-filter option for water and stretcher

[Graziano P.]

Hi All,
I need to introduce sequences by standard input. I have found the -filter
qualifier in
the -help -verbose options. For example, if I use this qualifier for
"transeq" I write:
transeq -filter

then I have to insert my sequence (in fasta format for example) pasting or
writing it. When I have finished writing or pasting the sequences, I have to
press CTRL-D to terminate the standard input introduction. Finally  the
program return the standard output.

I have tried to use the -filter qualifier with "water" and "stretcher".
These two programs require two sequences in input in different files.
If I write as standard input:

>HTRE_ECOLI P33129 OUTER MEMBRANE USHER PROTEIN ...
PGVYDVSVYVNDQPIINQSITFVAIEGKKNAQACITLKNLLQFHINSPDINNEKAVLLAR
DETLGNCLNLTEIIPQASVRYDVNDQRLDIDVPQAWVMKNYQNYVDPSLWENGINAAMLS
NDQRLDIDVP

>YCJV_ECOLI P77481 HYPOTHETICAL ABC TRANSPORTER ...
MAQLSLQHIQKIYDNQVHVVKDFNLEIADKEFIVFVGPSGCGKSTTLRMIAGLEEISGGD
LLIDGKRMNDVPAKARNIAMVFQNYALYPHMTVYDNMAFGLKMQKIAKEVIDERVNWAAQ
KISVAELTGAEFMLYTTVGGTS

when I press CTRL-D I get the following error message:

Error: Unable to read sequence ''

How can I tell to standard input that what I paste or write are two
different sequences?
Is there any separator character that do it?

Best regards
Graziano

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