fasta format?

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fasta format?

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01-28-2009

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fasta format?

Hi,
I'm in need of creating a file in the fasta format:

Code:

>1A6A.A      
HVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALANIAVDKANLEIMTKRSNYTPITN
VPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCR
VEHWGLDEPLLKHWEF
>1A6A.B    
PRFLEYSTSECHFFNGTERVRYLDRYFHNQEENVRFDSDVGEFRAVTELGRPDAEYWNSQKDLLEQKRGRVDNYCRHNYG

Thinking it could be possible using awk... Just don't have it right at all below since it's only printing the first 60 positions in the line and not making the full line into several lines of 60 positions.

Code:

cat filename | awk '{print substr($1,1,60)}'

I also need to add a '>' to the first line with the lineID
Right now my file is in this format:

Code:

DRB1_010101
MVCLKLPGGSCMTALTVTLMVLSSPLALAGDTRPRFLWQLKFECHFFNGTERVRLLERCIYNQEESVRFDSDVGEYRAVTELGRPDAEYWNSQKDLLEQRRAAVDTYCRHNYGVGESFTVQRRVEPKVTVYPSKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSVTSPLTVEWRARSESAQSKMLSGVGGFVLGLLFLGAGLFIYFRNQKGHSGLQPTGFLS

Help! and thanks!

lost

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Not sure how you identify your header; anyway, to break that line down into 60 characters per line and assuming that a line with more than 20 characters must be such a data line and with 1-20 characters should get that > in front of it:

Code:

sed -e '/^.\{20,\}$/ { s/.\{60\}/&\n/g}; /^.\{1,20\}$/ { s/^.*$/>&/}' infile
>DRB1_010101
LKLPGGSCMTALTVTLMVLSSPLALAGDTRPRFLWQLKFECHFFNGTERVRLLERCIYNQ
EESVRFDSDVGEYRAVTELGRPDAEYWNSQKDLLEQRRAAVDTYCRHNYGVGESFTVQRR
VEPKVTVYPSKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNGDWT
FQTLVMLETVPRSGEVYTCQVEHPSVTSPLTVEWRARSESAQSKMLSGVGGFVLGLLFLG
AGLFIYFRNQKGHSGLQPTGFLS

zaxxon

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01-28-2009

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Thanks!
I'm unfortunately not very familiar with sed and the given command won't run...

Code:

sed: command garbled: sed -e '/^.\{20,\}$/ { s/.\{60\}/&\n/g}; /^.\{1,20\}$/ { s/^.*$/>&/}'

can't figure out where the mistake is..

lost

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I've written it in GNU sed; maybe you got one your box or can install one. Maybe someone else knows that has to be tweaked so it runs with other versions of sed, sorry.

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So if the command gsed isn't recognised, I don't have GNU sed on the terminal? or is there other short cuts to make a GNU sed command executable in non-GNU environment?
Dang it... Any way, THANKS!

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It can either be not installed or not in the path. I don't know your OS, but maybe a search with it's package manager for gsed could help.

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