http://blog.gmane.org/gmane.comp.lang.perl.bio.general hourly 1 1901-01-01T00:00+00:00 http://gmane.org/img/gmane-25t.png http://gmane.org http://comments.gmane.org/gmane.comp.lang.perl.bio.general/26664 <pre>HI, First of all i am really sorry for sending this mail here, i am not sure if this is the right forum. I know lot of people work on similar stuff. I wrote to NCBI but nobody replied. Actually i am looking for all bacterial/microbial gene annotation nucleotide fasta files. Does anyone knows where to download these kind of files. I tried *ffn files but they are not annotated. Or is there any module in bioperl that i can use ? I would really appreciate your help. Thanks Shalabh </pre> shalabh sharma 2013-05-17T14:54:55 http://comments.gmane.org/gmane.comp.lang.perl.bio.general/26657 <pre>Hi all, I get this message when compiling Bio::DB::Sam: Building Bio-SamTools gcc -g -Wall -O2 -fPIC -o bam2bedgraph bam2bedgraph.o -L/var/lib/gbrowse2/databases/samtools/samtools-0.1.19 -lbam -lm -lz /var/lib/gbrowse2/databases/samtools/samtools-0.1.19/libbam.a(bgzf.o): In function `mt_destroy': /var/lib/gbrowse2/databases/samtools/samtools-0.1.19/bgzf.c:458: undefined reference to `pthread_join' /var/lib/gbrowse2/databases/samtools/samtools-0.1.19/libbam.a(bgzf.o): In function `bgzf_mt': /var/lib/gbrowse2/databases/samtools/samtools-0.1.19/bgzf.c:445: undefined reference to `pthread_create' collect2: ld returned 1 exit status make: *** [bam2bedgraph] Error 1 Is this error related to the module or some dependencies? or maybe a problem with my system? Any help appreciated, thanks! </pre> Miquel Ràmia 2013-05-16T10:42:29 http://comments.gmane.org/gmane.comp.lang.perl.bio.general/26654 <pre>Hi when accessing entrez gene using eutils to get multiple genes, NCBI now returns an Entrezgene-Set[1] rather than a list of EntrezGene. This change must have happened sometime on the last 2 months. Compare: use Bio::DB::EUtilities; my %sets = ( eutil =&gt; 'efetch', db =&gt; 'gene', retmode =&gt; 'text', rettype =&gt; 'asn1', email =&gt; 'bioperl-l&lt; at &gt;lists.open-bio.org', ); ## this mimics the previous behaviour of the NCBI server but the multiple requests will annoy their servers my &lt; at &gt;ids = (3014, 85235); my $response; foreach (&lt; at &gt;ids) { my $fetcher = Bio::DB::EUtilities-&gt;new(%sets, id =&gt; $_); $response .= $fetcher-&gt;get_Response-&gt;content; } print $fetcher-&gt;get_Response-&gt;content; ## this used to be the right way to do it, but now returns an Entrezgene-Set my $fetcher = Bio::DB::EUtilities-&gt;new(%sets, id =&gt; \&lt; at &gt;ids); $response .= $fetcher-&gt;get_Response-&gt;content; print $fetcher-&gt;get_Response-&gt;content; There is no module to read these Entrezgene-Set in Perl at the moment, since Bio::ASN1::EntrezGene; is not able to handle them. I have contacted the module author and set him a fix[2] and he said he'll try to look into it next week. However, even with the fix there is another problem. How would one access a set of sequences using the Bio::SeqIO API? There is no method to do that. One could say, to ignore them, and make next_seq return the next sequence of the set. But then we are losing data. After all, it's perfectly viable to have multiple Entrezgene-Set in one file. What would be the right way to do this? Carnë [1] http://0-www.ncbi.nlm.nih.gov.elis.tmu.edu.tw/IEB/ToolBox/CPP_DOC/asn_spec/Entrezgene-Set.html [2] https://github.com/carandraug/bio-asn1-entrezgene/commit/69d505056d8b7897df6271ffb7a5f39d58873c6b </pre> Carnë Draug 2013-05-16T01:53:55 http://comments.gmane.org/gmane.comp.lang.perl.bio.general/26653 <pre>Hi,all, I had done a blastall search and got a xml output file. How could i parse