Question :
Update : 7.11.18
You can also use AWK to solve this problem
awk '/^>/ {printf("\n%s\n",$0);next; } { printf("%s",$0);} END {printf("\n");}' < file.fa >result
I've a multi- fasta file with several unique names, (e.g. > Cryptococcus gattii ), and I need to generate another file with single line sequence i.e. header in one line sequence in single line below.
>Cryptococcus gattii
MGIKGLTGLLSENAPKCMKDHEMKTLFGRKVAIDASMSIYQFLIAVRQQDGQMLMNESGDVTSHLMGFFYRTIRMVDHGIKPCYIFDGKPPELKGSVLAKRFARREEAKEGEEEAKETGTAEDVDKLARRQVRVTREHNEECKKLLSLMGIPVVTAPGEAEAQCAELARAGKVYAAGSEDMDTLTFHSPILLRHLTFSEAKKMPISEIHLDVALRDLEMSMDQFIELCILLGCDYLEPCKGIGPKTALKLMREHGTLGKVVEHIRGKMAEKAEEIKAAADEEAEAEAEAEKYDSDPENEEGGETMINSDGEEVPAPSKPKSPKKKAPAKKKKIASSGMQIPEFWPWEEAKQLFLKPDVVNGDDLVLEWKQPDTEGLVEFLCRDKGFNEDRVRAGAAKLSKMLAAKQQGRLDGFFTVKPKEPAAKDAGKGKGKDTKGEKRKAEEKGAAKKKTKK
>Daphnia pulex
MGIKGLTQVIGDTAPTAIKENEIKNYFGRKVAIDASMSIYQFLIAVRSEGAMLTSADGETTSHLMGIFYRTIRMVDNGIKPVYVFDGKPPDMKGGELTKRAEKREEASKQLVLATDAGDAVEMEKMNKRLVKVNKGHTDECKQLLTLMGIPYVEAPCEAEAQCAALVKAGKVYATATEDMDSLTFGSNVLLRYLTYSEAKKMPIKEFHLDKILDGLSYTMDEFIDLCIMLGCDYCDTIKGIGAKRAKELIDKHRCIEKVIENLDTKKYTVPENWPYQEARRLFKTPDVADAETLDLKWTQPDEEGLVKFMCGDKNFNEERIRSGAKKLCKAKTGQTQGRLDSFFKVLPSSKPSTPSTPASKRKVGCIIYLFLYF
Answer
Multi fasta or multi line fasta is a useful file format where fasta header is followed by sequence in several lines instead of in single line. But some softwares accept sequences in a single lines so we need to compress sequences in a single line. Following PERL script can help to do that
singleline.pl
| Script name | Download |
|---|---|
| singleline.pl |  |
Considering sequences are stored in 'input.txt' , result will be stored in 'output.txt' and given PERL script is stored at your 'desktop' named as 'singleline.pl', you can use this script as follows
perl singleline.pl input.txt > output.txt
Result will be like that
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