Please send your questions to the mailing list - I cannot be the only person answering questions. Begin forwarded message: 0000,0000,0000From: Arya Akmal < 0000,0000,0000Date: February 7, 2005 10:46:04 AM EST 0000,0000,0000To: Jason Stajich < 0000,0000,0000Subject: 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+ribonucleoprotein+A1+(Helix-destabilizing+protein)+(Single-strand+binding+protein)+(hnRNP+core+protein+A1).%0ASKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQEMASASSSQRGRSGSGNFGGGRGGGFGGNDNFGRGGNFSGRGGFGGSRGGGGYGGSGDGYNGFGNDGGYGGGGPGYSGGSRGYGSGGQGYGNQGSGYGGSGSYDSYNNGGGRGFGGGSGSNFGGGGSYNDFGNYNNQSSNFGPMKGGNFGGRSSGPYGGGGQYFAKPRNQGGYGGSSSSSSYGSGRRF&FORMAT_OBJECT=Alignment&COMPOSITION_BASED_STATISTICS=off&FILTER=L&CDD_SEARCH=off&PROGRAM=blastp&CMD=Put&DATABASE=nr&EXPECT=1e-10 < <<An Error Occurred<< < <

An Error Occurred<

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 .) < < --------------------------------------------------- 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%7C1786183%7Cgb%7CAAC73113.1%7C+(AE000111)+aspartokinase+I%2C+homoserine+dehydrogenase+I+%5BEscherichia+coli%5D%0AMRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDALPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGVGGALLEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV&FORMAT_OBJECT=Alignment&EXPECT=1e-10&DATABASE=ecoli&SERVICE=plain&CMD=Put&PROGRAM=blastp < <<An Error Occurred<< < <

An Error Occurred<

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) < < --------------------------------------------------- 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$