Perl Code: Help Needed for Sequence Extraction.

[csmbiotech]

Hi,

Please let me know how the coding can be done for extracting each sequence in separate files, from a single file (*.txt or *.fa) containing those multiple sequences in Fasta formay.

Now, please let me elaborate this:

Suppose I have a file MultiFasta.txt which containes these three sequences in Fasta format:

> Species1
GTTGATGTAGCTTAAACTTAAAGCAAGGCA... ...AACAGACTTACACATGCAAGCATCCACGCCCCGGTGAG

> Species2
CGCTTAACCACACCC... ... ...CCATAA

> Species3
ATTAGATACCCC... ...TATATACCGCCATCTTCAGCAAACCC

Now I want these sequences should be extracted in separate files (eithe text format or fasta format). Please let me know what should be the code for the same. I was trying but, all in vein.

Thanks in advance.

[GenoMax]

See if this works for you: https://bioexpressblog.wordpress.com...sequence-file/ No code needed.

Warning: You will get generically named files (1.fa, 2.fa etc) with this one liner.

If you need file names to be set to the fasta headers (instead of the generic solution above) then it would be best to use faSplit utility from Jim Kent @UCSC (http://hgdownload.cse.ucsc.edu/admin...x86_64/faSplit). faSplit can be used in many ways by in this specific instance, use as follows (out_folder has to be made before running the following command):

$ faSplit byname in.fasta out_folder/

[csmbiotech]

Thanks for the help. But I use Windows OS. Can I run awk in Windows?

[GenoMax]

http://www.bioinformatics-made-simple.com/2013/07/how-to-split-multi-line-fasta-files.html

http://kirill-kryukov.com/study/tools/fasta-splitter/

[csmbiotech]

Thank you so much for updating me regarding this Perl script.
regards,

Chandra