get-gff-info - Extract informations to GFF annotations

Overview

Extract information from GFF files

sequence command

Used to extract the nucleotidic sequences from GFF annotations. It requires the fasta file containing the sequences referenced in the GFF seq_id attribute (first column of the raw GFF).

The sequnces extract have as identifier the uid stored in the GFF file and by default the sequnece is not reverse complemented if the annotation is on the - strand, but this can be changed by using the -r option.

The sequences are wrapped at 60 characters, as per FASTA specs, but this behavior can be disabled by specifing the -w option.

Warning

The reference file is loaded in memory

dbm command

Creates a dbm DB using the semidbm package. The database can then be loaded using mgkit.db.dbm.GFFDB

mongodb command

Outputs annotations in a format supported by MongoDB. More information about it can be found in mgkit.db.mongo

gtf command

Outputs annotations in the GTF format

split command

Splits a GFF file into smaller chunks, ensuring that all of a sequence annotations are in the same file.

cov command

Calculate annotation coverage for each contig in a GFF file. The command can be run as strand specific (not by default) and requires the reference file to which the annotation refer to. The output file is a tab separated one, with the first column being the sequence name, the second is the strand (+, -, or NA if not strand specific) and the third is the percentage of the sequence covered by annotations.

Warning

The GFF file is assumed to be sorted, by sequence or sequence-strand if wanted. The GFF file can be sorted using sort -s -k 1,1 -k 7,7 for strand specific, or sort -s -k 1,1 if not strand specific.

Changes

Changed in version 0.3.4: using click instead of argparse, renamed split command –json to –json-out

Changed in version 0.3.1: added cov command

Changed in version 0.3.0: added –split option to sequence command

Changed in version 0.2.6: added split command, –indent option to mongodb

Changed in version 0.2.3: added –gene-id option to gtf command

New in version 0.2.2: added gtf command

New in version 0.2.1: dbm and mongodb commands

New in version 0.1.15.

Options

get-gff-info

Main function

get-gff-info [OPTIONS] COMMAND [ARGS]...

Options

--version

Show the version and exit.

--cite

cov

Report on how much a sequence length is covered by annotations in [gff-file]

get-gff-info cov [OPTIONS] [GFF_FILE] [OUTPUT_FILE]

Options

-v, --verbose

-f, --reference <reference>

Required Reference FASTA file for the GFF

-j, --json-out

The output will be a JSON dictionary

-s, --strand-specific

If the coverage must be calculated on each strand

-r, --rename

Emulate BLAST output (use only the header part before the first space)

--progress

Shows Progress Bar

Arguments

GFF_FILE

Optional argument

OUTPUT_FILE

Optional argument

dbm

Creates a dbm database with annotations from file [gff-file] into db [output-dir]

get-gff-info dbm [OPTIONS] [GFF_FILE]

Options

-v, --verbose

-d, --output-dir <output_dir>

Directory for the database

Default

gff-dbm

Arguments

GFF_FILE

Optional argument

gtf

Extract annotations from a GFF file [gff-file] to a GTF file [gtf-file]

get-gff-info gtf [OPTIONS] [GFF_FILE] [GTF_FILE]

Options

-v, --verbose

-g, --gene-id <gene_id>

GFF attribute to use for the GTF gene_id attribute

Default

gene_id

Arguments

GFF_FILE

Optional argument

GTF_FILE

Optional argument

mongodb

Extract annotations from a GFF [gff-file] file and makes output for MongoDB [output-file]

get-gff-info mongodb [OPTIONS] [GFF_FILE] [OUTPUT_FILE]

Options

-v, --verbose

-t, --taxonomy <taxonomy>

Taxonomy used to populate the lineage

-c, --no-cache

No cache for the lineage function

-i, --indent <indent>

If used, the json will be written in a human readble form

--progress

Shows Progress Bar

Arguments

GFF_FILE

Optional argument

OUTPUT_FILE

Optional argument

sequence

Extract the nucleotidic sequences of annotations from [gff-file] to [fasta-file]

get-gff-info sequence [OPTIONS] [GFF_FILE] [FASTA_FILE]

Options

-v, --verbose

-r, --reverse

Reverse complement sequences on the - strand

-w, --no-wrap

Write the sequences on one line

-s, --split

Split the sequence header of the reference at the first space, to emulate BLAST behaviour

-f, --reference <reference>

Fasta file containing the reference sequences of the GFF file

--progress

Shows Progress Bar

Arguments

GFF_FILE

Optional argument

FASTA_FILE

Optional argument

split

Split annotations from a GFF file [gff-file] to several files starting with [prefix]

get-gff-info split [OPTIONS] [GFF_FILE]

Options

-v, --verbose

-p, --prefix <prefix>

Prefix for the file name in output

Default

split

-n, --number <number>

Number of chunks into which split the GFF file

Default

10

-z, --gzip

gzip output files

Arguments

GFF_FILE

Optional argument