bwast

Blast Wrapper And Sequence Trimmer

Performs command-line BLAST using Fasta/Genbank/EMBL files and loads the comparison up in ACT, in just one step.

Why use bwast?

Allows:

• A subregion of genbank or fasta file to be specified after filename (start..stop)
• Automated loading of the sequences and comparison into the Artemis Comparison Tool (ACT) - act must be on your PATH (Please use -a flag)
• An infinite number of input sequences, depending on memory available

Produces (Output files):

• Fasta version of genbank/embl file supplied
• Blast tab delimited (-outfmt 6) output with blast options used, in the filename
• A new genbank/embl/fasta file of a specified subregion, if coordinates were given

Requirements

Dependencies

• NCBI's blast+

  (blastn and tblastx need to be on your path, conda install -c bioconda blast)

• Artemis Comparison Tool (ACT)

  (act needs to be on your path, conda install -c bioconda artemis)

• Biopython

  (I use conda to install biopython, conda install -c bioconda biopython )

If you are using Conda with Apple Silicon Macs (M1/M2), see this

Input format requirements

• Input files should have a recognisable suffix (e.g. gb, gbk, gbff, emb, embl, fas, fasta, fna, fa)
• Genbank and EMBL files must be formatted according to Biopython requirements. Valid headers must be present. Genbank output from Artemis and RAST are known to cause issues.

Quick Start Instructions

Blast two genbank files

bwast.py <genbank1> <genbank2>

Blast more than two files

bwast.py <genbank1> <genbank2> <fasta1> <genbank3>

Blast two or more genbank files and load in Artemis Comparison Tool

bwast.py -a <genbank1> <genbank2>

Blast subregions of genbank files

bwast.py <genbank1> 200..2000 <genbank2> 7000..9000

Blast with blastn instead of megablast and use a custom e-value cutoff

bwast.py <genbank1> <genbank2> -f '-task blastn -evalue 0.0001'

See optional arguments and usage

bwast.py -h

Detailed Instructions

Getting bwast

To use, simply use git clone https://github.com/bawee/bwast.git, if you have Git installed (recommended).

--or--

Just download the bwast.py Python script on it's own.

Running bwast

path/to/bwast.py sequence1.gbk sequence2.fna

Optional arguments

• -h, --help show this help message and exit

• -f FLAGS, --flags FLAGS Custom BLAST options, enclosed in quotes. E.g. -f '-task blastn -evalue 0.001'

• -v, --verbose Verbose mode

• -a, --act Run ACT after performing BLAST

• -b {blastn,tblastx}, --blast {blastn,tblastx} Blast program to use. Either tblastn or blastn. Default is blastn

• -o, --outfmt Change the output format. Default is --outfmt 6.

F.A.Q

1. I think I found a bug in the script. How do I let you know?

   Thanks for taking the time to report it! Please submit an issue on GitHub and I will be in touch shortly. You can also contact me on twitter @bawee.

2. Why do I get the error: BLAST engine error: Empty CBlastQueryVector or Command line argument error: Query is Empty!?

   Genbank files output by Artemis can sometimes cause this due to the absence of a valid header. Please contact me on twitter if you need a script to add a dummy header.

3. Can I use relative/absolute paths to point to input files?

   Yes you can!

4. How do I get ACT on my PATH?

   On a Mac OSX, run this command:

   export PATH="$PATH:/Applications/Artemis.app/Contents"
   

   or put this line into your ~/.profile to have it set permanently.

   On Windows 10, you can a combination of Windows Subsystem for Linux shell (e.g. ubuntu) and a window X-server such as VcXsrv or Xming. You will still need to add the ACT executable (for unix) to your path, for example:

   export PATH="$PATH:/path/to/artemis/download"
   

5. I get error messages when using a genbank or embl file. Is there something wrong with my file format?

   Biopython (used by bwast) is very fussy about the exact genbank/embl format used. Try manually adding the expected lines/text in the header. Genbank/embl files output by Artemis and RAST are known to be incompatible with biopython.

6. My BLAST hits were flipped and are matching the wrong end of the sequence

   If your query and reference are very similar in length, ACT can sometimes flip the BLAST hits incorrectly. I do not know how to prevent this from happening. If you are specifying a subregion, try changing the sequence length.

7. What does the name bwast mean?

   Blast Wrapper And Sequence Trimmer

Info

Written by Bryan Wee.

Inspired by EasyfigCL (MJ Sullivan) and Seqhandler (NF Alikhan)

Merge subroutine adapted from Seqhandler (NF Alikhan) github.com/happykhan/seqhandler

1. Version 0.0.1 - 1st version
2. Version 0.0.2 - added ability to detect and merge multifasta inputs - Thanks to B Forde for the suggestion.