[Bioperl-l] [Gmod-gbrowse] Landmark not recognized SeqFeature::Store database problem

Scott Cain scott at scottcain.net
Tue Jan 25 23:10:17 UTC 2011


Hi Darwin,

Bio::DB::SeqFeature::Store does not care about the order in which
entries appear in the GFF files, so the scaffold lines can be anywhere
(many people do put them in a separate file).

Scott


On Tue, Jan 25, 2011 at 5:54 PM, Darwin Sorento Dichmann
<dichmann at berkeley.edu> wrote:
> Worked. Thanks Scott!
>
> Now, when I expand to the whole genome do the scaffold lines need to be in the same gff as the other features and if so do they have to be immediately before the features of the scaffold similar to the test? or can they be in a separate file or appended at the top/end of the feature file.
>
> Darwin
>
> On Jan 25, 2011, at 2:36 PM, Scott Cain wrote:
>
>> Hi Darwin,
>>
>> In column 9, case matters.  That is, "name" != "Name".  Try changing
>> that for the scaffold.
>>
>> Scott
>>
>>
>> On Tue, Jan 25, 2011 at 4:59 PM, Darwin Sorento Dichmann
>> <dichmann at berkeley.edu> wrote:
>>> Hello,
>>>
>>> I am trying to set up a SeqFeature::Store database. However, I consistently get "Landmark named scaffold_something is not recognized. See the help pages for suggestions." Apache errorlog shows nothing. I am currently troubleshooting on a single scaffold and get same error.
>>>
>>> I've been banging my head against this for weeks and can't figure out what the problem is. Any help or pointers are greatly appreciated. Cc'ed to the bioperl list.
>>>
>>> Best wishes,
>>> Darwin
>>>
>>> The database seem to load properly and I can find the scaffold name:
>>> ---
>>> mysql> select seqname from locationlist;
>>> +--------------+
>>> | seqname      |
>>> +--------------+
>>> | scaffold_498 |
>>> +--------------+
>>> ---
>>> Command for loading the database and head of files:
>>> -----
>>> bp_seqfeature_load.pl -dsn frog3 -u darwin -p xxxxxxx -c -v fixed_scaffold_498.gff3 scaffold_498.fasta
>>> loading scaffold_498.gff3...
>>> Building object tree... 0.00s
>>> load time:  0.02s
>>> loading scaffold_498.fasta...
>>> Building object tree... 0.00s
>>> load time:  0.28s
>>>
>>>
>>> Macintosh:scaffold_498 darwin$ head -25 fixed_scaffold_498.gff3
>>> scaffold_498    pick    scaffold        1       875342  .       .       .       name=scaffold_498
>>> scaffold_498    pick    gene    5249    38060   1000    +       .       ID=CUFF.398955;Name=
>>> scaffold_498    pick    transcript      5249    38060   1000    +       .       ID=CUFF.398955.1;Name=;Parent=CUFF.398955
>>> scaffold_498    pick    exon    5249    5359    1000    +       .       ID=CUFF.398955.1.1;Name=;Parent=CUFF.398955.1
>>> scaffold_498    pick    exon    5508    5661    1000    +       .       ID=CUFF.398955.1.2;Name=;Parent=CUFF.398955.1
>>> scaffold_498    pick    exon    7474    7647    1000    +       .       ID=CUFF.398955.1.3;Name=;Parent=CUFF.398955.1
>>> scaffold_498    pick    exon    7819    8005    1000    +       .       ID=CUFF.398955.1.4;Name=;Parent=CUFF.398955.1
>>> scaffold_498    pick    exon    8254    8419    1000    +       .       ID=CUFF.398955.1.5;Name=;Parent=CUFF.398955.1
>>> scaffold_498    pick    exon    9997    10111   1000    +       .       ID=CUFF.398955.1.6;Name=;Parent=CUFF.398955.1
>>> scaffold_498    pick    exon    12104   12302   1000    +       .       ID=CUFF.398955.1.7;Name=;Parent=CUFF.398955.1
>>> scaffold_498    pick    exon    13854   13954   1000    +       .       ID=CUFF.398955.1.8;Name=;Parent=CUFF.398955.1