it to other format? I've found many scripts online, but no one worked. I am new to linux. Can anyone give me a good script to use? Thanks, Vivi </pre> Wenlan Tian 2013-04-29T18:17:08 http://comments.gmane.org/gmane.comp.lang.perl.bio.general/26651 <pre>FYI, if you haven't seen this yet: http://wssspe.researchcomputing.org.uk/ It seems to me that the Bio* projects, perhaps led by BioPerl as the oldest and thus longest running (nowadays more fancily called "sustained") of them would have a lot to say about the subject. Anyone interested in a joint submission? Also, I notice that Biojava's Andreas is on the organizing committee, so maybe he's been conspiring on something already :-) -hilmar </pre> Hilmar Lapp 2013-05-15T20:44:07 http://comments.gmane.org/gmane.comp.lang.perl.bio.general/26650 <pre>Hello All, I've a pairwise global alignemnet of two DNA sequences generated by the program NEEDLE of EMBOSS package. I wish to extract the sub-sequence that matches/aligns to a given region of the other sequence. In this alignment &lt;http://pastebin.com/wrhEDzJU&gt; (Pastebin Link) the given region (actually the CDS) falls between base number 24:485 in the original sequence with ID 'XM_001005073.' I wish to extract the sub-sequence in the sequence ID 'Homolog' that aligns with that 24:485 region of the other sequence. I'm using Bioperl to parse the alignment. I find out the the alignment column numbers corresponding to 24:485 region in the particular sequence, using 'column_from_residue_number'. Then I extract the sub-sequence from the 'aligned' other sequence(containing gaps) using the corresponding column numbers. Finally I remove the gap characters. Am I doing this thing correctly and are there any pitfalls ? Is there any better way to do it by (Bio)Perl/Python? The code goes here: use strict; use warnings; use Bio::AlignIO; # read in an alignment generated by the EMBOSS program Needle my $in = new Bio::AlignIO(-format =&gt; 'emboss', -file =&gt; 'test_needle.aln'); while( my $aln = $in-&gt;next_aln ) { #Seqnames: 'XM_001005073.'(CDS:24-485),'Homolog' my ($cds_start,$cds_end)=(24,485);# my $col_cdsstart = $aln-&gt;column_from_residue_number( 'XM_001005073.', $cds_start); my $col_cdsend= $aln-&gt;column_from_residue_number( 'XM_001005073.', $cds_end); foreach my $seq ($aln-&gt;each_seq) { if($seq-&gt;id() eq 'Homolog'){ my $homolog_cds=$seq-&gt;subseq($col_cdsstart,$col_cdsend); $homolog_cds=~s/\-//g; print $homolog_cds,"\n"; } } } -- View this message in context: http://bioperl.996286.n3.nabble.com/Extracting-matching-subsequence-from-pairwise-alignment-tp16935.html Sent from the Bioperl-L mailing list archive at Nabble.com. </pre> WoA 2013-05-08T19:24:53 http://comments.gmane.org/gmane.comp.lang.perl.bio.general/26648 <pre>Hello, I'm currently running Bio::Perl 1.6.1 on Ubuntu 12.04.2 LTS and have noticed a problem with Bio::SeqIO when writing genbank files using the write_seq() function; some of the files do not include an 'ORIGIN' tag or the sequence. I am using GI#s (50 at a time every 2 minutes) to retrieve genbank files via Bio::DB::GenBank. ----------------------------------------START CODE---------------------------------- my $gb = Bio::DB::GenBank-&gt;new(-verbose=&gt;-1);my $seqout = Bio::SeqIO-&gt;new(-file=&gt;"&gt;$fileName", '-format'=&gt;'Genbank', -alphabet=&gt;'dna', -flush=&gt;0, -verbose=&gt;-1);while(&lt; at &gt;ids){ my &lt; at &gt;batchArray = splice(&lt; at &gt;ids, 0, 50); my $batchArrayRef = \&lt; at &gt;batchArray; my $streamObj; my $pid = fork(); if($pid == 0){ eval{ $streamObj = $gb-&gt;get_Stream_by_id($batchArrayRef); }; if($&lt; at &gt;){ print "Error: ".$&lt; at &gt;."