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pyblastbio的Python项目详细描述
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Pyblast
这是其他应用程序在seqrecord对象和json对象上运行blast搜索的包装器。打算 用于小型python应用程序。
功能包括：
- 自动blast解析为json
- 使用线性或循环主题对齐循环查询
- 喷砂自安装
安装
您可以使用以下命令将blast安装到pyblast目录：
pyblast install
这将把它安装到python安装位置的pyblast/blast_bin中。如果要在其他地方安装blast，请移动ncbi-blast-x.x.x+文件夹 将path/to/ncbi-blast-x.x.x+/bin添加到您所需的位置。pyblast更喜欢使用存储的blast 在您的可执行路径中。如果在那里找不到blast可执行文件，它会在pyblast/blast_bin/_paths.txt中的路径中查找它。 文件。_当您运行install_blast.py时，paths.txt会自动更新，因此无需手动管理路径。
在安装并验证blastn命令在命令行工作之后，
pip install pyblastbio
用法
这个包是blast命令行的python包装器，打算与微服务（例如flask）一起运行，或者用于jupyter笔记本或小python脚本/应用程序中的快速对齐。
这个包还包括一个基本的基于python的安装脚本，用于单元测试。
对bio.seqrecord对象运行blast查询
我们可以使用下面的代码对一些序列进行快速对齐，这为我们提供了一个很好的结果字典：
frompyblastimportBioBlastfrompyblast.utilsimportmake_linear,make_circularfromBio.SeqRecordimportSeqRecordfromBio.SeqimportSeqqueries=[SeqRecord(Seq("ACGTGATTCGTCGTGTAGTTGAGTGTTACGTTGCATGTCGTACGTGTGTAGTGTCGTGTAGTGCTGATGCTACGTGATCG"))]subjects=[SeqRecord(Seq("ACGTGATTCGTCGTGTAGTTGAGTGTTACGTTGCATGTCGTTACGTGATCG"))]# pyblast requires a 'topology' annotation on the SeqRecords.# we can make records circular or linear using `make_linear` or `make_circular` methodssubjects=make_linear(subjects)queries=make_linear(queries)blast=BioBlast(subjects,queries)results=blast.quick_blastn()print(results)
[{"query":{"start":1,"end":46,"bases":"ACGTGATTCGTCGTGTAGTTGAGTGTTACGTTGCATGTCGT-ACGTG","strand":1,"length":80,"sequence_id":"11e17df2-579f-4234-a1e6-f4e3fadfe277","circular":false,"name":"<unknown name>","origin_key":"bbadd55c-9413-4394-a23c-0da983630b98","origin_record_id":"<unknown id>","origin_sequence_length":80},"subject":{"start":1,"end":47,"bases":"ACGTGATTCGTCGTGTAGTTGAGTGTTACGTTGCATGTCGTTACGTG","strand":1,"length":51,"sequence_id":"69248d23-1044-4a75-80c9-53b999796d48","circular":false,"name":"<unknown name>","origin_key":"1f627d51-93df-458b-ba36-9b5a7b483a4d","origin_record_id":"<unknown id>","origin_sequence_length":51},"meta":{"query acc.":"11e17df2-579f-4234-a1e6-f4e3fadfe277","subject acc.":"69248d23-1044-4a75-80c9-53b999796d48","score":43,"evalue":0,"bit score":80,"alignment length":47,"identical":46,"gap opens":1,"gaps":1,"query length":80,"q. start":1,"q. end":46,"subject length":51,"s. start":1,"s. end":47,"subject strand":"plus","query seq":"ACGTGATTCGTCGTGTAGTTGAGTGTTACGTTGCATGTCGT-ACGTG","subject seq":"ACGTGATTCGTCGTGTAGTTGAGTGTTACGTTGCATGTCGTTACGTG","span_origin":true}}]
对循环主题和查询运行blast
pyblast还处理循环主题和查询的对齐。如下所示，我们将主题（1到50）与循环查询（82/origin到30）完全对齐。循环主题和循环查询可以混合在一起，也可以是多个查询。
seq = "ACGTTGTAGTGTAGTTGATGATGATGTCTGTGTCGTGTGATGTGCTGTAGTGTTTAGGGGCGGCGCGGAGTATGCTG"
queries = [
SeqRecord(Seq(seq))
]
subjects = [
SeqRecord(Seq(seq[-20:] + seq[:30]))
]
# pyblast requires a 'topology' annotation on the SeqRecords.
# we can make records circular or linear using `make_linear` or `make_circular` methods
subjects = make_circular(subjects)
queries = make_circular(queries)
blast = BioBlast(subjects, queries)
results = blast.quick_blastn()
print(results)
[{"query":{"start":82,"end":30,"strand":1,"...":"..."},"subject":{"start":1,"end":50,"strand":1,"...":"..."},"meta":{"...":"..."}]
生物工厂
在某些情况下，我们希望为不同类型的路线共享相同的序列。例如，我们可能希望将一组底漆和一组模板与相同的查询记录对齐。在这种情况下，我们可以使用bioblastfactory：
frompyblastimportBioBlastFactory# initialize a new factoryfactory=BioBlastFactory()# add records accessible by keywordfactory.add_records(records1,"primers")factory.add_records(records2,"templates")factory.add_records(records3,"queries")# we spawn new BioBlast alignmers from the keywords aboveprimer_alignment=factory("primers","queries")template_alignment=factory("templates","queries")# we can then run alignments, ensuring the queries in both results# refer to the exact same queryprimer_results=primer_alignment.quick_short_blastn()template_results=template_alignment.quick_blastn()
读取文件的实用程序
pyblast包括用于读取fasta和genbank文件的实用程序。
frompyblast.utilsimportload_glob,load_genbank_glob,load_fasta_glob# load many genbank files into a list of SeqRecords# 'topology' is automatically detected here# we enforce all record_ids to be unique (a requirement for pyblast)records1=load_genbank_glob("~/mydesigns/*.gb",force_unique_ids=True)# load many fasta files into a list of SeqRecords# 'topology' is NOT detected# we enforce all record_ids to be unique (a requirement for pyblast)records2=make_linear(load_fasta_glob("~/mydesigns/*.fasta"),force_unique_ids=True)
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