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bp_genbank2gff.pl giving errors when using file....
by Gow
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Hi All, I am trying to use bp_genbank2gff.pl script to convert a locally downloaded genbank file. It is throwing stack errors. But, the script works beautifully when I use --accession option to download and convert. Any suggestions? Thanks very much for checking this. the command i use: perl bp_genbank2gff.pl --stdout --file NC_004329.nb and i am getting the following exception message: ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: EMBL stream with no ID. Not embl in my book STACK: Error::throw STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.5/Bio/Root/Root.pm:359 STACK: Bio::SeqIO::embl::next_seq /usr/lib/perl5/site_perl/5.8.5/Bio/SeqIO/embl.pm:189 STACK: Bio::DB::GFF::Adaptor::biofetch::load_from_file /usr/lib64/perl5/site_perl/5.8.5/x86_64-linux-thread-multi/Bio/DB/GFF/Adaptor/biofetch.pm:163 STACK: bp_genbank2gff.pl:274 ----------------------------------------------------------- Many thanks in advance, Gowtham _______________________________________________ Bioperl-l mailing list Bioperl-l@... http://lists.open-bio.org/mailman/listinfo/bioperl-l |
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Re: bp_genbank2gff.pl giving errors when using file....
by Scott Cain-3
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Hi Gotham,
I was going to send you an email to complain to the author, until I realized that it was me :-) It has been quite a while since I looked at the code for this script, as the one I typically use these days is bp_genbank2gff3.pl, but I think I have a "fix". Try changing the name of the file to NC_004329.gb or .gbk or .genbank. That is the (very weak) heuristic that the script uses to determine if a file is genbank formated versus embl (note that the error message says it's not an embl file--that's why). If that doesn't do it, let me (and the mailing list) know. Scott PS: I wasn't really going to say to complain to the author directly-- that was just me trying to be funny. PPS: As another side note, it is fairly funny to me that the code that this script depends upon, Bio::DB::GFF::Adaptor::biofetch, says in the documentation that it is proof-of-principle and should not be used in production. On Jul 7, 2009, at 1:59 PM, Gowthaman Ramasamy wrote: > > Hi All, > I am trying to use bp_genbank2gff.pl script to convert a locally > downloaded genbank file. It is throwing stack errors. But, the > script works beautifully when I use --accession option to download > and convert. > > Any suggestions? Thanks very much for checking this. > > the command i use: > perl bp_genbank2gff.pl --stdout --file NC_004329.nb > > and i am getting the following exception message: > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: EMBL stream with no ID. Not embl in my book > STACK: Error::throw > STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.5/Bio/ > Root/Root.pm:359 > STACK: Bio::SeqIO::embl::next_seq /usr/lib/perl5/site_perl/5.8.5/Bio/ > SeqIO/embl.pm:189 > STACK: Bio::DB::GFF::Adaptor::biofetch::load_from_file /usr/lib64/ > perl5/site_perl/5.8.5/x86_64-linux-thread-multi/Bio/DB/GFF/Adaptor/ > biofetch.pm:163 > STACK: bp_genbank2gff.pl:274 > ----------------------------------------------------------- > > > Many thanks in advance, > Gowtham > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@... > http://lists.open-bio.org/mailman/listinfo/bioperl-l ----------------------------------------------------------------------- Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research _______________________________________________ Bioperl-l mailing list Bioperl-l@... http://lists.open-bio.org/mailman/listinfo/bioperl-l |
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Re: bp_genbank2gff.pl giving errors when using file....