\n"; } else{ while(my $seqObj = $streamObj-&gt;next_seq()){ unless($seqObj-&gt;accession_number() =~ /N[A-Z]\_/){ #print "ID: ".$seqObj-&gt;id()."\n"; #print "Seq:\n".$seqObj-&gt;seq()."\n"; $seqout-&gt;write_seq($seqObj); } } } exit 0; }}waitpid($pid,0);sleep(120); ----------------------------------------END CODE---------------------------------- Most of the Genbank files written to the output file have sequences, but there is a small portion that do not, even though they should. For example, JX287367, in NCBI includes an 'ORIGIN' tag and sequence and when I use the print function before writing to file, the sequence is printed to STDOUT, but the 'ORIGIN' tag and sequence are not written to the output gbk file. The following is found in the final output file: ----------------------------------START GBK----------------------------------------- LOCUS JX287367 588 bp DNA linear BCT 19-DEC-2012DEFINITION Chlamydia trachomatis strain UW-5/CX pyruvoyl-dependent arginine decarboxylase (aaxB) gene, complete cds.ACCESSION JX287367VERSION JX287367.1 GI:404351720KEYWORDS .SOURCE Chlamydia trachomatis ORGANISM Chlamydia trachomatis Bacteria; Chlamydiae; Chlamydiales; Chlamydiaceae; Chlamydia/Chlamydophila group; Chlamydia.REFERENCE 1 (bases 1 to 588) AUTHORS Bliven,K.A., Fisher,D.J. and Maurelli,A.T. TITLE Characterization of the activity and expression of arginine decarboxylase in human and animal Chlamydia pathogens JOURNAL FEMS Microbiol. Lett. 337 (2), 140-146 (2012) PUBMED 23043454REFERENCE 2 (bases 1 to 588) AUTHORS Bl iven,K.A., Fisher,D.J. and Maurelli,A.T. TITLE Direct Submission JOURNAL Submitted (06-JUL-2012) Department of Microbiology and Immunology, F. Edward Hebert School of Med! icine, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD 20814, USAFEATURES Location/Qualifiers source 1..588 /mol_type="genomic DNA" /db_xref="taxon:813" /strain="UW-5/CX" /organism="Chlamydia trachomatis" /serovar="E" gene 1..588 /gene="aaxB" CDS 1..588 /protein_id="AFR60849.1" /gene="aaxB" /transl_table=11 /note="AaxB" /db_xref="GI:404351721" /codon_start=1 /product="pyruvoyl-dependent arginine decarboxylase" /translation="MPYGTRYPTLAFHTGGVGESDDGMPPQPFETFCYDSALLQAKIE NFNIVPYTSVLPKELFGNILPVDQCTKFFKHGAVLEVIMAGRGATVTDGTQAIATGVG ICWGKDKNGELIGGW! AAEYVEFFPTWIDDEIAESHAKMWLKKSLQHELDLRSVSKHSE FQYFHN YINIRKKFGFCLTALGFLNFENVAPAVIQ" // ----------------------------------END GBK----------------------------------------- Can anyone tell what I am missing or why this is happening? I don't know if this has happened in earlier BioPerl versions as up until now, I usually downloaded sequences straight from NCBI, but that became too time consuming....but this seems to be as well :S Thank you in advance for any help, Veronica </pre> Veronica A. 2013-05-08T00:32:22 http://comments.gmane.org/gmane.comp.lang.perl.bio.general/26647 <pre>The module pages on the wiki could look a little better, like this one for example: http://www.bioperl.org/wiki/Module:Bio::Tools::Run::RemoteBlast. There used to be a bunch of extra whitespace at the top of the page, which was caused by extra line breaks in Template:Doclink, which I just removed. But, I think there are other improvements that could be made. I would like to turn this into an infobox -- which are the helpful informative tables of info on Wikipedia that appear on many articles on the upper right. That would allow us to add more links -- like to metacpan, for example. It is not completely trivial to import infoboxes into a wiki though, I just discovered. I just went through the exercise on my home wiki, and it involves importing a lot of templates from Wikipedia, and fixing up the common.css. You can see the full list of imported templates here: