Question: (Closed) How can i extract only Few sequences from my fasta file ?
0
gravatar for k.kathirvel93
3.7 years ago by
k.kathirvel93210
India
k.kathirvel93210 wrote:

Hi, Everyone. I have a fasta file with thousands of sequences with peg IDs. Can anyone please help me to extract only particular sequences based on there peg ID........ Thanks in advance !!

.fasta file looks...

>fig|6666666.167416.peg.1
MYVAGHEGIELQPLSAADDAEARRLADEYFSRIDPAGR
>fig|6666666.167416.peg.2
MTHNQCLDLLESAEDTLDFLKSSLTYLGSPQKTENKAR
>fig|6666666.167416.peg.3
MIAHASTPYSRKRGEPGPPHGPGLRRNEPHSGSTPFSL
>fig|6666666.167416.peg.4
MLLAAGRNRSARAAAREATGQDRCGGKRTGRKSGFPE
>fig|6666666.167416.peg.5
MDVRAPRAAPTGSDWRCRGRFSFFPRRSSFRSGARRL
>fig|6666666.167416.peg.6
MQIMVIEAMKEGADPEALLSSAQKVIDERTKELDKLD
>fig|6666666.167416.peg.7
MHELQQALANLNTVLRRLDRNPAQYLLGGENIEETKP
>fig|6666666.167416.peg.8
MLGHGRLQGSVRWRGAARKAVGGFLPSGLRPHHEISE

From this, for example, I just want to extract the sequences of >fig|6666666.167416.peg.2 to >fig|6666666.167416.peg.7 based on their ID number. excepting some python script....

sequencing rna-seq next-gen • 1.3k views
ADD COMMENTlink modified 14 months ago by RamRS24k • written 3.7 years ago by k.kathirvel93210
4

Wow, it's not like anyone asked this question ever before..

ADD REPLYlink modified 14 months ago by RamRS24k • written 3.7 years ago by 5heikki8.6k

You can edit with certain linux command if ur working on linux system.

Or else there are some perl scrpits available online which can help you out

ADD REPLYlink modified 14 months ago by RamRS24k • written 3.7 years ago by raya.girish20

Pls show us what have your tried or what approach would be good. And you are expecting Python script?

ADD REPLYlink modified 14 months ago by RamRS24k • written 3.7 years ago by geek_y10.0k

Hello k.kathirvel93!

Questions similar to yours can already be found at:

We have closed your question to allow us to keep similar content in the same thread.

If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.

Cheers!

ADD REPLYlink modified 14 months ago by RamRS24k • written 3.7 years ago by Michael Dondrup46k
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