gff3_to_fasta readme

Extract sequences from specific regions of genome based on gff file.

Usage

gff3_to_fasta.py [-h] [-g GFF] [-f FASTA] [-st SEQUENCE_TYPE] [-u USER_DEFINED] [-d DEFLINE] [-o OUTPUT_PREFIX] [-noQC] [-v]

Testing enviroment

1. Python 2.7

Required inputs

1. GFF3: specify the file name with the -g argument
2. Fasta file: specify the file name with the -f argument. This file must be the Fasta file that the GFF3 seqids and coordinates refer to. For more information, refer to the GFF3 specification.
3. Output prefix: specify with the -o argument. All resulting fasta files will contain this prefix.

Outputs

1. Fasta formatted sequence file based on the gff3 file.

Example command

1. Specify the input, output file names and options using short arguments:
   • python2.7 bin/gff3_to_fasta.py -g example_file/example.gff3 -f example_file/reference.fa -st all -d simple -o test_sequences

Optional arguments

1. -h, –help

   • show this help message and exit

2. -g GFF, –gff GFF

   • Genome annotation file in GFF3 format

3. -f FASTA, –fasta FASTA

   • Genome sequences in FASTA format

4. -st SEQUENCE_TYPE, –sequence_type SEQUENCE_TYPE

   • Type of sequences you would like to extract:
     • “all” - FASTA files for all types of sequences listed below, except user_defined;
     • “gene” - gene sequence for each record;
     • “exon” - exon sequence for each record;
     • “pre_trans” - genomic region of a transcript model (premature transcript);
     • “trans” - spliced transcripts (only exons included);
     • “cds” - coding sequences;
     • “pep” - peptide sequences;
     • “user_defined” - specify parent and child features via the -u argument.

5. -u USER_DEFINED, –user_defined USER_DEFINED

   • Specify parent and child features for fasta extraction, format [parent feature type] [child feature type]. Required if -st user_defined is given.
     • Example: -st user_defined -u miRNA exon
   • Lines with the child feature type given in -u must contain a Parent attribute referencing the given Parent feature type. Hence, the parent lines must also contain an ID attribute.
   • If CDS is the child feature type, the program will take phase into account.

6. -d DEFLINE, –defline DEFLINE

   • Defline format in the output FASTA file:
     • “simple” - only ID is shown in the defline;
     • “complete” - complete information of the feature is shown in the defline.

7. -o OUTPUT_PREFIX, –output_prefix OUTPUT_PREFIX

   • Prefix of output file name

8. -noQC, –quality_control

   • Specify this option if you do not want to excute quality control for gff file. (default: QC is executed)

9. -v, –version

   • Show program version number and exit