Hi,
I'm new to perl. I recently installed RHEL 5.5 (it's the only Linux dist
allowed at my work place) and tried to upgrade from perl 5.8.8 (which came
with RHEL) to v 5.12.2. I didn't get any errors after going through the
config shell, make test, make install steps. But when I ask what the new
Hi,
I installed BioPerl on RHEL 5.5 (successfully I hope) and am trying to
execute a xml parser script that uses XML::Simple. I keep getting the
following error message:
could not find ParserDetails.ini in /usr/local/lib/perl5/site_
perl/5.12.2/XML/SAX
When I try to reinstall XML::Simple using C
son wrote:
> On 11/1/10 Mon Nov 1, 2010 10:01 AM, "galeb abu-ali" <
> abuali...@gmail.com>
> scribbled:
>
> > Hi,
> >
> > I installed BioPerl on RHEL 5.5 (successfully I hope) and am trying to
> > execute a xml parser script that uses XML::Simple.
re you running? It might be easier to go through the
> package manager and let it deal with dependencies. Under ubuntu, its
> libxml-parser-perl.
> On Nov 1, 2010 1:47 PM, "galeb abu-ali" wrote:
> > I do not have ParserDetails.ini in the SAX folder. I just tried
> installi
maintaining through yum.
> On Nov 1, 2010 2:56 PM, "galeb abu-ali" wrote:
> > I'm running Red Hat Enterprise Linux 5.5, and don't know how to go
> through
> > the package manager to get this done. Also, is it possible that I didn't
> > place the expat
awn wilson wrote:
> I'm just talking out of my ass here but, it sounds like either you need to
> install the sax module or your search path is messed up. The former should
> be easy enough to check, for the later try:
> perldoc -v
> And
> perldoc -f perlrun
> On Nov 1,
Hi,
I'm parsing an xml file and get an error when dereferencing a hash. I get an
error saying "Not a HASH reference as line 15."
Not sure where my syntax is off.
thanks,
galeb
My script is:
#!/usr/local/bin/perl
# parse_xml_OMap.pl
use strict; use warnings;
use Data::Dumper;
use XML::Simple
thanks, you're right. I took another look at the data structure and got the
script to work.
On Wed, Nov 3, 2010 at 6:07 PM, Jim Gibson wrote:
> On 11/3/10 Wed Nov 3, 2010 1:13 PM, "galeb abu-ali" >
> scribbled:
>
> > Hi,
> >
> > I'm parsing
Hi,
I'm trying to create a genbank library file that contains several genbank
records. I read in the genbank record names from a separate file into an
array and then loop through array of file names, open each file and read
contents into another array. The problem is in looping through the array a
Hi,
I am trying to use a script called VelvetOptmizer for optimizing assembly of
genome sequencing reads, which is part of the velvet assembler freeware.
This script uses modules 'threads' and 'threads::shared', both of which I
have installed. However, when I try to run the script, I get a message
Hi,
I'm trying to parse a table containing information about genes in a
bacterial chromosome. Below is a sample for several genes, and there's about
4500 such blocks in a file:
gene_oidLocus TagSourceCluster InformationGene
InformationE-value
642745051SeSA_B0001COG_cat
Hi,
I'm trying to parse a table containing information about genes in a
bacterial chromosome. Below is a sample for several genes, and there's about
4500 such blocks in a file:
gene_oidLocus TagSourceCluster InformationGene
InformationE-value
642745051SeSA_B0001COG_cat
Hi,
I'm trying to parse a table containing information about genes in a
bacterial chromosome. Below is a sample for several genes, and there's about
4500 such blocks in a file:
gene_oidLocus TagSourceCluster InformationGene
InformationE-value
642745051SeSA_B0001COG_cat
Hi,
I'm trying to parse a table containing information about genes in a
bacterial chromosome. Below is a sample for one gene, and there's about 4500
such blocks in a file:
gene_oidLocus TagSourceCluster InformationGene
InformationE-value
642745051SeSA_B0001COG_category
te:
> now, here's a homework question!! :)
>
> On Sat, Apr 23, 2011 at 10:27 AM, galeb abu-ali
> wrote:
> > Hi,
> >
> > I'm trying to parse a table containing information about genes in a
> > bacterial chromosome. Below is a sample for one gene, and there&#
t, Apr 23, 2011 at 11:56 AM, galeb abu-ali
> wrote:
>
> > BTW, it's not homework, It's supporting metadata for my research and I'm
> > trying to parse it in a format that will be easier to lookup later.
> >
>
> it was a joke. i figured you were either
rase/DNA polymerase involved in DNA repair
Many thanks again! Must've spent ~ 4 days on this. I've been flirting with
Perl less than a year, it's so seductive I find myself debating whether to
go back to school.
cheers
galeb
On Sat, Apr 23, 2011 at 3:30 PM, Mike McCl
thanks Peter,
code looks elegant now!
"like chiseling away everything that is not David from a block of marble :-)
"
very cool reference!
#!/usr/bin/perl
use Modern::Perl '2011';
use autodie;
my @a;
while( <> ) {
chomp;
my @temp if /^start$/;
if( /^end$/ ) {
push @a, [ @temp ];
} else {
push @temp, $_;
}
}
for my $name ( @a ) {
say join ", ", @$name;
}
On Fri, Jul 12, 2013 at 8:39 PM, John
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