Fwd: [Bioperl-l] bioperl on Mac OSX

Mon Feb 7 10:58:41 EST 2005

Please send your questions to the mailing list - I cannot be the only  
person answering questions.

Begin forwarded message:

> From: Arya Akmal <akmala at nmrc.navy.mil>
> Date: February 7, 2005 10:46:04 AM EST
> To: Jason Stajich <jason.stajich at duke.edu>
> Subject: Re: [Bioperl-l] bioperl on Mac OSX
>
> The modules you mentions can be loaded:
>
> >:~$ perl /Library/Perl/5.8.1/IO/String.pm
> >:~$ perl /Library/Perl/5.8.1/LWP
> >:~$ perl /Library/Perl/5.8.1/LWP.pm
> >:~$ perl /Library/Perl/5.8.1/LWP/UserAgent.pm
> >:~$
>
> The problem seems to be with HTML::Parser:
>
> >:~$ perldoc HTML::Parser
> >No documentation found for "HTML::Parser".
> >:~$
>
> The only modules I have under HTML are Form.pm and Tagset.pm.  
> Apparently, I am missing a module called HeadParser.pm:
>
>  DB<4> use Bio::Perl;
>
>  DB<5> $seq_object = get_sequence('swissprot',"ROA1_HUMAN");
>
>  DB<6> $blast_result = blast_sequence($seq_object)
>
>  -------------------- WARNING ---------------------
>  MSG: req was POST http://www.ncbi.nlm.nih.gov/blast/Blast.cgi
>  User-Agent: libwww-perl/5.803
>  Content-Length: 666
>  Content-Type: application/x-www-form-urlencoded
>
> SERVICE=plain&QUERY=%3EROA1_HUMAN+Heterogeneous+nuclear+ribonucleoprote 
> in+A1+(Helix-destabilizing+protein)+(Single- 
> strand+binding+protein)+(hnRNP+core+protein+A1).%0ASKSESPKEPEQLRKLFIGGL 
> SFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSR 
> EDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 
> IQKYHTVNGHNCEVRKALSKQEMASASSSQRGRSGSGNFGGGRGGGFGGNDNFGRGGNFSGRGGFGGSRGG 
> GGYGGSGDGYNGFGNDGGYGGGGPGYSGGSRGYGSGGQGYGNQGSGYGGSGSYDSYNNGGGRGFGGGSGSN 
> FGGGGSYNDFGNYNNQSSNFGPMKGGNFGGRSSGPYGGGGQYFAKPRNQGGYGGSSSSSSYGSGRRF&FOR 
> MAT_OBJECT=Alignment&COMPOSITION_BASED_STATISTICS=off&FILTER=L&CDD_SEAR 
> CH=off&PROGRAM=blastp&CMD=Put&DATABASE=nr&EXPECT=1e-10
>
> <HTML>
> <HEAD><TITLE>An Error Occurred</TITLE></HEAD>
> <BODY>
> <H1>An Error Occurred</H1>
> 500 Can't locate HTML/HeadParser.pm in @INC (@INC contains:  
> /sw/lib/perl5 /sw/lib/perl5/darwin  
> /System/Library/Perl/5.8.1/darwin-thread-multi-2level  
> /System/Library/Perl/5.8.1  
> /Library/Perl/5.8.1/darwin-thread-multi-2level /Library/Perl/5.8.1  
> /Library/Perl /Network/Library/Perl/5.8.1/darwin-thread-multi-2level  
> /Network/Library/Perl/5.8.1 /Network/Library/Perl .)
> </BODY>
> </HTML>
>
> ---------------------------------------------------
> Submitted Blast for [ROA1_HUMAN]
>
> Finally, here are the results of running the Remote Blast tests:
>
> :~/Desktop$ perl -I. -Ilib t/RemoteBlast.t
> 1..6
> ok 1
> ok 2
>
> -------------------- WARNING ---------------------
> MSG: req was POST http://www.ncbi.nlm.nih.gov/blast/Blast.cgi
> User-Agent: libwww-perl/5.803
> Content-Length: 1091
> Content-Type: application/x-www-form-urlencoded
>
> COMPOSITION_BASED_STATISTICS=off&CDD_SEARCH=off&FILTER=L&QUERY=%3Egi%7C 
> 1786183%7Cgb%7CAAC73113.1%7C+(AE000111)+aspartokinase+I%2C+homoserine+d 
> ehydrogenase+I+%5BEscherichia+coli%5D%0AMRVLKFGGTSVANAERFLRVADILESNARQG 
> QVATVLSAPAKITNHLVAMIEKTISGQDALPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIK 
> HVLHGISLLGQCPDSINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRR 
> IAASRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQVPDAR 
> LLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRDEDELPVKGISNLNNM 
> AMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISFCVPQSDCVRAERAMQEEFYLELKEGL 
> LEPLAVTERLAIISVVGDGMRTLRGISAKFFAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQ 
> MLFNTDQVIEVFVIGVGGVGGALLEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQA 
> KEPFNLGRLIRLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKS 
> RRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLAREMGYTEPDP 
> RDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMANLSQLDDLFAARVAKARDEGK 
> VLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLR 
> TLSWKLGV&FORMAT_OBJECT=Alignment&EXPECT=1e 
> -10&DATABASE=ecoli&SERVICE=plain&CMD=Put&PROGRAM=blastp
>
> <HTML>
> <HEAD><TITLE>An Error Occurred</TITLE></HEAD>
> <BODY>
> <H1>An Error Occurred</H1>
> 500 Can't locate HTML/HeadParser.pm in @INC (@INC contains: t . lib  
> /sw/lib/perl5 /sw/lib/perl5/darwin  
> /System/Library/Perl/5.8.1/darwin-thread-multi-2level  
> /System/Library/Perl/5.8.1  
> /Library/Perl/5.8.1/darwin-thread-multi-2level /Library/Perl/5.8.1  
> /Library/Perl /Network/Library/Perl/5.8.1/darwin-thread-multi-2level  
> /Network/Library/Perl/5.8.1 /Network/Library/Perl)
> </BODY>
> </HTML>
>
> ---------------------------------------------------
> ok 3
> ok 4 # Unable to run RemoteBlast tests - probably no network  
> connection.
> ok 5 # Unable to run RemoteBlast tests - probably no network  
> connection.
> ok 6 # Unable to run RemoteBlast tests - probably no network  
> connection.
> :~/Desktop$
>
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