[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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