but is there a way to do this without haveing to write down all the headers on the command line. i have a file with 100's of sequnces and i just want to make a new file for each sequence. the "split" command allows you to do this by specifiying the amount of files, but no matter what i do using this, the order does not seem to be preserved, and 1 file always contains 2 sequences. there is an option to split by header, but thought this would automatically pick up the individual headers and put them in their own files.
split the fasta file into one new file per header with “%(seqid)s” being filled into each filename.:
$ pyfasta split –header “%(seqid)s.fasta” original.fasta
You need to specify that sequence id (= the name of your fasta within multifasta file) will be used as the name of the new files. For that, seqid parameter is used.
I guess you need to say with what you wanna split the fasta:
extract sequence from the file. use the header flag to make a new fasta file. the args are a list of sequences to extract.
extract sequence from a file using a file containing the headers not wanted in the new file:
extract sequence from a fasta file with complex keys where we only want to lookup based on the part before the space.
but is there a way to do this without haveing to write down all the headers on the command line. i have a file with 100's of sequnces and i just want to make a new file for each sequence. the "split" command allows you to do this by specifiying the amount of files, but no matter what i do using this, the order does not seem to be preserved, and 1 file always contains 2 sequences. there is an option to split by header, but thought this would automatically pick up the individual headers and put them in their own files.