pseudoscaffold_annotator

A program to annotate an assembled pseudoscaffold

If this program fails on you, revert back to a previous release using the commands

git checkout -f
git reset --hard 25543ca66a9a1a7cc1ab8dc72f4c6e237e797478

This is a program for annotating an assembled pseudoscaffold using a reference genome and annotation file. Currently, this only supports using GFF3 files as input, but can output both GFF3 files and 3-column BED files. Increased support for the BED format will come later.

Running this program to annotate a pseudoscaffold is done using the following command:

./pseudoscaffold_annotator.py annotate -r REFERENCE_FASTA -a ORIGINAL_ANNOTATION -p PSEUDOSCAFFOLD_FASTA -o OUTFILE_NAME -c BLAST_CONFIG_FILE

The BLAST configuration file can be run using the following command:

./pseudoscaffold_annotator.py blast-config

Use the -h flag to see all options for configuring.

IMPORTANT

pseudoscaffold_annotator.py requires no new lines within the sequence of the pseudoscaffold. The following is not an allowed sequence:

    >pseudoscaffold
    ACTGTCAG
    GCTATCGA

The 'fix' subroutine removes new lines between sequence data, creating a fasta file that reads like: >pseudoscaffold ACTGTCAGGCTATCGA

To fix a pseudoscaffold, run the following command:

./pseudoscaffold_annotator.py fix -p PSEUDOSCAFFOLD_FASTA -n FIXED_FASTA

This program requires Python 2.7 or higher, or the argparse module installed for Python 2.6

NOTE: this has NOT been tested on Python 3.x

Other dependencies include:

NOTE: This program has only been tested with the Morex (Barley) genome, please use with caution

TODO

Add support for extracting information from BED file
Add parallelization support
Add BED to GFF annotating capabilities
Add GFF to BED annotating capabilities
~~Finish GFF to GFF annotation capabilities~~ DONE!
Add BED to BED annotating capabilities

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