Reformatting Fasta Files

Question

[Gritz122]

Hi,

I am new to regular expressions and programming in general and I need help with reformatting FASTA files from

>AB000667.1.2469.3417   root;Eukaryota;Chordata;Actinopteri;Pleuronectiformes;Paralichthyidae;Paralichthys;Paralichthys olivaceus
CAAAGGCTTGGTCCTGACTTTACTGTCGACTCTAACTAGACTTACACATGCAAGTATCCG
CCCCCCTGTGAGAATGCCCATAACGCCCTGCTCGGGAACAAGGAGCTGGCATCAGGCACA
...

some of them have:

>AB002132.1._1.403

in the header

and I want to change it to:

>AccessionNumber.Version SpeciesName
nucleotide sequence
nucleotide sequence, continued
nucleotide sequence, continued
etc...

The requirments include:

• The sequence name is just the Accession number followed by the version number
• This is followed by a space and then the species name. There should be a space between the genus and species name

Thanks!

Answer 1

[cpad0112]

$ sed '/>/ s/\(.*\)\s.*;\(.*\)$/\1\2/g' test.fa 

>AB000667.1.2469.3417  Paralichthys olivaceus
CAAAGGCTTGGTCCTGACTTTACTGTCGACTCTAACTAGACTTACACATGCAAGTATCCG
CCCCCCTGTGAGAATGCCCATAACGCCCTGCTCGGGAACAAGGAGCTGGCATCAGGCACA

input:

$ cat test.fa 

>AB000667.1.2469.3417   root;Eukaryota;Chordata;Actinopteri;Pleuronectiformes;Paralichthyidae;Paralichthys;Paralichthys olivaceus
CAAAGGCTTGGTCCTGACTTTACTGTCGACTCTAACTAGACTTACACATGCAAGTATCCG
CCCCCCTGTGAGAATGCCCATAACGCCCTGCTCGGGAACAAGGAGCTGGCATCAGGCACA

More the test data is provided, better would be the solution to OP. Gritz122

[Gritz122]

What would I have to change the regular expression to if I just need the

Genus_species

[cpad0112]

 $  sed '/>/ s/.*;\(.*\)$/>\1/g;s/ /_/g' test.fa

>Paralichthys_olivaceus
CAAAGGCTTGGTCCTGACTTTACTGTCGACTCTAACTAGACTTACACATGCAAGTATCCG
CCCCCCTGTGAGAATGCCCATAACGCCCTGCTCGGGAACAAGGAGCTGGCATCAGGCACA

[Gritz122]

Thanks so much, huge help!

[GenoMax]

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