是否可以用 python/biopython 进行 igblast(分析免疫球蛋白 (Ig) 序列)
is that possible to do igblast(Analyze immunoglobulin (Ig) sequences) with python/biopython
我刚接触 python/biopython 并尝试使用 biopython 进行 blast,如下所示:
from Bio.Blast import NCBIWWW
fasta_string = open("C:\xxxx\xxxx\xxxx\abc.fasta").read()
result_handle = NCBIWWW.qblast("blastp", "nr", fasta_string)
print result_handle.read()
我想知道是否可以 运行 igblast 使用 biopython。我已经搜索过这个,但似乎没有人真正这样做。
我没试过,但我发现:
PyIgBlast - Open source Parser to call IgBlast and parse results for
high-throughput sequencing. Uses Python multi-processing to get around
bottlenecks of IgBlast multi-threading. Parses blast output to
deliminated files (csv,json) for uploading to databases. Can connect
directly with mysql and mongo instances to insert directly.
代码使用Python 2.7和BioPython。
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.
代码使用Python3.6和BioPython。
这两个工具都使用本地安装的 igblastn
可执行文件。您可以使用 conda install igblast
.
在本地安装 igblastn
我刚接触 python/biopython 并尝试使用 biopython 进行 blast,如下所示:
from Bio.Blast import NCBIWWW
fasta_string = open("C:\xxxx\xxxx\xxxx\abc.fasta").read()
result_handle = NCBIWWW.qblast("blastp", "nr", fasta_string)
print result_handle.read()
我想知道是否可以 运行 igblast 使用 biopython。我已经搜索过这个,但似乎没有人真正这样做。
我没试过,但我发现:
PyIgBlast - Open source Parser to call IgBlast and parse results for high-throughput sequencing. Uses Python multi-processing to get around bottlenecks of IgBlast multi-threading. Parses blast output to deliminated files (csv,json) for uploading to databases. Can connect directly with mysql and mongo instances to insert directly.
代码使用Python 2.7和BioPython。
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.
代码使用Python3.6和BioPython。
这两个工具都使用本地安装的 igblastn
可执行文件。您可以使用 conda install igblast
.
igblastn