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annejong / FUNAGEPro

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FACoP.v2 web not parsing gff files correctly #2

Open iaindhay opened 5 months ago

iaindhay commented 5 months ago

Hi

When i supply a gff and fna file the web FACoP.v2 dose not seem to recover the locus_tags from the gff file (in the attributes column). it is assigning its own locus_tags called prodigal_1_xx I have tried changing the "locus_tag" to "locus-tag" and the behavior is identical. Any suggestions?

Gff lines fro example

##sequence-region contig_1 1 4517665
contig_1    Bakta   region  1   4517665 .   +   .   ID=contig_1;Name=contig_1
contig_1    Prodigal    CDS 359 1459    .   -   0   ID=eco15669_00010;Name=sodium-potassium/proton antiporter ChaA;locus_tag=eco15669_00010;product=sodium-potassium/proton antiporter ChaA;Dbxref=COG:COG0387,COG:P,GO:0005886,GO:0010446,GO:0015385,GO:0015386,RefSeq:WP_000063607.1,SO:0001217,UniParc:UPI000012776B,UniRef:UniRef100_P31801,UniRef:UniRef50_P31801,UniRef:UniRef90_P31801;gene=chaA
contig_1    Prodigal    CDS 1729    1959    .   +   0   ID=eco15669_00015;Name=putative cation transport regulator ChaB;locus_tag=eco15669_00015;product=putative cation transport regulator ChaB;Dbxref=COG:COG4572,COG:P,RefSeq:WP_001146444.1,SO:0001217,UniParc:UPI000012776C,UniRef:UniRef100_P0AE65,UniRef:UniRef50_P0AE65,UniRef:UniRef90_P0AE65;gene=chaB
contig_1    Prodigal    CDS 2096    2812    .   +   0   ID=eco15669_00020;Name=glutathione-specific gamma-glutamylcyclotransferase;locus_tag=eco15669_00020;product=glutathione-specific gamma-glutamylcyclotransferase;Dbxref=BlastRules:WP_001336325,COG:COG3703,COG:P,EC:4.3.2.7,GO:0003839,GO:0005737,GO:0006751,GO:0061928,RefSeq:WP_001350506.1,SO:0001217,UniParc:UPI0000168086,UniRef:UniRef100_UPI0000168086,UniRef:UniRef50_P39163,UniRef:UniRef90_P39163;gene=chaC
contig_1    Prodigal    CDS 2856    3209    .   -   0   ID=eco15669_00025;Name=DsrE/F sulfur relay family protein YchN;locus_tag=eco15669_00025;product=DsrE/F sulfur relay family protein YchN;Dbxref=BlastRules:WP_001169669,COG:COG1553,COG:P,GO:0005829,GO:0032991,GO:0042802,RefSeq:WP_001169669.1,SO:0001217,UniParc:UPI000013A6B5,UniRef:UniRef100_P0AB53,UniRef:UniRef50_P0AB53,UniRef:UniRef90_P0AB53;gene=ychN
iaindhay commented 5 months ago

Nevermind. I think it's just that it doesn't like "CDS" in the type column, seems it only wants "gene".

annejong commented 5 months ago

Good that you solved it. Typically locus_tags are described by type=gene. Facop also works with plain DNA without GFF if you don't have one. It will use Prodigal to predict CDSs and generate a GFF

any suggestions are welcome

Anne

Op wo 5 jun 2024 om 07:04 schreef ihay @.***>:

Nevermind. I think it's just that it doesn't like "CDS" in the type column, seems it only wants "gene".

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