Hello,
I would like to make a transcript database for Chinese hamster (Cricetulus griseus) using the function makeTranscriptDbFromGFF. Since it is the first time I use this function, I do this per the code in the vignette. However, I face some problems and would appreciate any pointer.

I started by downloading the GFF (ref_CriGri_1.0_scaffolds.gff3) from NCBI.
[ftp://ftp.ncbi.nlm.nih.gov/genomes/Cricetulus_griseus/GFF/]

Creating the txdb seems to go fine:

> txdb <- makeTranscriptDbFromGFF(file="ref_CriGri_1.0_scaffolds.gff3", format="gff3", dataSource="ftp://ftp.ncbi.nlm.nih.gov/genomes/Cricetulus_griseus/GFF/", species="Cricetulus griseus")
extracting transcript information
Extracting gene IDs
extracting transcript information
Processing splicing information for gff3 file.
Deducing exon rank from relative coordinates provided
Prepare the 'metadata' data frame ... metadata: OK
Now generating chrominfo from available sequence names. No chromosome length information is available.
Warning messages:
1: In .deduceExonRankings(exs, format = "gff") :
  Infering Exon Rankings.  If this is not what you expected, then please be sure that you have provided a valid attribute for exonRankAttributeName
2: In matchCircularity(chroms, circ_seqs) :
  None of the strings in your circ_seqs argument match your seqnames.

# Characterization txdb
> txdb
TranscriptDb object:
| Db type: TranscriptDb
| Supporting package: GenomicFeatures
| Data source: ftp://ftp.ncbi.nlm.nih.gov/genomes/Cricetulus_griseus/GFF/
| Organism: Cricetulus griseus
| miRBase build ID: NA
| transcript_nrow: 21612
| exon_nrow: 212163
| cds_nrow: 183531
| Db created by: GenomicFeatures package from Bioconductor
| Creation time: 2013-08-15 18:26:33 +0200 (Thu, 15 Aug 2013)
| GenomicFeatures version at creation time: 1.13.29
| RSQLite version at creation time: 0.11.4
| DBSCHEMAVERSION: 1.0
>
> columns(txdb)
[1] "CDSID"      "CDSNAME"    "CDSCHROM"   "CDSSTRAND"  "CDSSTART"   "CDSEND"     "EXONID"
 [8] "EXONNAME"   "EXONCHROM"  "EXONSTRAND" "EXONSTART"  "EXONEND"    "GENEID"     "TXID"
[15] "EXONRANK"   "TXNAME"     "TXCHROM"    "TXSTRAND"   "TXSTART"    "TXEND"
> keytypes(txdb)
[1] "GENEID"   "TXID"     "TXNAME"   "EXONID"   "EXONNAME" "CDSID"    "CDSNAME"
>

As a test, I would like to retrieve the transcript names for 3 Entrez Gene IDs. Note: I selected these 3 IDs randomly; they are in the top5 -listed IDs in the GFF.
Unfortunately, this doesn't seem to work:
> keys <- c("100754456", "100759368", "100760238")
> select(txdb, keys = keys, columns="TXNAME", keytype="GENEID")
[1] GENEID TXNAME
<0 rows> (or 0-length row.names)
>
Note: the human example from the vignette worked fine.

I think this is somehow due to the fact that during the parsing of the GFF the keytypes (?) are not properly recognized/linked. This is also reflected by the plain use of 'rna' and 'gene' as names/IDs:
> GR <- transcripts(txdb, columns=c("tx_id", "tx_name", "gene_id", "cds_id","cds_name"))
> head(GR)
GRanges with 6 ranges and 5 metadata columns:
            seqnames             ranges strand |     tx_id     tx_name         gene_id        cds_id
               <Rle>          <IRanges>  <Rle> | <integer> <character> <CharacterList> <IntegerList>
  [1] NW_003613580.1 [ 736932,  738552]      + |         1        rna0           gene2           1,2
  [2] NW_003613580.1 [2073869, 2085513]      + |         2        rna4           gene6     3,4,5,...
  [3] NW_003613580.1 [2143936, 2241368]      + |         3        rna6           gene8    8,9,10,...
  [4] NW_003613580.1 [2390123, 2449470]      + |         4        rna8          gene10  22,23,24,...
  [5] NW_003613580.1 [2390123, 2555467]      + |         5        rna7          gene10  22,23,24,...
  [6] NW_003613580.1 [3070833, 3147709]      + |         6        rna9          gene12  43,44,45,...
             cds_name
      <CharacterList>
  [1]              NA
  [2]              NA
  [3]              NA
  [4]              NA
  [5]              NA
  [6]              NA
  ---
  seqlengths:
   NW_003613580.1 NW_003613581.1 NW_003613582.1 ... NW_003698075.1 NW_003704321.1 NW_003717424.1
               NA             NA             NA ...             NA             NA             NA
>
> tail(GR)
GRanges with 6 ranges and 5 metadata columns:
            seqnames    ranges strand |     tx_id     tx_name         gene_id        cds_id
               <Rle> <IRanges>  <Rle> | <integer> <character> <CharacterList> <IntegerList>
  [1] NW_003694533.1 [29, 205]      - |     21607    rna22504       gene25148        183527
  [2] NW_003697941.1 [ 4, 135]      - |     21608    rna22505       gene25149        183528
  [3] NW_003698068.1 [ 1, 267]      + |     21609    rna22506       gene25150        183529
  [4] NW_003698075.1 [ 1, 267]      - |     21610    rna22507       gene25151            NA
  [5] NW_003704321.1 [24, 203]      - |     21611    rna22508       gene25152        183530
  [6] NW_003717424.1 [10, 189]      + |     21612    rna22509       gene25155        183531
             cds_name
      <CharacterList>
  [1]              NA
  [2]              NA
  [3]              NA
  [4]              NA
  [5]              NA
  [6]              NA
  ---
  seqlengths:
   NW_003613580.1 NW_003613581.1 NW_003613582.1 ... NW_003698075.1 NW_003704321.1 NW_003717424.1
               NA             NA             NA ...             NA             NA             NA
>



Any suggestions on how to properly generate a txdb from this GFF would be appreciated.

Thanks,
Guido

> sessionInfo()
R Under development (unstable) (2013-08-10 r63532)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] GenomicFeatures_1.13.29 AnnotationDbi_1.23.18   Biobase_2.21.6          GenomicRanges_1.13.36
[5] XVector_0.1.0           IRanges_1.19.21         BiocGenerics_0.7.3

loaded via a namespace (and not attached):
[1] biomaRt_2.17.2     Biostrings_2.29.14 bitops_1.0-5       BSgenome_1.29.1    DBI_0.2-7
 [6] RCurl_1.95-4.1     Rsamtools_1.13.28  RSQLite_0.11.4     rtracklayer_1.21.9 stats4_3.1.0
[11] tools_3.1.0        XML_3.98-1.1       zlibbioc_1.7.0
>


---------------------------------------------------------
Guido Hooiveld, PhD
Nutrition, Metabolism & Genomics Group
Division of Human Nutrition
Wageningen University
Biotechnion, Bomenweg 2
NL-6703 HD Wageningen
the Netherlands
tel: (+)31 317 485788
fax: (+)31 317 483342
email:      guido.hooiveld@wur.nl
internet:   http://nutrigene.4t.com
http://scholar.google.com/citations?user=qFHaMnoAAAAJ
http://www.researcherid.com/rid/F-4912-2010


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