blasttools 0.1.16

Commands for turning blast queries into pandas dataframes.

blasttools

Commands for turning blast queries into pandas dataframes.

Blast against any built blast databases

blasttools blast --out=my.pkl query.fasta my_blastdbs_dir/*.pot

Install

Install with

python -m pip install -U blasttools
# *OR*
python -m pip install -U 'git+https://github.com/arabidopsis/blasttools.git'

Once installed you can update with blasttools update

Common Usages:

Build some blast databases from Ensembl Plants.

blasttools plants --release=40 build triticum_aestivum zea_mays

Find out what species are available:

blasttools plants --release=40 species

Blast against my.fasta and save dataframe as a pickle file (the default is to save as a csv file named my.fasta.csv).

blasttools plants blast --out=dataframe.pkl my.fasta triticum_aestivum zea_mays

Get your blast data!

import pandas as pd
df = pd.read_pickle('dataframe.pkl')

Parallelization

When blasting, you can specify --num-threads which is passed directly to the underlying blast command. If you want to parallelize over species, databases or fasta files, I suggest you use GNU Parallel [Tutorial].

parallel has a much better set of options for controlling how the parallelization works and is also quite simple for simple things.

e.g. build blast databases from a set of fasta files concurrently:

parallel blasttools build ::: *.fa.gz

Or blast everything!

species=$(blasttools plants species)
parallel blasttools plants build ::: $species
# must have different output files here...
parallel blasttools plants blast --out=my{}.pkl my.fasta ::: $species
# or in batches of 4 species at a time
parallel -N4 blasttools plants blast --out='my{#}.pkl' my.fasta ::: $species

Then gather them all together...

blasttools concat --out=alldone.xlsx my*.pkl && rm my*.pkl

or programmatically:

from glob import glob
import pandas as pd
df = pd.concat([pd.read_pickle(f) for f in glob('my*.pkl')], ignore_index=True)

Remember: if you parallelize your blasts and use --num-threads > 1 then you are probably going to be fighting for cpu time amongst yourselves!

Best matches

Usually if you want the top/best --best=3 will select the lowest evalue's for each query sequence. However if you want say the best to, say, be the longest query match then you can add --expr='qstart - qend'. (Remember we are looking for the lowest values).

XML

Blast offers an xml (--xml) output format that adds query, match, sbjct strings. The other fields are equivalent to adding --columns='+score gaps nident positive qlen slen'.

It also offers a way to display the blast match as a pairwise alignment.

from blasttools.blastxml import hsp_match
df = pd.read_csv('results.csv')
df['alignment'] = df.apply(hsp_match, axis=1)
print(df.iloc[0].alignment)