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(Continued from previous question...)
How do you write sequences to different files instead of writing them
all to one file?
A) EMBOSS is not good at writing multiple sequences to different files.
You could try using 'nthseq' to pull out one sequence at a time.
You should consider using the '-ossingle' qualifier. This writes
sequences to separate FASTA files, but the file names depend on the
sequence ID. This is rarely used. It is there because -ossingle is the
default for GCG output format. The output filename is currently ignored
when ossingle is used, and the filename depends on each individual
sequence.
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