http://chrismaloney.org/wiki/index.php?title=Special:RecentChanges&amp;limit=100. I don't *think* this should cause any problems, but I'm not 100% sure. On the other hand, if it does, it should be easy to roll back </pre> Chris Maloney 2013-05-05T04:03:38 http://comments.gmane.org/gmane.comp.lang.perl.bio.general/26643 <pre> I'm trying to get alignment from tiled information generated out of a Blastx report, (for two sequences made by 'blas2seq'). I'm using ActivePerl 15.6.2 and Bioperl 1.6 in Windows 7 However I'm getting the following error: Can't locate object method "get_tiled_alns" via package "Bio::Search::Tiling::Ma pTiling" at tile_align_blastx.pm line 11, &lt;GEN1&gt; line 72. The code is as follows: use strict; use warnings; use Bio::SearchIO; use Bio::Search::Tiling::MapTiling; my $blio = Bio::SearchIO-&gt;new( -file =&gt; 'test.blastx2seq.out', -format =&gt;'blast'); my $result = $blio-&gt;next_result; my $hit = $result-&gt;next_hit; my $tiling = Bio::Search::Tiling::MapTiling-&gt;new($hit); my &lt; at &gt;alns = $tiling-&gt;get_tiled_alns('abc123'); my $concat_seq_obj = $alns[0]-&gt;get_seq_by_id('abc123'); </pre> WoA 2013-04-29T21:56:19 http://comments.gmane.org/gmane.comp.lang.perl.bio.general/26642 <pre> Hi All, I'm trying to get alignment from tiled information generated out of a Blastx report, (for two sequences made by 'blas2seq'). I'm using ActivePerl 15.6.2 and Bioperl 1.6 in Windows 7 However I'm getting the following error: Can't locate object method "get_tiled_alns" via package "Bio::Search::Tiling::Ma pTiling" at tile_align_blastx.pm line 11, &lt;GEN1&gt; line 72. The code is as follows: use strict; use warnings; use Bio::SearchIO; use Bio::Search::Tiling::MapTiling; my $blio = Bio::SearchIO-&gt;new( -file =&gt; 'test.blastx2seq.out', -format =&gt;'blast'); my $result = $blio-&gt;next_result; my $hit = $result-&gt;next_hit; my $tiling = Bio::Search::Tiling::MapTiling-&gt;new($hit); my &lt; at &gt;alns = $tiling-&gt;get_tiled_alns('abc123'); my $concat_seq_obj = $alns[0]-&gt;get_seq_by_id('abc123'); </pre> WoA 2013-04-29T21:54:12 http://comments.gmane.org/gmane.comp.lang.perl.bio.general/26641 <pre> Hi All, I'm trying to get alignment from tiled information generated out of a Blastx report, (for two sequences made by 'blas2seq'). I'm using ActivePerl 15.6.2 and Bioperl 1.6 in Windows 7 However I'm getting the following error: Can't locate object method "get_tiled_alns" via package "Bio::Search::Tiling::Ma pTiling" at tile_align_blastx.pm line 11, line 72. The code is as follows: use strict; use warnings; use Bio::SearchIO; use Bio::Search::Tiling::MapTiling; my $blio = Bio::SearchIO-&gt;new( -file =&gt; 'test.blastx2seq.out', -format =&gt;'blast'); my $result = $blio-&gt;next_result; my $hit = $result-&gt;next_hit; my $tiling = Bio::Search::Tiling::MapTiling-&gt;new($hit); my &lt; at &gt;alns = $tiling-&gt;get_tiled_alns('abc123'); my $concat_seq_obj = $alns[0]-&gt;get_seq_by_id('abc123'); </pre> WoA 2013-04-29T21:55:01 http://comments.gmane.org/gmane.comp.lang.perl.bio.general/26640 <pre>Hi All, Is there any module in Bioperl that can download sequences from NCBI's trace archive? Thanks Shalabh </pre> shalabh sharma 2013-04-29T20:25:58 http://comments.gmane.org/gmane.comp.lang.perl.bio.general/26639 <pre>Hi all, I am having some trouble running bioperl script bp_genbank2gff.pl. The script works fine, but I don't understand a warning message when retrieving a gff (in this case gff3). That message is: 'skipping a misc_feature' I have searched a lot on google but I didn't find an answer. I tried to look up the code.. http://doc.bioperl.org/bioperl-live/Bio/DB/GFF/Adaptor/biofetch.html but since I am not fluent in Perl I just saw that in case