Room for terdon and Ursula

terdon

14:26

@UrszulaUciechowska you can join me here if you want.

You might not be able to write when you fist come here. I can give you write access but you need to first log in to chat. As soon as I see your avatar in the room, I'll give you write access.

@UrszulaUciechowska you should be able to write now

You might need to reload the room.

Urszula Uciechowska

now I can write

I need to take the protein sequence and the protein ID out of ths file

terdon

@UrszulaUciechowska OK, so protein only? And all variants?

For some reason, your example shows a termiator and its translation!

Urszula Uciechowska

do not need them

the /protein_id="AAQ05968.1" and the sequence

terdon

@UrszulaUciechowska OK, so do you have a list of desired input ids?

Urszula Uciechowska

rest can be deleted

terdon

14:38

Do you have a list of the desired protein IDs? How can I know which sequences you want and which ones not?

Urszula Uciechowska

I want all

protein sequences that starts with /translation="

terdon

All what? All proteins coded for by the vector?

But if you want the protein only, why do you also want regulatory_class? That is a separate entry, it doesn't refer to the protein.

Urszula Uciechowska

/protein_id="AAQ05968.1"
/db_xref="GI:33320495"
/translation="MREAVIAEVSTQLSEVVGVIERHLEPTLLAVHLYGSAVDGGLKP
HSDIDLLVTVTVRLDETTRRALINDLLETSASPGESEILRAVEVTIVVHDDIIPWRYP
AKRELQFGEWQRNDILAGIFEPATIDIDLAILLTKAREHSVALVGPAAEELFDPVPEQ
DLFEALNETLTLWNSPPDWAGDERNVVLTLSRIWYSAVTGKIAPKDVAADWAMERLPA
QYQPVILEARQAYLGQEDRLASRADQLEEFVHYVKGEITKVVGK"

terdon

Ah, OK, so you were using the regulatory_class only to delimit the sequence?

Urszula Uciechowska

yes

terdon

14:42

OK, let me think about it. You might be able to use the fact that the sequence is in all CAPS

Urszula Uciechowska

yes you right

terdon

@UrszulaUciechowska try this:

sed -n '/\/protein_id=/,/^\s*[[:upper:]]\+"\s*$/{p}' two_seq.txt

Urszula Uciechowska

its working

at least for this file

can you explain me the command ?

terdon

@UrszulaUciechowska It's the same idea as the originals. It will print between the two matching patterns. The general format is

sed -n '/foo/,/bar/{p}`

the -n means "don't print unless explicitly told to do so, the {p} means "print"

So, that command will print all lines between foo and bar.

The one I am using prints all lines between /protein_id= and a line that starts with 0 or more whitespace characters (^\s*), then one or more upper case letters until a " and then 0 or more whitespace until the end of the line (\s*$)

Urszula Uciechowska

thanks a lot

terdon

14:55

@UrszulaUciechowska You're welcome. Could you please edit your question to use protein_id as the delimiter and clarify that you only want the sequence?

That way, I can edit my answer and you could accept it.

Urszula Uciechowska

terdon

@UrszulaUciechowska Thanks. Us bioinformaticians should stick together :)

Urszula Uciechowska

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