Perl Script 2 : Convert Multi Fasta file into a Single line FASTA File

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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9 comments:

  1. UnknownOctober 16, 2012 at 3:57 AM

    I noticed a few possible errors with your script (only by attempting to run it naively myself). I had to make a few small changes for this to actually work. I realized the issue arises from the way this website handles the use of '<', '>' characters. This effectively removes the file handlers from your script, resulting in it not working. You might want to consider hosting this elsewhere or finding a way around this. Either way, thank you for posting this, I too have been in the need to single line sequence files.

    ReplyDelete
  2. Priyanka PaulOctober 16, 2012 at 5:50 AM

    Hi jordyn,
    Thanks for your suggestion. I will consider it in future.

    ReplyDelete
  3. AnonymousNovember 9, 2012 at 8:41 PM

    Thanks. It's very useful

    ReplyDelete
  4. VondoJuly 1, 2013 at 5:16 PM

    Thanks, the template helped me a lot.

    ReplyDelete
  5. chucaoFebruary 19, 2014 at 12:10 AM

    Thank you. Your blog has been very useful. This script works very well

    ReplyDelete
    Replies
    1. संजयFebruary 19, 2014 at 8:12 AM

      Hi Chucao,
      Always welcome. Please to learn that PERL script worked for you.

      Delete
  6. UnknownJuly 6, 2018 at 1:20 AM

    No such file or directory at ./singleline.pl line 8.
    i am getting this error while running the script for multi to single fasta could you please help me to resolve this error.


    thanl you

    ReplyDelete
  7. UnknownJuly 6, 2018 at 1:22 AM

    No such file or directory at ./singleline.pl line 8.
    I am getting this error while converting multi to single fasta could you please help me to fix this error.

    thank you

    ReplyDelete
    Replies
    1. संजयJuly 11, 2018 at 8:34 PM

      Thanks for using this script. Error said that your input file is not present. Please make sure to give the proper path. Thanks

      Delete

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