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jydu / maffilter

The MafFilter genome alignment processor
GNU General Public License v3.0
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GFF3 Issue #10

Closed PlantDr430 closed 4 years ago

PlantDr430 commented 4 years ago

Sorry to trouble you again, but I ran into another issue. I am getting the following error when I try to extract features from a GFF3 file.

Adding filter..........................: ExtractFeature
WARNING!!! Parameter verbose not specified. Default used instead: 1
-- Verbose.............................: yes
-- Features to extract.................: Cpurp.gff3 (GFF)
-- Features are for species............: Cpurp
-- Features are strand-aware...........: yes
-- Extract incomplete features.........: no
-- Extract features of type............: mRNA
GffFeatureReader::nextFeature(). Wrong GFF3 file format: should have 9 tab delimited columns.

My GFF3 does have 9 columns and is tab delimited. For example,

Cpurp.1 funannotate gene    8   1406    .   -   .   ID=CPUR_00001;
Cpurp.1 funannotate mRNA    8   1406    .   -   .   ID=CPUR_00001-T1;Parent=CPUR_00001;product=hypothetical protein;
Cpurp.1 funannotate exon    1197    1406    .   -   .   ID=CPUR_00001-T1.exon1;Parent=CPUR_00001-T1;
Cpurp.1 funannotate exon    8   11  .   -   .   ID=CPUR_00001-T1.exon2;Parent=CPUR_00001-T1;
Cpurp.1 funannotate CDS 1197    1406    .   -   0   ID=CPUR_00001-T1.cds;Parent=CPUR_00001-T1;
Cpurp.1 funannotate CDS 8   11  .   -   0   ID=CPUR_00001-T1.cds;Parent=CPUR_00001-T1;
Cpurp.1 funannotate gene    3547    4147    .   -   .   ID=CPUR_00002;
Cpurp.1 funannotate mRNA    3547    4147    .   -   .   ID=CPUR_00002-T1;Parent=CPUR_00002;product=hypothetical protein;
Cpurp.1 funannotate exon    3938    4147    .   -   .   ID=CPUR_00002-T1.exon1;Parent=CPUR_00002-T1;
Cpurp.1 funannotate exon    3547    3867    .   -   .   ID=CPUR_00002-T1.exon2;Parent=CPUR_00002-T1;
Cpurp.1 funannotate CDS 3938    4147    .   -   0   ID=CPUR_00002-T1.cds;Parent=CPUR_00002-T1;
Cpurp.1 funannotate CDS 3547    3867    .   -   0   ID=CPUR_00002-T1.cds;Parent=CPUR_00002-T1;
Cpurp.1 funannotate gene    5877    6467    .   +   .   ID=CPUR_00003;
Cpurp.1 funannotate mRNA    5877    6467    .   +   .   ID=CPUR_00003-T1;Parent=CPUR_00003;product=hypothetical protein;
Cpurp.1 funannotate exon    5877    6086    .   +   .   ID=CPUR_00003-T1.exon1;Parent=CPUR_00003-T1;
Cpurp.1 funannotate exon    6147    6467    .   +   .   ID=CPUR_00003-T1.exon2;Parent=CPUR_00003-T1;
Cpurp.1 funannotate CDS 5877    6086    .   +   0   ID=CPUR_00003-T1.cds;Parent=CPUR_00003-T1;
Cpurp.1 funannotate CDS 6147    6467    .   +   0   ID=CPUR_00003-T1.cds;Parent=CPUR_00003-T1;

Here is my maf_filter call just in case, but it appears to be a problem with my GFF file format, which is a v3.0 file format so I am not sure why I am getting an error about the file format. 

maf.filter= \
    ExtractFeature( \
        ref_species=Cpurp, \
        feature.file=Cpurp.gff3, \
        feature.file.compression=none, \
        feature.format=GFF, \
        feature.type=mRNA, \
        compression=none, \
        complete=yes, \
        ignore_strand=no), \
    Output( \
        file=population_filtered_mRNAs.maf) \
jydu commented 4 years ago

Did this issue resolve by itself ;) ?