SeqHandler

SeqHandler provides low level operations on sequence files (FASTA, GenBank or EMBL files).

Requires Biopython, see: http://biopython.org/wiki/Main_Page & Python 2.7.3 or similar

SPLIT MODULE

Use this Module if you want to split a gbk/embl file on a particular feature. e.g. source, fasta_record

An example would be : python SeqHandler.py split test.embl splitTest -f source -i embl

Where:

• test.embl is the input file you want to split (gbk or embl).
• -i flag, specifies the input file type (genbank/embl) If none is specified the script will assume input is a Genbank file
• splitTest is the output directory for all the resulting files.
• -o flag, specifies the output file type (genbank/embl/fasta)
• -f flag, denotes the feature you want to split on (In this case 'source'). If none is specified the script will split on 'fasta_record'

N.B The script will try to rename the split files using the 'note' attached to the feature you're trying to split on.

If no output format is specified (-o) flag, the file format for split files will be the same as the input. i.e embl input, get embl output.

MERGE MODULE

Use this module if you want to merge a genbank, embl or fasta records.

An example would be: python SeqHandler.py merge test.gbk -i genbank test2.fna -o fasta

Where:

• test.gbk is the input file you want to merge (gbk/embl/fasta).
• test2.fna is the output file.
• -i flag, specifies the input file type (genbank/embl/fasta) If none is specified the script will assume input is a Genbank file
• -o flag, specifies the output file type (genbank/embl/fasta)

N.B Input only takes one file. If you want to merge multiple seperate files together you'll need to first concatenate them together.

If no output format is specified (-o) flag, the file format for split files will be the same as the input. i.e embl input, get embl output.

CONVERT MODULE

Use this module if you want to convert a sequence file.

An example would be: python SeqHandler.py convert test.gbk test2.fna -o fasta -i genbank

Where:

• test.gbk is the input file you want to merge
• test2.fna is the output file.
• -i flag, specifies the input file type If none is specified the script will assume input is a Genbank file
• -o flag, specifies the output file type If none is specified the script will assume input is a fasta file

See USAGE (python SeqHandler.py convert -h) for full list of supported files.

CHANGE LOG

2013-04-16 Nabil-Fareed Alikhan <n.alikhan@uq.edu.au>

• Version 0.3
• Initial build

2013-04-17 Nabil-Fareed Alikhan <n.alikhan@uq.edu.au>

• Version 0.5
• Reworked GBKSplit to SeqHandler
• Created sub modules: split, merge & convert files
• Explicit control of Input/Output for modules

2013-09-05 Nabil-Fareed Alikhan <n.alikhan@uq.edu.au>-

• Changed fasta header handling for Prokka input in merge
• Added header override flags for merge

2013-09-05 Mitchell Stanon-Cook <m.stantoncook@uq.edu.au>-

• Made into an installable package
• Installs a script (SeqHandler) system wide
• Small improvements in terms of using __init__ as a meta container

2013-09-06 Mitchell Stanon-Cook <m.stantoncook@uq.edu.au>-

• Added option to convert to/from gff

LICENCE

Nabil-Fareed Alikhan <n.alikhan@uq.edu.au>. (C) 2012-2013.

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.