feature is a misc feature, warning is raised. Now, maybe I misunderstood, but the misc feature is one from column 9 tag as described in http://gmod.org/wiki/GFF ? If yes, shouldn't its name be printed out when it is being skipped, to let the user know which feature has been removed from gff? Thanks </pre> francesco.brundu< at >gmail.com 2013-04-29T16:36:42 http://comments.gmane.org/gmane.comp.lang.perl.bio.general/26635 <pre>Dear bioperlers, I am facing a problem I used to encounter in the past and failed to report it properly. I am either mis-using it or there is a bug, I would like your feedback. Consider the alignment between sequence A and B in test.ali, and the bioperl_test.pl as examples (attached to this mail). I would like to know at position i what is the amino acid of seq A, and what is the amino acid in position i in sequence B (of course these residues may not be aligned). The problem is: a) I cannot parse the first residue of the alignment, it has to start at 1, otherwise I have: ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Second argument residue number missing STACK: Error::throw STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:472 STACK: Bio::SimpleAlign::column_from_residue_number /usr/share/perl5/Bio/SimpleAlign.pm:2626 STACK: ./bioperl_test.pl:19 ----------------------------------------------------------- b) Although, if I understand correctly, this function should return only the residues, sometimes I have a gap inserted, so the function is not working properly: ./bioperl_test.pl |grep '-' P:11 for seq 1 and -:30 for seq 2 S:76 for seq 1 and -:96 for seq 2 -:124 for seq 1 and L:146 for seq 2 -:150 for seq 1 and K:170 for seq 2 -:175 for seq 1 and I:190 for seq 2 -:202 for seq 1 and L:215 for seq 2 -:224 for seq 1 and G:233 for seq 2 W:264 for seq 1 and -:263 for seq 2 S:296 for seq 1 and -:297 for seq 2 -:343 for seq 1 and S:345 for seq 2 -:369 for seq 1 and H:361 for seq 2 Can we discuss it here or I have to open a bug report? Thanks in advance, Stéphane </pre> Téletchéa Stéphane 2013-04-23T16:10:23 http://comments.gmane.org/gmane.comp.lang.perl.bio.general/26629 <pre>I just noticed this event, and I see that genehack posted about it to the list back in February. Nevertheless, I thought it was worth an update / reminder: http://www.yapcna.org/yn2013/talk/4687. Is anyone planning on going? I'm thinking about it, but it's a long shot. Chris Maloney </pre> Chris Maloney 2013-04-22T21:00:50 http://comments.gmane.org/gmane.comp.lang.perl.bio.general/26623 <pre>At the HIV Sequence and Immunolgogy Databases (http://www.hiv.lanl.gov) where I work, we have used a bit of creativity to solve some difficult problems in multiple sequence alignment, because we often want to produce an alignment of gene sequences from more than 20,000 different isolates of HIV-1 in less than a few minutes time. We are very good at "deep" multiple alignment, thousands of copies of the same small genome. My problem comes when I want to align the genomes of other viruses or similar sized gene regions (the complete mitochondrial genomes of vertebrates for example, which are roughly 17 kb in size), they don't always have the same gene order. A good example are the mitochondrial genomes of birds and mammals, which are mostly co-linear, but with the NADH6 gene moved to a different location. See attached JPG of Aardvark and Japanese Eagle-Hawk mitochondrial genomes. In other cases, I think it is the primate mitochondrial genomes, the authors all used a different site for the "base #1" in the circular genome. So although the primate mitochondrial genomes are 100% co-linear with other vertebrates, we have to chop several thousand bases off