Open cjfields opened 8 years ago
cjfields
commented
8 years ago Original Redmine Comment Author Name: Chris Fields Original Date: 2009-10-26T00:54:37Z
Dan, just to follow SOP, can you attach a report and describe what you did to cause the fail?
cjfields
commented
8 years ago Original Redmine Comment Author Name: Dan Bolser Original Date: 2009-10-26T13:52:59Z
I was blasting phase 3 BACs from Tomato against Phase 1 BACs from Potato. Everything was going great. I produced blast-tabular output and applied some filters.
Now I wanted to visualize the results, and what better way than in GBrowse, I thought. So I ran the following:
bp_search2gff.pl —version 3 \ -i Results/blast_table_filtered -f blasttable \ -o Results/blast_table_filtered.gff \ —method match_part \ —type hit \ —target
I explicitly set the “—method” field, because the default is non-standard for GFF3.
To my dismay, when the resulting GFF was loaded into GBrowse (into a ‘clean’ Bio::DB::SeqFeature::Store database), I saw the dreaded ‘landmark not found’ error. This is because GB needs a ‘landmark’ entry for each sequence that you want to use as a reference. I tried to get the script to add these ‘landmarks’ for me using the “—component” option. From the manual
—component - generate GFF component fields (chromosome)
I assumed that this would generate a landmark for each ‘hit’ (or query), but the results were unchanged with or without this setting.
Also, I see TONS of errors like this…
——————————- WARNING ——————————- MSG: Removing score value(s) —————————————————————————-
How can I silence these errors or just see a summary of them or something like that?
Cheers, Dan.
perl -pi -e ‘s/Target=Sequence:/Target=/’ Results/blast_table_filtered.gff
perl -pi -e ‘s/Target=Sequence:/Target=/’ Results/blast_table_filtered.query.gff
perl -pi -e ‘s/Target=Sequence:/Target=/’ Results/blast_table_bac_filtered.gff
perl -pi -e ‘s/Target=Sequence:/Target=/’ Results/blast_table_bac_filtered.query.gff
P.S. Why would I need to do this?
perl -pi -e ‘s/Target=Sequence:/Target=/’ Results/blast_table_filtered.gff
perl -pi -e ‘s/Target=Sequence:/Target=/’ Results/blast_table_filtered.query.gff
perl -pi -e ‘s/Target=Sequence:/Target=/’ Results/blast_table_bac_filtered.gff
perl -pi -e ‘s/Target=Sequence:/Target=/’ Results/blast_table_bac_filtered.query.gff
Author Name: Dan Bolser (Dan Bolser) Original Redmine Issue: 2900, https://redmine.open-bio.org/issues/2900 Original Date: 2009-08-05 Original Assignee: Bioperl Guts
No components are added… I need the components (if I understand correctly) to view the blast results in GBrowse … i.e. I need the GFF to give me a reference sequence.