2 <TITLE> Alternative ways of invoking ALSCRIPT</TITLE>
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10 <H2><A NAME=SECTION00016800000000000000> Alternative ways of invoking ALSCRIPT</A></H2>
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14 The documentation above describes the interactive mode of running ALSCRIPT.
15 However, it may be more convenient to run the program as a pipe under
16 Unix or MS-DOS. Examples are shown here.
18 ALSCRIPT is a program for producing pretty versions of multiple
19 sequence aligments. ALSCRIPT will also format single sequences. A
20 full description of the program is given in the file "alscript.doc".
22 Ways of running alscript:
25 Interactive mode: just type alscript.
26 You will be prompted for a command file name. The command file will
27 define the AMPS blocfile, and name of the file to store the PostScript
28 output - see alscript.doc for details.
31 alscript <command_file> has same effect as 1, But does not prompt for
33 e.g. alscript example1.als
36 alscript -q < <blocfile> > <PostScript>
37 Quick mode - uses default commands, reads alignment from stdin,
38 writes PostScript to stdout. This mode creates a command file
41 e.g. alscript -q < example1.blc > example1.ps
44 alscript -f <command_file>
48 alscript -f <command_file> -s
49 Silent operation: No messages are written to stderr, unless fatal.
50 Silent operation may be toggled by the silent_mode command
54 alscript -f <command_file> -p < <blocfile> > <PostScript>
55 Make alscript work like a pipe - blocfile is read from stdin,
57 to stdout. Messages are written to stderr. To supress messages include
60 e.g. alscript -f example1.als -p -s < example1.blc > example1.ps
64 Using alscript as a pipe has the advantage of allowing the blocfile to
65 be created on the fly by the programs msf2blc or clus2blc. For example
66 if we have a GCG .msf file called "pileup.msf" we can run alscript with
67 default shading/fonts and send the results straight to the PostScript
68 printer "lpr" as follows:
70 msf2blc -q <pileup.msf | alscript -q -s | lpr
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