by Gow
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Hi Scott,
Thanks for the mail. Its funny. Knowing you (at GMOD meeting) I wouldn't mistake it in any other ways. I was rushing back to email the list to tell I got it working. There is NOTHING wrong with script. Its perfectly good. (not many scripts stands the time. This one does). Its the genbank record. Some of the genbank records I tried did produce that error, while others did not. I'll dig into those files to see if anything is obvious (to my eyes) that causes this error. PS1: I tried changing the name, and that did NOT solve the problem. Thanks once again, Gowtham On 7/7/09 12:18 PM, "Scott Cain" <cain.cshl@...> wrote: > Hi Gotham, > > I was going to send you an email to complain to the author, until I > realized that it was me :-) > > It has been quite a while since I looked at the code for this script, > as the one I typically use these days is bp_genbank2gff3.pl, but I > think I have a "fix". Try changing the name of the file to > NC_004329.gb or .gbk or .genbank. That is the (very weak) heuristic > that the script uses to determine if a file is genbank formated versus > embl (note that the error message says it's not an embl file--that's > why). If that doesn't do it, let me (and the mailing list) know. > > Scott > > PS: I wasn't really going to say to complain to the author directly-- > that was just me trying to be funny. > > PPS: As another side note, it is fairly funny to me that the code that > this script depends upon, Bio::DB::GFF::Adaptor::biofetch, says in the > documentation that it is proof-of-principle and should not be used in > production. > > > On Jul 7, 2009, at 1:59 PM, Gowthaman Ramasamy wrote: > >> >> Hi All, >> I am trying to use bp_genbank2gff.pl script to convert a locally >> downloaded genbank file. It is throwing stack errors. But, the >> script works beautifully when I use --accession option to download >> and convert. >> >> Any suggestions? Thanks very much for checking this. >> >> the command i use: >> perl bp_genbank2gff.pl --stdout --file NC_004329.nb >> >> and i am getting the following exception message: >> >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: EMBL stream with no ID. Not embl in my book >> STACK: Error::throw >> STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.5/Bio/ >> Root/Root.pm:359 >> STACK: Bio::SeqIO::embl::next_seq /usr/lib/perl5/site_perl/5.8.5/Bio/ >> SeqIO/embl.pm:189 >> STACK: Bio::DB::GFF::Adaptor::biofetch::load_from_file /usr/lib64/ >> perl5/site_perl/5.8.5/x86_64-linux-thread-multi/Bio/DB/GFF/Adaptor/ >> biofetch.pm:163 >> STACK: bp_genbank2gff.pl:274 >> ----------------------------------------------------------- >> >> >> Many thanks in advance, >> Gowtham >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l@... >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > ----------------------------------------------------------------------- > Scott Cain, Ph. D. scott at scottcain dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > > > > _______________________________________________ Bioperl-l mailing list Bioperl-l@... http://lists.open-bio.org/mailman/listinfo/bioperl-l |
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Re: bp_genbank2gff.pl giving errors when using file....
by Gow
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And bp_genbank2gff3.pl script handled them very well.......
Thanks again, gowtham On 7/7/09 12:18 PM, "Scott Cain" <cain.cshl@...> wrote: > Hi Gotham, > > I was going to send you an email to complain to the author, until I > realized that it was me :-) > > It has been quite a while since I looked at the code for this script, > as the one I typically use these days is bp_genbank2gff3.pl, but I > think I have a "fix". Try changing the name of the file to > NC_004329.gb or .gbk or .genbank. That is the (very weak) heuristic > that the script uses to determine if a file is genbank formated versus > embl (note that the error message says it's not an embl file--that's > why). If that doesn't do it, let me (and the mailing list) know. > > Scott > > PS: I wasn't really going to say to complain to the author directly-- > that was just me trying to be funny. > > PPS: As another side note, it is fairly funny to me that the code that > this script depends upon, Bio::DB::GFF::Adaptor::biofetch, says in the > documentation that it is proof-of-principle and should not be used in > production. > > > On Jul 7, 2009, at 1:59 PM, Gowthaman Ramasamy wrote: > >> >> Hi All, >> I am trying to use bp_genbank2gff.pl script to convert a locally >> downloaded genbank file. It is throwing stack errors. But, the >> script works beautifully when I use --accession option to download >> and convert. >> >> Any suggestions? Thanks very much for checking this. >> >> the command i use: >> perl bp_genbank2gff.pl --stdout --file NC_004329.nb >> >> and i am getting the following exception message: >> >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: EMBL stream with no ID. Not embl in my book >> STACK: Error::throw >> STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.5/Bio/ >> Root/Root.pm:359 >> STACK: Bio::SeqIO::embl::next_seq /usr/lib/perl5/site_perl/5.8.5/Bio/ >> SeqIO/embl.pm:189 >> STACK: Bio::DB::GFF::Adaptor::biofetch::load_from_file /usr/lib64/ >> perl5/site_perl/5.8.5/x86_64-linux-thread-multi/Bio/DB/GFF/Adaptor/ >> biofetch.pm:163 >> STACK: bp_genbank2gff.pl:274 >> ----------------------------------------------------------- >> >> >> Many thanks in advance, >> Gowtham >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l@... >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > ----------------------------------------------------------------------- > Scott Cain, Ph. D. scott at scottcain dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > > > > _______________________________________________ Bioperl-l mailing list Bioperl-l@... http://lists.open-bio.org/mailman/listinfo/bioperl-l |
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Re: bp_genbank2gff.pl giving errors when using file....
