Removing a DOT after each sequence

Question

[Ric]

Hi, I have a FASTA file which contains a . after each sequence. How is it possilble to remove the dot?

>gene39576 gene=rps16
MVKLRLKRCGRKQRAVYRIVAIDVRSRREGKDLRKVGFYDPIKNQTYLNVPAILYFLEKG
AQPTGTVQDILKKAEVFKELRPNQS.
>gene39578 gene=psbK
MLNTFSLIGICLNSTLFSSSFFFGKLPEAYAFLNPIVDIMPVIPLFFFLLAFVWQAAVSF
R.
>gene39579 gene=psbI
MLTLKLFVYTVVIFFVSLFIFGFLSNDPGRNPGREE.
>gene39580 gene=NitoCp007
MIPDVILDVKNKIKRGFPCLIFKFSYDLVYSTHLTKNKNKGFRNLKKKNQVINGKRGIRT
LGTINSYNGLAIRRFSPLSHLSQLKKIITT.
>gene39584 gene=atpA
MVTIRADEISNIIRERIEQYNREVKVVNTGTVLQVGDGIARIHGLDEVMAGELVEFEEGT
IGIALNLESNNVGVVLMGDGLLIQEGSSVKATGRIAQIPVSEAYLGRVINALAKPIDGRG
EISASEFRLIESAAPGIISRRSVYEPLQTGLIAIDSMIPIGRGQRELIIGDRQTGKTAVA
TDTILNQQGQNVICVYVAIGQKASSVAQVVTTLQERGAMEYTIVVAETADSPATLQYLAP
YTGAALAEYFMYRERHTLIIYDDPSKQAQAYRQMSLLLRRPPGREAYPGDVFYLHSRLLE
RAAKLSSSLGEGSMTALPIVETQSGDVSAYIPTNVISITDGQIFLSADLFNSGIRPAINV
GISVSRVGSAAQIKAMKQVAGKLKLELAQFAELEAFAQFASDLDKATQNQLARGQRLREL
LKQSQSAPLTVEEQIMTIYTGTNGYLDSLEVGQVRKFLVELRTYLKTNKPQFQEIISSTK
TFTEEAEALLKEAIQEQTDRFILQEQA.

Thank you in advance,

[kishorssf91]

I have tried both the cmd suggested above.

seqkit replace -sp "\." -r "" test.fa and grep -v "\." test.fa

&

seqkit replace -sp "\." -r "" test.fa and grep -v "\." test.fa

But i am still having the dots. I am adding the sequence here for you convenience (9th charecter on the string）.

Can i please get any suggestions? @pierre lindenbaum cpad0112

>asap_1791
LTICQSKS.LCLGLGINLHLMYLGEIAPKRMRGILTLTCAVYLSIGKLLAQVIGLKELMGTEDMWPYLLA

[Jeremy]

You can use the following:

sed 's/\.//g' test.fa > test2.fa

Answer 1

[Pierre Lindenbaum]

sed :

 sed '/^[^>]/s/\.$//'

[Ric]

It turns out a DOT is also available in the middle of each sequence. How it be possible to extend the sed command?

[cpad0112]

Did you try sed '/^[^>]/s/\.//' ? @ Ric

Answer 2

[cpad0112]

try seqkit replace -sp "\." -r "" test.fa and grep -v "\." test.fa on OP fasta sequences.