[Gmod-help] Re: [Gmod-gbrowse] bp_genbank2gff3.pl bugs?

[Alessandra]

Hi Dave,

well, I resolved for me with a script that it validates gff3 and
adds/changes errors.. now, I nearly completed human gff3 files. After
I upload gff3 into ftp.gbrowse.org

what do you think about gbrowse.org survey? :-P

cheerio,
alessandra.

On Fri, Dec 11, 2009 at 3:34 PM, Dave Clements, GMOD Help Desk
<help at gmod.org> wrote:
> Hi Alessandra,
>
> I don't know of any other scripts for this conversion.
>
> Dave C.
>
> On Wed, Dec 9, 2009 at 3:43 AM, Alessandra <alessandra.bilardi at gmail.com> wrote:
>> Hi all,
>>
>> I'm using bp_genbank2gff3.pl to convert more GenBank entries into GFF3 files.
>> when I use command-line with NC_000001.gbk and NC_000010.gbk (human
>> chr1 and chr10):
>> bp_genbank2gff3.pl --dir ./ --outdir ./
>> I observed that:
>> * Name tag is away and it is required at least in chromosome type
>> track.. if you use bp_seqfeature_gff3.pl script to upload data into
>> mysql database or in gene type track.. if you need to search gene name
>> by searchform landmark_search_field
>> * after adding to Name tag, NC_000010.gbk.gff is right and I can
>> upload it by bp_seqfeature_gff3.pl (with more warnings and one error,
>> easily solvable)
>> * NC_000001.gbk.gff has got any problem:
>> ** exon type track is away
>> ** gene type track has got gene_name.t01, gene_name.t02, and
>> gene_name.p01, gene_name.p02 when, into GenBank, gene has got one mRNA
>> and CDS
>> ** gene type track has got gene_name.t01, gene_name.t02,
>> gene_name.t03, gene_name.t04 and gene_name.p01, gene_name.p02,
>> gene_name.p03, gene_name.p04 when, into GenBank, gene has got two mRNA
>> and CDS  (I did not check others..)
>> ** CDS and mRNA type tracks record lines are present with 1,5x or 2x
>> ** mRNA type track has got data puzzle: mRNA attributes, exon
>> positions and exon Parent values into ID values
>> ** in mRNA and CDS type tracks have got more ID and Parent values (and
>> into NC_000010.gbk.gff, this format is not used)
>> ** in CDS type track has got repeat ID/Parent values
>> (ID=LOC100287102.p01,LOC100287102.p02,LOC100287102.p02;Parent=LOC100287102.t01,LOC100287102.t02,LOC100287102.t02;)
>>
>> I tested command-line:
>> bp_genbank2gff3.pl --dir ./ --outdir ./
>> bp_genbank2gff3.pl --dir ./ --outdir ./ --noCDS
>> bp_genbank2gff3.pl --dir ./ --outdir ./ --CDS
>> and I observed similar problems.. so that polypeptide type track has
>> got egual problem like CDS type track.
>> Genbank entries are similar and I did not understand where there are
>> the differences..
>>
>> Are there other scripts to convert GenBank entries in GFF3 files?
>>
>> Thanks,
>> Alessandra.
>>
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>
>
>
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-- 
 Alessandra Bilardi, Ph. D.
----
 CRIBI, University of Padova, Italy
 Via Ugo Bassi, 58/B - 35121 Padova
 Tel +390498276165 Fax +390498276159
  http://www.linkedin.com/in/bilardi
----
La semplicità è la più alta forma di perfezione (Leonardo Da Vinci)
Keep simple, stupid (KISS, IT)
----