Any ideas on how to transform a fasta file (in .fasta extension) to a tab-delimited file (in .txt extension)? Thanks.
Here is a small script in R that does the job. Could probably be transposed in many other languages quite easily. Could also be improved to split information from the first line or each fasta record...
Here is a small script in R that does the job. Could probably be transposed in many other languages quite easily. Could also be improved to split information from the first line or each fasta record...
If you install biopieces (biopieces.org), you can do:
read_fasta -i file.fasta | write_tab -x -K SEQNAME,SEQTYPE, SEQ
Try biostars.org for this kind of questions.
If you work under Linux (which I highly recommend for serious bioinformatics work), you can use a tool that is part of the fastx toolkit found at http://hannonlab.cshl.edu/fastx_toolkit/ The program itself is named fasta_formatter (http://hannonlab.cshl.edu/fastx_toolkit/commandline.html#fasta_formatter_usage). Cheers.
You can use Bioedit, it's a free software for Windows, and You can use it to work with your sequence and to save it in differents extentions ( including .txt).
One can also use the FASTA-to-tabular converter from the Galaxy bioinformatics suite:
https://usegalaxy.org/
The easiest if you work under linux:
tr '\n' '\t' output.txt . This command converts the new line after fasta header into tab. Thus, each row contains fasta header in first column and sequence in second column.
Does anyone have a script that will convert in the other direction? i.e. csv to fasta? I tried reversing the commands, but that did not work.
I also found code that included
example
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