upgrade to perl 5.12.2 on RHEL 5.5

2010-10-29 Thread galeb abu-ali
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

need help with XML::Simple

2010-11-01 Thread galeb abu-ali
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

Re: need help with XML::Simple

2010-11-01 Thread galeb abu-ali
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: need help with XML::Simple

2010-11-01 Thread galeb abu-ali
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

Re: need help with XML::Simple

2010-11-01 Thread galeb abu-ali
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

Re: need help with XML::Simple

2010-11-02 Thread galeb abu-ali
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,

issue with dereferencing a hash

2010-11-03 Thread galeb abu-ali
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

Re: issue with dereferencing a hash

2010-11-04 Thread galeb abu-ali
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

genbank library file

2011-01-16 Thread galeb abu-ali
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

threading perl 5.12

2011-02-17 Thread galeb abu-ali
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

parse complicated table

2011-04-23 Thread galeb abu-ali
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

Fwd: parse complicated table

2011-04-23 Thread galeb abu-ali
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

Fwd: parse complicated table

2011-04-23 Thread galeb abu-ali
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

how to parse complex table

2011-04-23 Thread galeb abu-ali
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

Re: how to parse complex table

2011-04-23 Thread galeb abu-ali
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&#

Re: how to parse complex table

2011-04-23 Thread galeb abu-ali
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

Fwd: how to parse complex table

2011-04-24 Thread galeb abu-ali
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

Re: Fwd: how to parse complex table

2011-04-25 Thread galeb abu-ali
thanks Peter, code looks elegant now! "like chiseling away everything that is not David from a block of marble :-) " very cool reference!

Re: grab pattern from start and end block

2013-07-12 Thread galeb abu-ali
#!/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