the right end and past them onto the left end (5' end, beginning) to make them align with the mt-genomes of other mammals. So, it seems to me that there ought to be a multiple sequence alignment tool, that can read GenBank files with their annotation, and use the annotation to help with the alignment process. One tool that I am aware of, which can help a lot, is the "Artemis Genome Comparison Tool" (ACT) and its associated DOUBLE-ACT server: http://www.hpa-bioinfotools.org.uk/pise/double_act.html The DOUBLE-ACT server uses BLAST to find regions on a pair of genomes which are homologous/similar and creates a table of these matched regions. The Artemis Comparison Tool then loads both genomes into an ARTEMIS Genome Browser tool and uses the BLAST hit table to help the browser get both genomes "in synch" with each other as you browse the genomes. Although the DOUBLE-ACT BLAST step here is not dependent on annotations at all, the annotations are visible when browsing the genomes in ACT. I am quite sure that I am not the only one in the world who needs this type of tool. I am increasingly seeing large multiple sequence alignments being done for classification of organisms, where the authors could have used such a tool. Please let me know if you have any ideas about where to look for such a tool, or which groups of bioinformatics workers might be able to develop one. Brian T. Foley, PhD HIV Databases Los Alamos National Laboratory btf&lt; at &gt;lanl.gov 505 665-1970 _______________________________________________ Bioperl-l mailing list Bioperl-l&lt; at &gt;lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l</pre> Brian Foley 2013-04-18T23:17:59 http://comments.gmane.org/gmane.comp.lang.perl.bio.general/26612 <pre>Hi All. I have a default blastx report and i want to get taxa ids from it along with other usual information. I am using Bioperl to parse the blast report, but i don't know how to get taxa ids. Thanks Shalu </pre> shalu sharma 2013-04-18T15:17:02 http://comments.gmane.org/gmane.comp.lang.perl.bio.general/26608 <pre>I am not much of a Perl coder and I have a few questions. First, I would like to write a script that will go to NCBI genebank and get the base number for the start of the CDS region, e.g. 235 (given a particular accession number). I have looked at HOWTO's and documentation for Bio::SeqIO and Bio::DB::GenBank and I can cut and paste the examples and they work, but I can not figure out how to get what I want; the CDS start site. I have difficulty knowing what all the methods and their options are for the seqio object and seq_object. Most of the examples seem to be using a file to get information and not a website. Actually, what I have to start with is a TAIR locus number such as AT4g08500, but I can not search on this at NCBI and come up with a unique entry. I may have to have a table of conversions from TAIR locus number to accession numbers. Also, I was looking for a bit of advice. What I am doing is getting data off another web site. I have a script using the WWW::Mechanize module in which I can input a link and go to that webpage, and then go down a line of links (over 100) getting information from each link. As part of that information that I am getting is the number base of a binding site, but I want to know if that binding site is in the CDS. The start number is the start of the gene, so say if the binding site is 235, then I want to know if this is in the CDS. This data is not provided by the website, that is why I want to go to NCBI and get the start of the CDS. The data at NCBI for 'gene' has the same length as the first webpage, but also contains the beginning of the CDS, say 299, so with this information I can