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Utilizing external gene calls #368

meren opened this issue Jun 9, 2016 · 2 comments


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@meren meren commented Jun 9, 2016

This has to be done during the generation of the contigs database. I will specify a format, and make necessary changes so anvi-gen-contigs-database can work with that.

@meren meren added feature core labels Jun 9, 2016
@meren meren added this to the v2.0.0 milestone Jun 9, 2016
@meren meren self-assigned this Jun 9, 2016
meren added a commit that referenced this issue Jun 10, 2016
meren added a commit that referenced this issue Jun 10, 2016

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@meren meren commented Jun 10, 2016


External gene calls can be imported the following way:

anvi-gen-contigs-database -f FASTA.fa -o CONTIGS.db --external-gene-calls TAB-DELIM-FILE

Here is the details of the external gene calls file:

$ anvi-gen-contigs-database -h
usage: anvi-gen-contigs-database [-h] -f FASTA [-L INT] [-K INT]
                                 [--external-gene-calls GENE-CALLS]
                                 [--skip-mindful-splitting] [-o DB_FILE_PATH]

Generate a new anvio contigs database.

optional arguments:
  --external-gene-calls GENE-CALLS
                        A TAB-delimited file to utilize external gene calls.
                        The file must have these columns: 'gene_callers_id' (a
                        unique integer number for each gene call, start from
                        1), 'contig' (the contig name the gene call is found),
                        'start' (start position, integer), 'stop' (stop
                        position, integer), 'direction' (the direction of the
                        gene open reading frame; can be 'f' or 'r'), 'partial'
                        (whether it is a complete gene call, or a partial one;
                        must be 1 for partial calls, and 0 for complete
                        calls), 'source' (the gene caller), and 'version' (the
                        version of the gene caller, i.e., v2.6.7 or v1.0). An
                        example file can be found via the URL

As the help menu suggests, an example file is here for now:

@tdelmont will test this and let us know!

@tdelmont tdelmont closed this Jun 22, 2016

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@ShaiberAlon ShaiberAlon commented Oct 24, 2019

This link which is reported in the help menu leads nowhere and should be updated:

@ShaiberAlon ShaiberAlon reopened this Oct 24, 2019
@meren meren closed this in 8beb272 Oct 25, 2019
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