>>> scaffold_498    pick    exon    14810   14989   1000    +       .       ID=CUFF.398955.1.9;Name=;Parent=CUFF.398955.1
>>> scaffold_498    pick    exon    15310   15394   1000    +       .       ID=CUFF.398955.1.10;Name=;Parent=CUFF.398955.1
>>> scaffold_498    pick    exon    15938   16044   1000    +       .       ID=CUFF.398955.1.11;Name=;Parent=CUFF.398955.1
>>> scaffold_498    pick    exon    17997   18072   1000    +       .       ID=CUFF.398955.1.12;Name=;Parent=CUFF.398955.1
>>> scaffold_498    pick    exon    18364   18472   1000    +       .       ID=CUFF.398955.1.13;Name=;Parent=CUFF.398955.1
>>> scaffold_498    pick    exon    19364   19488   1000    +       .       ID=CUFF.398955.1.14;Name=;Parent=CUFF.398955.1
>>> scaffold_498    pick    exon    21402   21549   1000    +       .       ID=CUFF.398955.1.15;Name=;Parent=CUFF.398955.1
>>> scaffold_498    pick    exon    27620   27726   1000    +       .       ID=CUFF.398955.1.16;Name=;Parent=CUFF.398955.1
>>> scaffold_498    pick    exon    29322   29436   1000    +       .       ID=CUFF.398955.1.17;Name=;Parent=CUFF.398955.1
>>> scaffold_498    pick    exon    29958   30129   1000    +       .       ID=CUFF.398955.1.18;Name=;Parent=CUFF.398955.1
>>> scaffold_498    pick    exon    30947   31055   1000    +       .       ID=CUFF.398955.1.19;Name=;Parent=CUFF.398955.1
>>> scaffold_498    pick    exon    31247   31309   1000    +       .       ID=CUFF.398955.1.20;Name=;Parent=CUFF.398955.1
>>> scaffold_498    pick    exon    31461   31526   1000    +       .       ID=CUFF.398955.1.21;Name=;Parent=CUFF.398955.1
>>> scaffold_498    pick    exon    32478   32625   1000    +       .       ID=CUFF.398955.1.22;Name=;Parent=CUFF.398955.1
>>>
>>> Macintosh:scaffold_498 darwin$ head -25 scaffold_498.fasta
>>>> scaffold_498
>>> TAATATTGTGATGGTCGGCCCTGTAGCTCCTGCTCTAATACAGAACCATTTTCCATTGTG
>>> GTTTTCCAGTGAGATAAACCCTTAATCAAACTGCATAATAAACTGACGGTAGCACACTAG
>>> CACTGGCTGTATCCCTTCTTGAGTAAAAAAAATAAATGGATCTGCCCTTGCTCTTTACCT
>>> CATTAGGCCAGTGGAGTAGATTTGGCATTGGATCATAGCAACGTATGTTTCCAACACAAG
>>> TGACACATTGCTGATTCAGTCCATCTTGACCAGGGCAAAGTTATTAGGTCATATATGGAG
>>> TGAAAACAATGGATTTCCCTACTATTATCTAATCTGGGCTTGTTTGGATATGGATTGGGC
>>> AAGCTGGAAATTGCCATTGGCTGAGGATCATATCAGGCTGTGGAGGCAGCCCATGAACAA
>>> AAGGTCTTCATGAGCTTTTTAAATGATCATATTATTTCAGCCAAGCTTGACCCAACACTA
>>> AGGTGGCTAAATGGGACGGAAGAGTTCTTGCGTGGCAGCAAAAATGAGACGGATCTTCTC
>>> AAACTGCACAGCTTTAATTCTTAGAACATGTTTTCCTAGAGGTCAATACTTTGCATGTCT
>>> GAGTTACCACATGATCGACTCAATCCCATGCTGTAGCCCTCAAGCTCACTGAGCCTTATT
>>> ATCTTATTATTTATACTCTGTAGCCTCTTTGGTGCCAAATGTTCTATTGCATAGATGGCA
>>> CAGGGTAACTTTCTGAGTGAGGTTCCTCAGAAATAAATTGAATATATGTCTGCGCTGCTG
>>> ATGCTTAAAGTTTGGCTTGGGAACCCCACATTGGCACACTATTTATAGCCAGTGAGAGGT
>>> AATTGCTAATATGAAGTGGATTGCCAAACTCATTCTATTTTGGATCACAGAGTGGTACat
>>> acaggtatgggacccgttattcagaatgctcgggaccaagggtattctggataaggggtc
>>> tttccgtaatttggatctccatacattaagtccactaaaaaatcaataaaacgttaataa
>>> aacccagtaggactgttctgccccaataaagattaattatattttagttgggatcaagta
>>> caggtactgttttattattacagagaaaagggaatcatttaaccattaaataaacccaat
>>> aggactgttctgcccccaataaggggtaattatatcttagttgggatcaagtacaggtac
>>> tgttttattattacagagaaaagggaatcatttaaccattaaataaacccaataggactg
>>> ttctgcccccaataaggggtaattatatcttagttgggatcaagtacaggtactgtttta
>>> ttattacAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
>>> NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCCA
>>>
>>>
>>> ----
>>>
>>>
>>>
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>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> 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




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