by Scott Cain-4
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Hi Gowthaman,
I thought I knew you but wasn't sure; hi again. About the problematic genbank files: was it something that the genbank parser should have handled but did not? If so, we should get that fixed anyway. Scott On Jul 7, 2009, at 4:06 PM, Gowthaman Ramasamy wrote: > Hi Scott, > Thanks for the mail. Its funny. Knowing you (at GMOD meeting) I > wouldn't > mistake it in any other ways. > > I was rushing back to email the list to tell I got it working. There > is > NOTHING wrong with script. Its perfectly good. (not many scripts > stands the > time. This one does). > > Its the genbank record. Some of the genbank records I tried did > produce that > error, while others did not. I'll dig into those files to see if > anything is > obvious (to my eyes) that causes this error. > > PS1: I tried changing the name, and that did NOT solve the problem. > > Thanks once again, > Gowtham > > > On 7/7/09 12:18 PM, "Scott Cain" <cain.cshl@...> wrote: > >> Hi Gotham, >> >> I was going to send you an email to complain to the author, until I >> realized that it was me :-) >> >> It has been quite a while since I looked at the code for this script, >> as the one I typically use these days is bp_genbank2gff3.pl, but I >> think I have a "fix". Try changing the name of the file to >> NC_004329.gb or .gbk or .genbank. That is the (very weak) heuristic >> that the script uses to determine if a file is genbank formated >> versus >> embl (note that the error message says it's not an embl file--that's >> why). If that doesn't do it, let me (and the mailing list) know. >> >> Scott >> >> PS: I wasn't really going to say to complain to the author directly-- >> that was just me trying to be funny. >> >> PPS: As another side note, it is fairly funny to me that the code >> that >> this script depends upon, Bio::DB::GFF::Adaptor::biofetch, says in >> the >> documentation that it is proof-of-principle and should not be used in >> production. >> >> >> On Jul 7, 2009, at 1:59 PM, Gowthaman Ramasamy wrote: >> >>> >>> Hi All, >>> I am trying to use bp_genbank2gff.pl script to convert a locally >>> downloaded genbank file. It is throwing stack errors. But, the >>> script works beautifully when I use --accession option to download >>> and convert. >>> >>> Any suggestions? Thanks very much for checking this. >>> >>> the command i use: >>> perl bp_genbank2gff.pl --stdout --file NC_004329.nb >>> >>> and i am getting the following exception message: >>> >>> ------------- EXCEPTION: Bio::Root::Exception ------------- >>> MSG: EMBL stream with no ID. Not embl in my book >>> STACK: Error::throw >>> STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.5/Bio/ >>> Root/Root.pm:359 >>> STACK: Bio::SeqIO::embl::next_seq /usr/lib/perl5/site_perl/5.8.5/ >>> Bio/ >>> SeqIO/embl.pm:189 >>> STACK: Bio::DB::GFF::Adaptor::biofetch::load_from_file /usr/lib64/ >>> perl5/site_perl/5.8.5/x86_64-linux-thread-multi/Bio/DB/GFF/Adaptor/ >>> biofetch.pm:163 >>> STACK: bp_genbank2gff.pl:274 >>> ----------------------------------------------------------- >>> >>> >>> Many thanks in advance, >>> Gowtham >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l@... >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> ----------------------------------------------------------------------- >> Scott Cain, Ph. D. scott at scottcain dot net >> GMOD Coordinator (http://gmod.org/) 216-392-3087 >> Ontario Institute for Cancer Research >> >> >> >> > ----------------------------------------------------------------------- Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research _______________________________________________ Bioperl-l mailing list Bioperl-l@... http://lists.open-bio.org/mailman/listinfo/bioperl-l |
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Re: bp_genbank2gff.pl giving errors when using file....
