGAAATCATTTTTGGGCGCGAGGCTATTTTGTGGATACGGTAGGTGTAAATGAAGAAATCATTAGACGGTATGTACGGCATCAAGACAAAAAAGAGCTTGAGCAAGAGCAGCAGTTAGAGTTATTGAGAGACTAACAGCGTCGTGGCCCCCTTTTAGGGGGCTTATATTAAAACCGCCTTCTAAGAAGGCGGATTTTT
>IS1004_IS200/IS605_IS200
TGTCATCCCTAAACCACCGCTTTTAGCGGTGGTGATTGTCCCTAGGGGCTTTTGCCCGAAAATGCGCCCATGTTAGAAGACAAACTCTTATTCACCATAAGTAAGAGGATTCAAATAACATGGGCGACTACAGAAGTTCATCACACGTCTATTGGCGTTGCAAATATCATATCGTTTGGACACCAAAATTTCGTTTTAAGATCTTAAAAGGTAATGTTGCCAAAGAGCTAAATCGTTCGATCTACATTCTTTGTAATATGAAAGATTGTGAAGTTTTGGAACTCAATGTTCAGCCAGATCATGTCCACTTAGTTGCGATAATTCCGCCCAAAGTATCGATTTCGACGTTGATGGGAGTTTTAAAGGGTAGGAGTGCAATTAGGCTATTCAACAAGTTTCCACATATCAGGAAAAAGTTATGGGGAAATCATTTTTGGGCGCGAGGCTATTTTGTGGATACGGTAGGTGTAAATGAAGAAATCATTAGACGGTATGTACGGCATCAAGACAAAAAAGAGCTTGAGCAAGAGCAGCAGTTAGAGTTATTGAGAGACTAACAGCGTCGTGGCCCCCTTTTAGGGGGCTTATATTAAAACCGCCTTCTAAGAAGGCGGATTTTT

[thsyd]

Actually,
using https://github.com/b-brankovics/fasta_tools/blob/master/bin/fasta_unique I find that
there are 767 sequences that are present in multiple copies and 5291 (of 5685) are unique.

usage of fasta_unique

fasta_unique input.fas >unique.fas 2>unique.tab

where input.fas = input file in fasta format
unique.fas = output file (a file containing unique sequences)
unique.tab = tab separated file of the sterr warnings of sequences that occur multiple times

code:

wget https://raw.githubusercontent.com/thanhleviet/ISfinder-sequences/master/IS.fna
perl fasta_unique.perl IS.fna > IS_fasta_unique.perl.fna 2>IS_fasta_unique.perl.unique.tsv

grep "^>" IS.fna | wc -l
5685

grep "^>" IS_fasta_unique.perl.fna | wc -l
5291

wc -l IS_fasta_unique.perl.unique.tsv
767 IS_fasta_unique.perl.unique.tsv

Output files (.txt added for compatibility with github):

IS_fasta_unique.perl.fna.txt
IS_fasta_unique.perl.unique.tsv.txt

[tianmao233666]

Thank you very much！

[zzlzef]

good man!