Camelia, the Perl 6 bug

IRC log for #bioperl, 2009-06-09

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All times shown according to UTC.

Time Nick Message
11:54 alper_ joined #bioperl
12:22 alper_ joined #bioperl
18:29 student joined #bioperl
18:30 student hello is anyone around?
18:31 student I've got a question, is there a bioperl module that converts gff files to fasta?
18:35 deafferret sure. lemme get you the link
18:36 deafferret http://www.bioperl.org/wiki/Bioperl_scripts    scripts/seq/seqconvert.PLS
18:37 rbuels but...gff?  there isn't usually sequence data in a gff unless it's gff3 with a fasta section....
18:37 student hmm
18:38 student i'm all new to this stuff
18:38 student i'm a computer science student
18:38 student working on a bioinformatic project
18:38 perl_splut joined #bioperl
18:38 student its for the barcode of life project, i'm working on finding a new region for fungi
18:39 deafferret oh, I misread. sorry. anyway, that wiki page has tons of conversions
18:39 student i'll show you the files i need to convert
18:39 deafferret gff usually doesn't have sequence data, which is usually the meat of fasta
18:40 student here is the link
18:40 student http://genomeportal.jgi-psf.org/​Crypa1/Crypa1.download.ftp.html
18:40 student so here is the file i need to convert
18:40 student http://genomeportal.jgi-psf.org/​Crypa1/Crypa1.download.ftp.html
18:41 student oops thats the same link...well on that page its the Genes: Cparasitica.FilteredModels1.gff.gz file
18:41 deafferret so you want fasta -> gff, not gff -> fasta   :)
18:42 student nono, i do want gff to fasta
18:43 student i've just looked thru that file and there doesn't seem to be any fasta information in it
18:43 student so i guess its like your guyz where saying, i need gff3 files
18:43 deafferret on third thought, that web page has both fasta and gff, so I don't know why you're trying to convert anything to anything
18:43 deafferret those fasta files are the sequences
18:43 deafferret those gff files are the location maps
18:44 deafferret ?
18:44 student ok, going back to my project
18:44 student i need to assemble a working set of protien and gene fasta files for fungi to analyze
18:45 student also contig and super contig files will be usefull
18:45 student so from that page i'm using:
18:45 student Proteins: Cparasitica.FilteredModels.aa.fasta.gz
18:45 student Assembled scaffolds (unmasked): Cryphonectria_parasitica.fasta.gz as the contig
18:45 student and Genes: Cparasitica.FilteredModels1.gff.gz as the gene file
18:46 student the gene file is the only one in gff format
18:47 student but your saying the gene file is just a map with no fasta info... correct?
18:47 deafferret Dunno. I haven't opened the files. have you?
18:48 student yes...it looks nothing like a fasta file
18:48 student as in no sequence information
18:48 deafferret Cparasitica.FilteredModels.aa.fasta.gz ?
18:48 student no Genes: Cparasitica.FilteredModels1.gff.gz
18:49 student the file you pasted is the protein file
18:49 deafferret right. GFF files looks like this:  http://www.bioperl.org/wiki/GFF
18:49 student yeh
18:49 deafferret GFF is basically a big location map sort of format. It tells you *where* things are, not the details of what they are
18:50 deafferret browsers (like GBrowse) display GFF files, making pretty maps of location data
18:50 student ic
18:52 student how do i get to the location you posted
18:52 student http://www.bioperl.org/wiki/Bioperl_scripts    scripts/seq/seqconvert.PLS
18:52 deafferret go to the first URL, then scroll down until you see seqconvert.PLS
18:53 student ah found it
18:59 student would there be an easy way to download sequence files from NCBI
19:00 student for example, Broad Institute has director download links which i've put into an excel file then made a perl script to grab each file and populate a directory structure with the files
19:01 student but on NCBI there can be many many protein files for example and the download link is a java script, not just a url
19:06 deafferret http://search.cpan.org/~cjfields/Bio​Perl-1.6.0/Bio/Perl.pm#get_sequence ?
19:13 student thank you very much for your assitance, definitively gave me some things to look into
19:14 deafferret sure.   :)
19:14 student so are you familiar with BOL?
19:15 deafferret nope
19:16 student http://www.dnabarcodes.org/
19:17 student basically they are they tried to use a small region from a gene and use it to identify species
19:18 deafferret sorry, I'm already 10 tangets deep here at $work, trying not to drown today   :)
19:18 student but this region didn't work out for some fungi and i'm looking into an alternate region
19:18 student ah, its cool :-)
19:19 deafferret stupid $mortgage  :)
19:20 rbuels deafferret: i bet you got a lot of hair off that yak though
19:21 rbuels deafferret: too bad there's another yak right behind it...
19:33 deafferret stupid yaks

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