Files pertaining to the manuscript High frequency of shared clonotypes in human B cell receptor repertoires
Immunoglobulin and T-Cell receptor rearrangement software
A Python wrapper for IgBLAST that scales to allow for the parallel processing of millions of reads on shared memory computers. All output is stored in a convenient JSON format.
- Python 3.6
- Pip version 10.0.1 or greater (python 3.6)
- MacOSX or Linux
- wget - Installed on many linux distributions by default. Available for mac through the homebrew package manager
Download the repository
This repository can be downloaded by selecting "Download ZIP" from the "Clone and Download" menu at the top right of this github page or by using git from command line.
If you have git installed you may use the command in order to place a copy of the github repo into your current directory.
git clone https://github.com/crowelab/PyIR
Ensure that pip is associated with the correct verison of python. If pip --version says that it is asscoiated with python version 2 then pip3 should be explicityly used instead of pip.
cd PyIR/
sudo pip install .
Ensure that pip is associated with the correct verison of python. If pip --version says that it is asscoiated with python version 2 then pip3 should be explicityly used instead of pip.
cd PyIR/
pip install --user .
If installing locally confirm pythons local bin is in your path. If not you can add the the following to your ~/.bashrc
export PY_USER_BIN=$(python -c 'import site; print(site.USER_BASE + "/bin")')
export PATH=$PY_USER_BIN:$PATHA shell script has been included in this repository which will build the databases and check to make sure that your installation is functioning properly. You may run the included "SetupGermlineLibrary.sh" script in order to build the gerline library and load test data. If the setup is successful then a file will be created which is a gunzipped json file containing the output of PyIR for the setup scripts testcase.
bash SetupGermlinLibrary.sh
usage: pyir [-h] -d DATABASE [-r {Ig,TCR}] [-s {human,mouse}]
[-nV NUM_V_ALIGNMENTS] [-nD NUM_D_ALIGNMENTS]
[-nJ NUM_J_ALIGNMENTS] [-mD MIND] [-cz CHUNK_SIZE] [-x EXECUTABLE]
[-m MULTI] [-o inputfile.json.gz] [--debug]
[--additional_field ADDITIONAL_FIELD] [-f json] [--pretty]
[--silent]
query.fasta
A Python wrapper for IgBLAST that scales to allow for the parallel processing
of millions of reads on shared memory computers. All output is stored in a
convenient JSON format. Authors - Andre Branchizio, Jordan Willis, Jessica
Finn
optional arguments:
-h, --help show this help message and exit
Necessary Arguments:
Arguments that must be included
query.fasta The fasta or fastq file to be run through the protocol
File paths and types:
Database paths, search types
-d DATABASE, --database DATABASE
Path to your blast database directory
-r {Ig,TCR}, --receptor {Ig,TCR}
The receptor you are analyzing, immunoglobulin or t
cell receptor
-s {human,mouse}, --species {human,mouse}
The Species you are analyzing
-cz CHUNK_SIZE, --chunk_size CHUNK_SIZE
How many sequences to work on at once. The higher the
number the more memory needed. If none specified chunk
size will be determined based on input file size
BLAST Specific Arguments:
Arguments Specific to IgBlast
-nV NUM_V_ALIGNMENTS, --num_V_alignments NUM_V_ALIGNMENTS
How many V genes do you want to match?
-nD NUM_D_ALIGNMENTS, --num_D_alignments NUM_D_ALIGNMENTS
How many D genes do you want to match?, does not apply
for kappa and lambda
-nJ NUM_J_ALIGNMENTS, --num_J_alignments NUM_J_ALIGNMENTS
How many J genes do you want to match?
-mD MIND, --minD MIND
The amount of nucleotide matches needed for a D gene
match. >= 5 right now
-x EXECUTABLE, --executable EXECUTABLE
The location of IGBlastn binary, the default location
is determined based on the OS and uses the igblast
binaries included in this application.
General Arguments:
Output and Miscellaneous Arguments
-m MULTI, --multi MULTI
Multiprocess by the amount of CPUs you have. Or you
can enter a number or type 0 to turn it off
-o inputfile.json.gz, --out inputfile.json.gz
Output_file_name, defaults to inputfile.json.gz
--debug Debug mode, this will not delete the temporary blast
files and will print some other useful things, like
which regions did not parse
--additional_field ADDITIONAL_FIELD
A comma key,value pair for an additional field you
want to add to the output json. Example '--
additional_field=donor,10` adds a donor field with
value 10.
-f json, --out-format json
Output file format, only json currently supported
--pretty Pretty json output
--silent Silence stdout
import json
import pyir.factory
import tempfile
input_file = open('1K_Seqs.fasta', 'r')
out_file = tempfile.NamedTemporaryFile(delete=True)
num_procs = 4
argument_overrides = {
'silent': True,
'database': 'Path/To/Database',
'query': input_file,
'out': out_file.name,
'multi': num_procs
}
py_ir = pyir.factory.PyIr(argument_overrides)
result = py_ir.run()
for line in result:
seq = json.loads(line)
# Do whatever you need with the resulting sequence
print(seq['Sequence ID'], seq['Top V gene match'] if 'Top V gene match' in seq else 'No match' )Files associated with the manuscript High frequency of shared clonotypes in human B cell receptor repertoires
Synthetic clonotype data sets:
Recombinator & additional scripts: