Private Sub CommandButton1_Click()
Dim cmd As String
Dim ret As Double
Dim WshShell As Object
Dim plink_object As Object
' Run Linux Commands
Set WshShell = CreateObject("WScript.Shell")
On Error Resume Next
Set plink_object = WshShell.Run("C:\cygwin\bin\mintty.exe C:\cygwin\home\cmccabe\windows_annovar.pl 66 ""50602_15:56:31_15:56:11_15:56:21;50602_15:57:07_15:56:47_15:56:57""", 1)
On Error GoTo 0
End Sub
Code:
C:\cygwin\home\cmccabe\windows_annovar.pl: line 36: perl: command not found
perl code:
Code:
match() {
printf "\n\n"
printf "DEBUG INFO: VALUE OF \$id: %s, VALUE OF \$panel: %s\n" $id $panel
printf "What is the id of the patient to be matched : "; read id
printf "What panel: "; read panel
[ -z "$id" ] && printf "\n No ID supplied. Leaving match function." && sleep 2 && menu
[ "$id" = "end" ] && printf "\n Leaving match function." && sleep 2 && menu
cd 'C:\Users\cmccabe\Desktop\annovar'
OMR=Output_Mutation_Report
perl -aF/\\t/ -lne 'BEGIN{%m=map{chomp;s/\cM|\cJ//g;$p=join("\t",(split/\t/)[4,5]);($p,$_)} <>;$m{"#CHROM\tINFO"}=$m{"Chr\tSegment Position"}};/SEGPOS=(\d+)/ || /\t(INFO)\t/ or next;$p=$F[0]."\t".$1;exists $m{$p} and print join("\t",$_,$m{$p})' ${id}_${panel}_${OMR}.txt < ${id}_${panel}_${OMR}_Filtered.vcf > ${id}_matched.vcf
convert
from the perl code I removed the $( ). Thank you .
Guys,
I need to find all the files ending with either dmp or dmp.Z. This command is giving me error.
@files =`find $path \(-name "*.dmp" -o -name "*.dmp.Z"\) -mtime +30`;
sh: 0403-057 Syntax error at line 1 : `(' is not expected.
Thanks in advance (4 Replies)
I am trying to use a script to replace the header of each file, whose filename are stored within the array $test, using the sed command within a Perl script as follows:
$count = 0;
while ( $count < $#test )
{
`sed -e 's/BIOGRF 321/BIOGRF 332/g' ${test} > 0`;
`cat 0 >... (2 Replies)
Hi Gurus,
I've a find command that gets the list of files from a source directory where the extension is not html, xml, jsp, shtml or htaccess. The below find command runs fine from the command prompt or in a shell script. I need to eventually run it in a PERL script and am getting the... (5 Replies)
Hi Everyone,
i have a string 00:44:40
so:
$tmp=~ s/://gi;
$tmp=~s/({2})({2})({2})/$1*3600+$2*60+$3/e;
the output is 2680.
Any way to combine this two lines into a single line?
Thanks (4 Replies)
Hello,
Can any perl experts help me convert my sed string to perl. I am unsuccessful with this.
I have to remove this string from html files OAS_AD('Top');
I have come up with this. However the requirement is in perl.
for find in $(find . -type f -name "file1.html") ; do cat $find |... (2 Replies)
Good morning!
Imtrying to run:
#!/usr/bin/perl
perl -nle 'print if /\var\/log/' /etc/syslog.confBut I keep getting error: Do you need to predeclare -nle.Im trying to create a script that read the contents of /etc/syslog.conf and print out every line that contains /var/log. (1 Reply)
Experts,
We used to receive our source files with '~^' as row delimiter. This file contains 2500K records and two of the columns having value in HTML formats within the file.
While running the below commands against the file, we are encountering out of memory, could you please help to... (3 Replies)
so in unix this command works works and shows me a list of directories
find . -name \*.xls -exec dirname {} \; | sort -u | > list.txt
but when i try running a perl script to run this command
my $query = 'find . -name \*.xls -exec dirname {} \; | sort -u | > list.txt';... (2 Replies)
In the below perl executes if one file is processed perfect. However, when multiple files are processed in batch which is preferred I get the below error that I can not seem to fix it as the '' necessary for the command to execute, but seem to only work for one -arg option. Thank you :).
... (2 Replies)
This's my problem
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LC_ALL = "en_US.UTF-8",
LC__FASTMSG = "true",
LC_MESSAGES = "",
LC_CTYPE = "en_US.UTF-8",
LC_TYPE = "en_US.UTF-8",
LANG = "EN_US"... (1 Reply)
Discussion started by: bobochacha29
1 Replies
LEARN ABOUT OPENSOLARIS
ppmtosixel
ppmtosixel(1) General Commands Manual ppmtosixel(1)NAME
ppmtosixel - convert a portable pixmap into DEC sixel format
SYNOPSIS
ppmtosixel [-raw] [-margin] [ppmfile]
DESCRIPTION
Reads a portable pixmap as input. Produces sixel commands (SIX) as output. The output is formatted for color printing, e.g. for a DEC
LJ250 color inkjet printer.
If RGB values from the PPM file do not have maxval=100, the RGB values are rescaled. A printer control header and a color assignment table
begin the SIX file. Image data is written in a compressed format by default. A printer control footer ends the image file.
OPTIONS -raw If specified, each pixel will be explicitly described in the image file. If -raw is not specified, output will default to com-
pressed format in which identical adjacent pixels are replaced by "repeat pixel" commands. A raw file is often an order of magni-
tude larger than a compressed file and prints much slower.
-margin
If -margin is not specified, the image will be start at the left margin (of the window, paper, or whatever). If -margin is speci-
fied, a 1.5 inch left margin will offset the image.
PRINTING
Generally, sixel files must reach the printer unfiltered. Use the lpr -x option or cat filename > /dev/tty0?.
BUGS
Upon rescaling, truncation of the least significant bits of RGB values may result in poor color conversion. If the original PPM maxval was
greater than 100, rescaling also reduces the image depth. While the actual RGB values from the ppm file are more or less retained, the
color palette of the LJ250 may not match the colors on your screen. This seems to be a printer limitation.
SEE ALSO ppm(5)AUTHOR
Copyright (C) 1991 by Rick Vinci.
26 April 1991 ppmtosixel(1)
11-21-2014
.