i have a fasta file with following format
>gi|321257144|ref|XP_003193485.1| flap endonuclease [Cryptococcus gattii WM276] MGIKGLTGLLSENAPKCMKDHEMKTLFGRKVAIDASMSIYQFLIAVRQQDGQMLMNESGDVTSHLMGFFY RTIRMVDHGIKPCYIFDGKPPELKGSVLAKRFARREEAKEGEEEAKETGTAEDVDKLARRQVRVTREHNE ECKKLLSLMGIPVVTAPGEAEAQCAELARAGKVYAAGSEDMDTLTFHSPILLRHLTFSEAKKMPISEIHL DVALRDLEMSMDQFIELCILLGCDYLEPCKGIGPKTALKLMREHGTLGKVVEHIRGKMAEKAEEIKAAAD EEAEAEAEAEKYDSDPENEEGGETMINSDGEEVPAPSKPKSPKKKAPAKKKKIASSGMQIPEFWPWEEAK QLFLKPDVVNGDDLVLEWKQPDTEGLVEFLCRDKGFNEDRVRAGAAKLSKMLAAKQQGRLDGFFTVKPKE PAAKDAGKGKGKDTKGEKRKAEEKGAAKKKTKK >gi|321473340|gb|EFX84308.1| hypothetical protein DAPPUDRAFT_47502 [Daphnia pulex] MGIKGLTQVIGDTAPTAIKENEIKNYFGRKVAIDASMSIYQFLIAVRSEGAMLTSADGETTSHLMGIFYR TIRMVDNGIKPVYVFDGKPPDMKGGELTKRAEKREEASKQLVLATDAGDAVEMEKMNKRLVKVNKGHTDE CKQLLTLMGIPYVEAPCEAEAQCAALVKAGKVYATATEDMDSLTFGSNVLLRYLTYSEAKKMPIKEFHLD KILDGLSYTMDEFIDLCIMLGCDYCDTIKGIGAKRAKELIDKHRCIEKVIENLDTKKYTVPENWPYQEAR RLFKTPDVADAETLDLKWTQPDEEGLVKFMCGDKNFNEERIRSGAKKLCKAKTGQTQGRLDSFFKVLPSS KPSTPSTPASKRKVGCIIYLFLYF
but i wanna to look sequence in a single line, not in many line as they are. any quick method??
Suggestion for Windows --> Switch to Linux :p
Good solution but be careful. If you redirect the result to a file,
the first line is left empty.
+1 for the windows fix :-)
There will be an empty line at the beginning it should be removed like:
tail -n +2 filein.fa > fileout.fa
yeah.. that was ~6 years ago. Now: http://stackoverflow.com/documentation/bioinformatics/4194
my bad I just saw it :)
...the link is dead and I still get the first line empty after redirecting the output into a file - could you update the answer if there is a more elegant way (not piping through tail) to avoid this?
Modified the original awk code from @Pierre Lindenbaum to below
Uses NR (numbered row) to print a newline only for non-first fasta record. Not the most elegant but I hope this will help someone out there.
you can use the answer provided by Jorge Amigo below. (it's not using tail)
Unfortunately i am a window lover. plz suggests something for window..plzzzz