Fasta to text format

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3.5 years ago

clarkanna150 • 0

Is there a quick way to convert fasta formats into text files? I need to convert whole genome sequences into .txt files for some software I am using, so need to remove scaffold assignments, so that the structure is the species name, followed by the entire sequence on "one line".

genome text fasta format • 4.2k views

ADD COMMENT • link 3.5 years ago by clarkanna150 • 0

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You're describing a custom plain text format, possibly space or tab separated with the species in the first field and the whole sequence in the second field, correct?

Where would you get the species name from?

ADD REPLY • link 3.5 years ago by Ram 43k

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Yes that is correct. Pref space delimited, with species name deriving from the 'filename' that the sequence is from.

ADD REPLY • link 3.5 years ago by clarkanna150 • 0

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Use this code courtesy of @Pierre. You can then cat the linearized files together. Change \t to space if you need that :

ADD REPLY • link 3.5 years ago by GenoMax 141k

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