31 Jan 2013 00:13
Re: Bioperl-l Digest, Vol 117, Issue 13
Fields, Christopher J <cjfields <at> illinois.edu>
2013-01-30 23:13:49 GMT
2013-01-30 23:13:49 GMT
We certainly accept support for updates to the code. In fact, if you are familiar with git/github the process is fairly straightforward: 1) Fork the code to your github account 2) Make and commit changes 3) Submit a pull request 4) Post something to the list just in case. We also accept code patches; the best way to submit these is as a bug report to the redmine repository (doesn't hurt to post here as well): https://redmine.open-bio.org/ chris On Jan 30, 2013, at 3:40 PM, Dan kilburn <dr_kilburn59 <at> yahoo.com> wrote: > Hi Jason, > > Are there any plans to keep SearchIO up to date with ncbi blast? I know they change formats ridiculously often, but I had to write my own parser to get sequence identity, which I would rather not have done. I realize that this job would be a big load on anyone who takes it, but it's so fundamental. Maybe I can help. > > --Dan > Sent from my iPhone > > On Jan 30, 2013, at 12:00 PM, bioperl-l-request <at> lists.open-bio.org wrote: > >> Send Bioperl-l mailing list submissions to >> bioperl-l <at> lists.open-bio.org >> >> To subscribe or unsubscribe via the World Wide Web, visit >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> or, via email, send a message with subject or body 'help' to >> bioperl-l-request <at> lists.open-bio.org >> >> You can reach the person managing the list at >> bioperl-l-owner <at> lists.open-bio.org >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of Bioperl-l digest..." >> >> >> Today's Topics: >> >> 1. Re: Parsing Blast-Report extracting "Features flanking .." >> (Jason Stajich) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Tue, 29 Jan 2013 11:00:16 -0800 >> From: Jason Stajich <jason.stajich <at> gmail.com> >> Subject: Re: [Bioperl-l] Parsing Blast-Report extracting "Features >> flanking .." >> To: buschj <at> hhu.de >> Cc: bioperl-l <at> lists.open-bio.org >> Message-ID: <6E83E3F3-C304-4DC4-9A11-FE1CA90F207D <at> gmail.com> >> Content-Type: text/plain; charset=us-ascii >> >> We don't parse the NCBI feature info from the BLAST reports per your query. To look up a specific feature you can use Bio::DB::GenBank to query for sequence from a specific feature by accession number - see the HOWTOs for that. >> >> However, most people use tools that generate SAM/BAM files with short reads - then you can use a tool like bedtools to find overlaps of reads with the locations of features. >> >> basically: >> - download the genome and GFF for arabidopsis >> - align your sRNA to the genome with a short read aligner - bowtie, bwa, others >> - convert your sam to bam file with SAMtools or picard >> - compare the location of features with the reads to get expression summaries or individuals reads with BEDTools >> >> >> On Jan 25, 2013, at 2:20 AM, jobu <buschj <at> hhu.de> wrote: >> >>> Am 22.01.2013 19:03, schrieb Mgavi Brathwaite: >>>> What upstream and downstream elements are you interested in? >>> >>> >>> I've got a huge pile of short RNA reads. >>> Part of the question now is whether those RNA fragments originate from >>> siRNA events, >>> or may represent miRNAs / parts of pre-miRNAs. >>> >>> So I did an online blast search against database nt. >>> The resulting report quite often just gives subject information like this: >>> >>> ----- >>>> gb|CP002686.1| Arabidopsis thaliana chromosome 3, complete sequence >>> Length=23459830 >>> ----- >>> >>> Now I would like to get the hit's neighbouring regions for further >>> analysis. >>> Preferably I would like to do that in an automized way, but the only >>> possible action with this kind of subject gi | description would be to >>> fetch the entire chromosomal sequence I guess ? >>> >>> However, >>> right below the line above, the report states more precisely: >>> >>> ------ >>> Features flanking this part of subject sequence: >>> 8872 bp at 5' side: cytochrome P450 90B1 >>> 402 bp at 3' side: U1 small nuclear ribonucleoprotein-70K >>> ------ >>> >>> Still I would like to have the possibility to automatically fetch the >>> subject's sequence(s), >>> as of now I think parsing the report with SearchIO won't let me aquire >>> that information, because SearchIO does not recognize report sections >>> like those. >>> >>> I hope I did not miss any of SearchIOs capabilities, but I could not >>> find any method covering my wish?! >>> >>> Right now maybe the only way to get the information I want is to >>> construct my own parser and write it out into a separate file, which in >>> turn again I could read into a hash before processing the Blast-Report >>> with SearchIO to combine both data for further automized work. >>> >>> I am aware though that even successfully getting the flanking features >>> would leave me with the more or less wide intergenic gap my hsp is >>> located in. >>> >>> However I'm in need of a way to get the flanking features including >>> their annotation and the region spanning between them. >>> But I hope I do not have to get complete sequences to accomplish that, >>> as this would be kind of an overkill. >>> >>> with kind regards >>> Jochen >>> >>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l <at> lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> Jason Stajich >> jason.stajich <at> gmail.com >> jason <at> bioperl.org >> >> >> >> >> ------------------------------ >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l <at> lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> End of Bioperl-l Digest, Vol 117, Issue 13 >> ****************************************** > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l <at> lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l
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