tell if the binding site is in the CDS. Do you think the best way to do this is extract the info from the link on the first web page, then go to NCBI and extract the CDS, then back to the original web page and the next link, and so on, for a couple of hundred links ? Or is there a better way ? I am concerned about a script that will keep going back to NCBI. Matthew The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. </pre> Matthew McCormack 2013-04-17T23:08:22 http://comments.gmane.org/gmane.comp.lang.perl.bio.general/26607 <pre>Hello, I've just updated to bioperl-run (1.006900) and perl (v5.14.2) installed on a Linux machine running Ubuntu 12.04. I have perl scripts that use Bio::Tools::Run::Primer3 and before the updates, ran as expected. However, they are now failing. While testing primer3_core on the command line, I realized the problem was the PRIMER_THERMODYNAMIC_PARAMETERS_PATH setting. I added this to my primer3_core input file and primers were designed. I.T. then moved the primer3_config directory to /opt/primer3_config as instructed and this helped running primer3_core on the command line as I no longer needed to include PRIMER_THERMODYNAMIC_PARAMETERS_PATH to the input file. However, the perl scripts still do not work. Is there a BioPerl config file that requires the PRIMER_THERMODYNAMIC_PARAMETERS_PATH setting? Or did something not install correctly? Thank you, Veronica </pre> Veronica A. 2013-04-17T16:32:53 http://comments.gmane.org/gmane.comp.lang.perl.bio.general/26600 <pre>Hi, I have perlbrew with perl-5.8.9 installed. And I tried to get the bioperl-live via Git following the instruction on bioperl official site: http://www.bioperl.org/wiki/Using_Git However, it seems the testing bioperl version encountered error (below) immediately. Manually checking the cloned bioperl-live revealed there is only one module HTTPget.pm under Bio/Root (see below), I also check the online Github bioperl-live repository, the Bio/Root folder indeed only contain only one modeul: HTTPget.pm is this normal or I need to use some alternative approach to get the bioperl (the CPAN package is rather old though)? Thanks John *% perl -MBio::Perl -le 'print Bio::Perl-&gt;VERSION;'* ------------------------------------------------------------------------------------------------------------ Base class package *"Bio::Root::Root" is empty.* (Perhaps you need to 'use' the module which defines that package first, or make that module available in &lt; at &gt;INC (&lt; at &gt;INC contains: $HOME/src/bioperl-live/ $HOME/perlbrew//perls/perl-5.8.9/lib/5.8.9/x86_64-linux $HOME/perlbrew//perls/perl-5.8.9/lib/5.8.9 $HOME/perlbrew//perls/perl-5.8.9/lib/site_perl/5.8.9/x86_64-linux $HOME/perlbrew//perls/perl-5.8.9/lib/site_perl/5.8.9 .). at $HOME/src/bioperl-live//Bio/Location/WidestCoordPolicy.pm line 80 BEGIN failed--compilation aborted at $HOME/src/bioperl-live//Bio/Location/WidestCoordPolicy.pm line 80. Compilation failed in require at $HOME/src/bioperl-live//Bio/Location/Atomic.pm line 79. BEGIN failed--compilation aborted at $HOME/src/bioperl-live//Bio/Location/Atomic.pm line 79. Compilation failed in require at (eval 1) line 3. ...propagated at $HOME/perlbrew//perls/perl-5.8.9/lib/5.8.9/base.pm line 93. BEGIN failed--compilation aborted at $HOME/src/bioperl-live//Bio/Location/Simple.pm line 87. Compilation failed in require at $HOME/src/bioperl-live//Bio/Factory/FTLocationFactory.pm line 97. BEGIN failed--compilation aborted at $HOME/src/bioperl-live//Bio/Factory/FTLocationFactory.pm line 97. Compilation failed in require at $HOME/src/bioperl-live//Bio/SeqIO.pm line 328. BEGIN failed--compilation aborted at $HOME/src/bioperl-live//Bio/SeqIO.pm line 