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Question: Error in normSplitFactor(f, x)
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gravatar for mictadlo
11 days ago by
mictadlo0
mictadlo0 wrote:

Hi, I found the below code here:

> library(GenomicRanges)
> library(rtracklayer)
> library(Rsamtools)
Loading required package: Biostrings
Loading required package: XVector
> 
> GFFfile = "snap_augustus.gff"
> FASTAfile = "genome_29155.faa"
> 
> #Load the annotation and reduce it
> GFF <- import.gff(GFFfile, format="gff", feature.type="exon")
> head(GFF)
GRanges object with 6 ranges and 6 metadata columns:
              seqnames         ranges strand |   source     type     score     phase                        ID
                 <Rle>      <IRanges>  <Rle> | <factor> <factor> <numeric> <integer>               <character>
  [1] lcl|ScwjSwM_3729 [15533, 15536]      - |    maker     exon      <NA>      <NA> sp0000001-mRNA-1:exon:210
  [2] lcl|ScwjSwM_3729 [14631, 14650]      - |    maker     exon      <NA>      <NA> sp0000001-mRNA-1:exon:209
  [3] lcl|ScwjSwM_3729 [12563, 14608]      - |    maker     exon      <NA>      <NA> sp0000001-mRNA-1:exon:208
  [4] lcl|ScwjSwM_3729 [11160, 11346]      - |    maker     exon      <NA>      <NA> sp0000001-mRNA-1:exon:207
  [5] lcl|ScwjSwM_3729 [10840, 10985]      - |    maker     exon      <NA>      <NA> sp0000001-mRNA-1:exon:206
  [6] lcl|ScwjSwM_3729 [10109, 10739]      - |    maker     exon      <NA>      <NA> sp0000001-mRNA-1:exon:205
                Parent
       <CharacterList>
  [1] sp0000001-mRNA-1
  [2] sp0000001-mRNA-1
  [3] sp0000001-mRNA-1
  [4] sp0000001-mRNA-1
  [5] sp0000001-mRNA-1
  [6] sp0000001-mRNA-1
  -------
  seqinfo: 4724 sequences from an unspecified genome; no seqlengths
> 
> grl <- reduce(split(GFF, elementMetadata(GFF)$gene_id))

Unfortunately it produce the following error:

Error in normSplitFactor(f, x) : 
  split factor has length 0 but 'NROW(x)' is > 0

My GFF file looks like this:

lcl|ScwjSwM_3729        maker   gene    9131    15536   .       -       .       ID=sp0000001;Name=sp0000001
lcl|ScwjSwM_3729        maker   mRNA    9131    15536   .       -       .       ID=sp0000001-mRNA-1;Parent=sp0000001;Name=sp0000001-mRNA-1;_AED=0.28;_eAED=0.28;_QI=0|0|0|0.14|1|1|7|0|1016
lcl|ScwjSwM_3729        maker   exon    15533   15536   .       -       .       ID=sp0000001-mRNA-1:exon:210;Parent=sp0000001-mRNA-1
lcl|ScwjSwM_3729        maker   exon    14631   14650   .       -       .       ID=sp0000001-mRNA-1:exon:209;Parent=sp0000001-mRNA-1
lcl|ScwjSwM_3729        maker   exon    12563   14608   .       -       .       ID=sp0000001-mRNA-1:exon:208;Parent=sp0000001-mRNA-1
lcl|ScwjSwM_3729        maker   exon    11160   11346   .       -       .       ID=sp0000001-mRNA-1:exon:207;Parent=sp0000001-mRNA-1
lcl|ScwjSwM_3729        maker   exon    10840   10985   .       -       .       ID=sp0000001-mRNA-1:exon:206;Parent=sp0000001-mRNA-1
lcl|ScwjSwM_3729        maker   exon    10109   10739   .       -       .       ID=sp0000001-mRNA-1:exon:205;Parent=sp0000001-mRNA-1
lcl|ScwjSwM_3729        maker   exon    9131    9147    .       -       .       ID=sp0000001-mRNA-1:exon:204;Parent=sp0000001-mRNA-1
lcl|ScwjSwM_3729        maker   CDS     15533   15536   .       -       0       ID=sp0000001-mRNA-1:cds;Parent=sp0000001-mRNA-1
lcl|ScwjSwM_3729        maker   CDS     14631   14650   .       -       2       ID=sp0000001-mRNA-1:cds;Parent=sp0000001-mRNA-1
lcl|ScwjSwM_3729        maker   CDS     12563   14608   .       -       0       ID=sp0000001-mRNA-1:cds;Parent=sp0000001-mRNA-1
lcl|ScwjSwM_3729        maker   CDS     11160   11346   .       -       0       ID=sp0000001-mRNA-1:cds;Parent=sp0000001-mRNA-1
lcl|ScwjSwM_3729        maker   CDS     10840   10985   .       -       2       ID=sp0000001-mRNA-1:cds;Parent=sp0000001-mRNA-1
lcl|ScwjSwM_3729        maker   CDS     10109   10739   .       -       0       ID=sp0000001-mRNA-1:cds;Parent=sp0000001-mRNA-1
lcl|ScwjSwM_3729        maker   CDS     9131    9147    .       -       2       ID=sp0000001-mRNA-1:cds;Parent=sp0000001-mRNA-1

What did I miss?

Thank you in advance

ADD COMMENTlink modified 11 days ago by Michael Lawrence9.6k • written 11 days ago by mictadlo0
2
gravatar for Michael Lawrence
11 days ago by
United States
Michael Lawrence9.6k wrote:

I guess we could make this more obvious but the problem is that there is no gene_id column.

ADD COMMENTlink written 11 days ago by Michael Lawrence9.6k

Thank you: `grl <- reduce(split(GFF, elementMetadata(GFF)$ID))`

ADD REPLYlink written 11 days ago by mictadlo0
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