Dear all, I have the following script (see below) that I would like to
interface.
#!/bin/csh -f
column.pl $1 50 > tmp1 # perl program. tmp1 is a one column file
H.py $1 > tmp2<<eof # python program. tmp2 is a one column file
eof
paste tmp2 tmp1 > $1.out <<eof # $1.out is a two column file
eof
gnuplot << eof
set terminal postscript landscape "courier" 10
set output "$1.ps"
set tics out
load "$1.label"
set xlabel "X"
set ylabel "Y"
plot "$1.out" notitle with impulses lt 1 lw 1
#plot "$1.out" notitle with histeps 1
eof
rm tmp[12]
Briefly the script takes an input file ("$1") and run two program on it,
column.pl (a perl script) and H.py (a python program), then it combines
the output of the two programs ("$1.out") and finally it plots the data
in "$1.out" using gnu-plot. The output of gnu-plot is a postcript file
("$1.ps"). In addition to tmp1, column.pl also generates the file
"$1.label", that is used by gnu-plot to set the xtics. Probably, this is
not the more elegant of the cshell programs but it is doing the job
under the unix prompt.
I have apache installed in my computer and I have been able to run the
program throguh the following form.
<html>
<head>
<html>
<head>
<title>nothing</title>
</head>
</head>
<body bgcolor="#B1AFCD" link="#0000FF">
<!--
<BODY BGCOLOR="#B1AFCD" LINK="#0000FF"
BACKGROUND="/graphics/background.gif">
-->
<form ENCTYPE="multipart/form-data"
ACTION="/cgi-bin/plot_vc.cgi"
METHOD="POST">
<table BORDER=0 >
<caption><!-- INPUT FROM LOCAL FILE -->
<br><!-- PASTING SEQUENCE -->
<br><!-- How do you make space in a table?? -->
<br><!-- OTHER OPTIONS --></caption>
<tr>
<p><b>Enter a short name for your alignment: </b><BR>
<INPUT SIZE=20 NAME="name"><P>
<p> <b>Enter your Local alignment file (CLUSTALW format): <br>
<input SIZE=50 NAME="alnfile" TYPE="file"></td>
<p>OR paste your INPUT alignment:<br>
<textarea NAME="alignment" ROWS=10 COLS=70></textarea>
<br><HR SIZE=2 WIDTH="100%">
<!-- OPTIONS END --><!-- SUBMIT/CLEAR panel -->
<input TYPE="submit" VALUE="Submit"><input TYPE="reset" VALUE="Clear">
</tr>
</table>
</form>
As I said, I can run the script (plot_vc.csh) using the above web form.
However, the program should be generating the files "$1.label", (where
$1 is the input) and "$1.ps" (postscript plot with the $1.labels on it).
Instead I am getting the files ".label", and ".ps" (the plot with no
label). So, I am not passing the arguments from one program to the
other, and I would like to know how to do it. Also, I would like to know
how to serve the results to the user (showing a link to the "$1.ps" file
will be enough). I know these question are too general, and I am sorry
about my lack of knowledge. I have tried to do it by myself, but with no
success, I am basically lost. However, I am person that works very well
with examples, and if you could give an example of how this thing could
be done it will be of great help.
Best regards,
Pedro
***************************************************************************
PEDRO a. RECHE gallardo, pHD TL: 617 632
3824
Scientist, Mol.Immnunol.Foundation, FX: 617 632 3351
Dana-Farber Cancer Institute, EM:
[EMAIL PROTECTED]
Harvard Medical School, URL: http://www.reche.org
44 Binney Street, D610C,
Boston, MA 02115
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