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karkman / gff_parser

Parser to add external gene calls and functional annotation from Prokka to Anvi'o.
GNU General Public License v3.0
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Not working , any idea ? #8

Closed davidvilanova closed 3 years ago

davidvilanova commented 3 years ago

Hi, While trying to parse my prokka gff file it fails 

python gff_parser.py --gene-calls gene.txt --annotation ano.txt --process-all files/prokka/1/PROKKA_02012021.gff
Traceback (most recent call last):
  File "gff_parser.py", line 52, in <module>
    source, version = feature.source.split(':')
ValueError: not enough values to unpack (expected 2, got 1)

Here is the gff header file

gnl|Prokka|SAMPLE_1_3   prokka  gene    1013    1198    .   -   .   ID=SAMPLE_1_00001_gene;locus_tag=SAMPLE_1_00001
gnl|Prokka|SAMPLE_1_3   Prodigal:002006 CDS 1013    1198    .   -   0   ID=SAMPLE_1_00001;Parent=SAMPLE_1_00001_gene;inference=ab initio prediction:Prodigal:002006;locus_tag=SAMPLE_1_00001;product=hypothetical protein;protein_id=gnl|Prokka|SAMPLE_1_00001
gnl|Prokka|SAMPLE_1_3   prokka  gene    1313    1786    .   -   .   ID=SAMPLE_1_00002_gene;Name=sarA;gene=sarA;locus_tag=SAMPLE_1_00002
gnl|Prokka|SAMPLE_1_3   Prodigal:002006 CDS 1313    1786    .   -   0   ID=SAMPLE_1_00002;Parent=SAMPLE_1_00002_gene;Name=sarA;gene=sarA;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:UniProtKB:A0A0F6B506;locus_tag=SAMPLE_1_00002;product=Salmonella anti-inflammatory response a
davidvilanova commented 3 years ago

grep -v "prokka" mygff_file > new_gff and then it works.....