by Chris Fields-5
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I may take a look at that one as well (it would be nice to know if
this is something that's popping up in newer records). chris On Jul 7, 2009, at 3:06 PM, Gowthaman Ramasamy wrote: > Hi Scott, > Thanks for the mail. Its funny. Knowing you (at GMOD meeting) I > wouldn't > mistake it in any other ways. > > I was rushing back to email the list to tell I got it working. There > is > NOTHING wrong with script. Its perfectly good. (not many scripts > stands the > time. This one does). > > Its the genbank record. Some of the genbank records I tried did > produce that > error, while others did not. I'll dig into those files to see if > anything is > obvious (to my eyes) that causes this error. > > PS1: I tried changing the name, and that did NOT solve the problem. > > Thanks once again, > Gowtham > > > On 7/7/09 12:18 PM, "Scott Cain" <cain.cshl@...> wrote: > >> Hi Gotham, >> >> I was going to send you an email to complain to the author, until I >> realized that it was me :-) >> >> It has been quite a while since I looked at the code for this script, >> as the one I typically use these days is bp_genbank2gff3.pl, but I >> think I have a "fix". Try changing the name of the file to >> NC_004329.gb or .gbk or .genbank. That is the (very weak) heuristic >> that the script uses to determine if a file is genbank formated >> versus >> embl (note that the error message says it's not an embl file--that's >> why). If that doesn't do it, let me (and the mailing list) know. >> >> Scott >> >> PS: I wasn't really going to say to complain to the author directly-- >> that was just me trying to be funny. >> >> PPS: As another side note, it is fairly funny to me that the code >> that >> this script depends upon, Bio::DB::GFF::Adaptor::biofetch, says in >> the >> documentation that it is proof-of-principle and should not be used in >> production. >> >> >> On Jul 7, 2009, at 1:59 PM, Gowthaman Ramasamy wrote: >> >>> >>> Hi All, >>> I am trying to use bp_genbank2gff.pl script to convert a locally >>> downloaded genbank file. It is throwing stack errors. But, the >>> script works beautifully when I use --accession option to download >>> and convert. >>> >>> Any suggestions? Thanks very much for checking this. >>> >>> the command i use: >>> perl bp_genbank2gff.pl --stdout --file NC_004329.nb >>> >>> and i am getting the following exception message: >>> >>> ------------- EXCEPTION: Bio::Root::Exception ------------- >>> MSG: EMBL stream with no ID. Not embl in my book >>> STACK: Error::throw >>> STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.5/Bio/ >>> Root/Root.pm:359 >>> STACK: Bio::SeqIO::embl::next_seq /usr/lib/perl5/site_perl/5.8.5/ >>> Bio/ >>> SeqIO/embl.pm:189 >>> STACK: Bio::DB::GFF::Adaptor::biofetch::load_from_file /usr/lib64/ >>> perl5/site_perl/5.8.5/x86_64-linux-thread-multi/Bio/DB/GFF/Adaptor/ >>> biofetch.pm:163 >>> STACK: bp_genbank2gff.pl:274 >>> ----------------------------------------------------------- >>> >>> >>> Many thanks in advance, >>> Gowtham >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l@... >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> ----------------------------------------------------------------------- >> Scott Cain, Ph. D. scott at scottcain dot net >> GMOD Coordinator (http://gmod.org/) 216-392-3087 >> Ontario Institute for Cancer Research >> >> >> >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@... > http://lists.open-bio.org/mailman/listinfo/bioperl-l _______________________________________________ Bioperl-l mailing list Bioperl-l@... http://lists.open-bio.org/mailman/listinfo/bioperl-l |
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