328. Compilation failed in require at $HOME/src/bioperl-live//Bio/Perl.pm line 120. BEGIN failed--compilation aborted at $HOME/src/bioperl-live//Bio/Perl.pm line 120. Compilation failed in require. BEGIN failed--compilation aborted. ------------------------------------------------------------------------------------------------------------ %ls $HOME/src/bioperl-live/Bio/Root/ HTTPget.pm ------------------------------------------------------------------------------------------------------------ </pre> John Chen 2013-04-13T17:37:36 http://comments.gmane.org/gmane.comp.lang.perl.bio.general/26599 <pre>Hi, I find a bug when I use Bio::SearchIO to parse Hmmscan. The result of my Hmmscan has 2 hits against 1 query ,but the module of Bio::SearchIO can only parse 1 hit in the output file. eg: hmmscan result: # hmmscan :: search sequence(s) against a profile database # HMMER 3.0 (March 2010); http://hmmer.org/ # Copyright (C) 2010 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query sequence file: pro_2.fa # target HMM database: /leofs/biodenovo/fangl/data/Pfam/Pfam-A.hmm # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: PEG03688 [L=200] Scores for complete sequence (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Model Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0.00038 20.7 0.1 0.00054 20.2 0.1 1.3 1 SnoaL_2 SnoaL-like domain ------ inclusion threshold ------ 0.068 12.9 0.0 0.43 10.3 0.0 2.0 1 FAD_binding_8 FAD-binding domain Domain annotation for each model (and alignments): # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 20.2 0.1 7.9e-08 0.00054 11 86 .. 59 157 .. 46 172 .. 0.72 Alignments for each domain: == domain 1 score: 20.2 bits; conditional E-value: 7.9e-08 T-HHHHHHTEEEEEEEE............CT.S--..E---HHHHHHHTTHHHCEECEEEEEEEEESSTTEEEEEEEEE-E........ESBS--EEEE CS SnoaL_2 11 gdldalaallapdvvwe............dp.fge..lrGrealraffrallaafpdlrfevedviadgdrvvvrwtvtgt........ipptgrgvtv 86 d l +l++ d+++ +p +g+ + G++a+ + f ++ + f+++++++d+ v++++ +t+t i p ++ +v PEG03688 59 PDYNLLKELVTYDCTYIsltfdnptlhgiMPwAGThtHVGPQAFIDIFTRVGLYWDRGPFSIDHIFGDDGNVTAWGSFTATsrtlgktvISPWAARARV 157 3666888999999999877777555545545544488******************************************98555555554444444444 PP # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 10.3 0.0 6.3e-05 0.43 19 63 .. 77 128 .. 63 197 .. 0.69 Alignments for each domain: == domain 1 score: 10.3 bits; conditional E-value: 6.3e-05 FAD_binding_8 19 lklkkpkks.......lkykpGqyvfini.pslsklflqsHPFtiasapeddk 63 l++ p+ ++ + G +fi i ++ l+++ PF+i dd PEG03688 77 LTFDNPTLHgimpwagTHTHVGPQAFIDIfTRVG-LYWDRGPFSIDHIFGDDG 128 555555444444444468899999*****66666.99********88777664 PP Internal pipeline statistics summary: ------------------------------------- Query sequence(s): 1 (200 residues) Target model(s): 13672 (2396357 nodes) Passed MSV filter: 244 (0.0178467); expected 273.4 (0.02) Passed bias filter: 219 (0.0160181); expected 273.4 (0.02) Passed Vit filter: 14 (0.00102399); expected 13.7 (0.001) Passed Fwd filter: 2 (0.000146284); expected 0.1 (1e-05) Initial search space (Z): 13672 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.15u 0.13s 00:00:00.28 Elapsed: 00:00:06.72 # Mc/sec: 71.32 // my parse result: query len hit len query_start query_end query_match_len hit_start hit_end hit_match_len evalue cov PEG03688 200 SnoaL_2 0 59 157 99 11 86 76 7.9e-08 0.49 pleast to solve this problem! Thanks! Best wishes! fangl _______________________________________________ Bioperl-l mailing list Bioperl-l&lt; at &gt;lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l</pre> fangl 2013-04-15T08:13:05 Search the mailing list at Gmane query http://search.gmane.org/?group=$group=gmane.comp.lang.perl.bio.general