Utilities¶
There are several scripts that maybe useful to users to convert between different formats, these scripts are housed in the funannotate util submenu.
$ funannotate util
Usage: funannotate util <arguments>
version: 1.8.16
Commands:
stats Generate assembly and annotation stats
contrast Compare annotations to reference (GFF3 or GBK annotations)
tbl2gbk Convert TBL format to GenBank format
gbk2parts Convert GBK file to individual components
gff2prot Convert GFF3 + FASTA files to protein FASTA
gff2tbl Convert GFF3 format to NCBI annotation table (tbl)
bam2gff3 Convert BAM coord-sorted transcript alignments to GFF3
prot2genome Map proteins to genome generating GFF3 protein alignments
stringtie2gff3 Convert GTF (stringTIE) to GFF3 format
quarry2gff3 Convert CodingQuarry output to proper GFF3 format
gff-rename Sort GFF3 file and rename gene models
Generate genome assembly stats¶
To generate genome assembly stats in a JSON file.
$ funannotate util stats
Usage: funannotate util stats <arguments>
version: 1.8.16
Description: Generate JSON file with genome assembly and annotation stats.
Arguments:
-f, --fasta Genome FASTA file (Required)
-o, --out Output file (JSON format)
-g, --gff3 Genome Annotation (GFF3 format)
-t, --tbl Genome Annotation (NCBI TBL format)
--transcript_alignments Transcript alignments (GFF3 format)
--protein_alignments Protein alignments (GFF3 format)
Comparing/contrast annotations to a reference¶
To compare/contrast genome annotations between different GFF3 or GBK files.
$ funannotate util contrast
Usage: funannotate util contrast <arguments>
version: 1.8.16
Description: Compare/constrast annotations to reference. Annotations in either GBK or GFF3 format.
Arguments: -r, --reference Reference Annotation. GFF3 or GBK format
-f, --fasta Genome FASTA. Required if GFF3 used
-q, --query Annotation query. GFF3 or GBK format
-o, --output Output basename
-c, --calculate_pident Measure protein percent identity between query and reference
Format Conversion¶
$ funannotate util tbl2gbk
Usage: funannotate util tbl2gbk <arguments>
version: 1.8.16
Description: Convert NCBI TBL annotations + Genome FASTA to GenBank format.
Required: -i, --tbl Annotation in NCBI tbl format
-f, --fasta Genome FASTA file.
-s, --species Species name, use quotes for binomial, e.g. "Aspergillus fumigatus"
Optional:
--isolate Isolate name
--strain Strain name
--sbt NCBI Submission Template file
-t, --tbl2asn Assembly parameters for tbl2asn. Example: "-l paired-ends"
-o, --output Output basename
$ funannotate util gbk2parts
Usage: funannotate util gbk2parts <arguments>
version: 1.8.16
Description: Convert GenBank file to its individual components (parts) tbl, protein
FASTA, transcript FASTA, and contig/scaffold FASTA.
Arguments: -g, --gbk Input Genome in GenBank format
-o, --output Output basename
$ funannotate util gff2prot
Usage: funannotate util gff2prot <arguments>
version: 1.8.16
Description: Convert GFF3 file and genome FASTA to protein sequences. FASTA output to stdout.
Arguments: -g, --gff3 Reference Annotation. GFF3 format
-f, --fasta Genome FASTA file.
--no_stop Dont print stop codons
$ funannotate util gff2tbl
Usage: funannotate util gff2tbl <arguments>
version: 1.8.16
Description: Convert GFF3 file into NCBI tbl format. Tbl output to stdout.
Arguments:
-g, --gff3 Reference Annotation. GFF3 format
-f, --fasta Genome FASTA file.
$ funannotate util bam2gff3
Usage: funannotate util bam2gff3 <arguments>
version: 1.8.16
Description: Convert BAM coordsorted transcript alignments to GFF3 format.
Arguments: -i, --bam BAM file (coord-sorted)
-o, --output GFF3 output file
$ funannotate util protein2genome
Usage: funannotate util prot2genome <arguments>
version: 1.8.16
Description: Map proteins to genome using exonerate. Output is EVM compatible GFF3 file.
Arguments: -g, --genome Genome FASTA format (Required)
-p, --proteins Proteins FASTA format (Required)
-o, --out GFF3 output file (Required)
-f, --filter Pre-filtering method. Default: diamond [diamond,tblastn]
-t, --tblastn_out Output to save tblastn results. Default: off
--tblastn Use existing tblastn results
--ploidy Ploidy of assembly. Default: 1
--maxintron Max intron length. Default: 3000
--cpus Number of cpus to use. Default: 2
--EVM_HOME Location of Evidence Modeler home directory. Default: $EVM_HOME
--tmpdir Volume/location to write temporary files. Default: /tmp
--logfile Logfile output file
$ funannotate util stringtie2gff3
Usage: funannotate util stringtie2gff3 <arguments>
version: 1.8.16
Description: Convert StringTIE GTF format to GFF3 funannotate compatible format. Output
to stdout.
Arguments: -i, --input GTF file from stringTIE
$ funannotate util quarry2gff3
Usage: funannotate util quarry2gff3 <arguments>
version: 1.8.16
Description: Convert CodingQuarry output GFF to proper GFF3 format. Output to stdout.
Arguments: -i, --input CodingQuarry output GFF file. (PredictedPass.gff3)
.. code-block:: none
$ funannotate util gff-rename
Usage: funannotate util gff-rename <arguments>
version: 1.8.16
Description: Sort GFF3 file by contigs and rename gene models.
Arguments: -g, --gff3 Reference Annotation. GFF3 format
-f, --fasta Genome FASTA file.
-o, --out Output GFF3 file
-l, --locus_tag Locus tag to use. Default: FUN
-n, --numbering Start number for genes. Default: 1