streamlit的参考资料
https://docs.streamlit.io/library/get-started/create-an-app
st.button https://docs.streamlit.io/library/api-reference/widgets/st.button
st.text_area https://docs.streamlit.io/library/api-reference/widgets/st.text_area
python io https://docs.python.org/3/library/io.html
io.StringIO 主要作用 python subprocess 调用blastn，blastn输出效果不生存到文件里，而是输出到屏幕，输出到屏幕的内容必要用io.StringIO转化一下才能被NCBIXML分析
https://janakiev.com/blog/python-shell-commands/
这个链接主要先容的是python subprocess 调用blastn，blastn输出效果不生存到文件里，而是输出到屏幕 ，然后怎样将输出到屏幕的内容生存到一个python 对象里
https://stackabuse.com/the-python-tempfile-module/
这个链接主要先容了怎样天生临时文件（用于存储用户上传的fasta文件）
https://stackoverflow.com/questions/23212435/permission-denied-to-write-to-my-temporary-file
临时文件写入内容的时间不知道为啥总是提示没有权限，这个链接里稍微有点先容
st.datatable https://docs.streamlit.io/1.3.0/library/api-reference/data/st.dataframe
https://www.metagenomics.wiki/tools/blast/blastn-output-format-6
blastn output format 6 的表头
st.file_uploader https://docs.streamlit.io/library/api-reference/widgets/st.file_uploader
完备代码
(还很不美满，只是勉强可以运行)
import streamlit as stimport tempfileimport osimport iofrom Bio import SeqIOimport subprocessfrom Bio.Blast import NCBIXMLimport pandas as pdst.title("Learn how to build web blast app using streamlit")# abc = st.text_area(label="paste your fasta here",# value=">seq1\nATCGA",# height=200)# #print(abc)# if st.button('save'):# # for line in abc:# # st.write(line)# with open('abc.txt','w') as fw:# fw.write(abc) # st.write("OK")# result = st.button("Click Here")# # # st.write(result)# print(os.getcwd())# if result:# with tempfile.TemporaryFile() as fp:# tmp = tempfile.NamedTemporaryFile(suffix=".fasta",delete=False)# st.write(tmp.name)# tmp.write(bytes(abc,'utf-8'))# tmp.seek(0)# with open(tmp.name,'r') as fr:# for line in fr:# st.write(line)# #os.write(new_file,b'abcde')# #st.write("OK")# #os.close(new_file)# # with open(tmp.name,'w') as fw:# # fw.write(abc)# st.write(":smile:") # you need to change this path to you ownblastn = "D:/Biotools/blast/ncbiblast/bin/blastn"db = 'D:/Bioinformatics_Intro/streamlit/uploadfiles/blastdb/cpvirus'tempfile.tempdir = "D:/Bioinformatics_Intro/streamlit/uploadfiles/temp"fasta = st.text_area(label="you can paste your fasta here", value=">seq1\nATCGA", height=400)runblastn = st.button("run blastn")names = "qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore".split()if runblastn: tmp = tempfile.NamedTemporaryFile(suffix=".fasta",delete=False) st.write(tmp.name) tmp.write(bytes(fasta,'utf-8')) tmp.seek(0) for rec in SeqIO.parse(tmp.name,'fasta'): st.write(rec.id) cmd = [blastn,'-db',db,'-query',tmp.name,'-evalue','0.0001','-outfmt','6'] process = subprocess.Popen(cmd,stdout=subprocess.PIPE, stderr=subprocess.PIPE, universal_newlines=True) stdout,stderr = process.communicate() # for record in NCBIXML.parse(io.StringIO(stdout)): # st.write(record.query) df = pd.read_csv(io.StringIO(stdout),sep="\t",header=None,names=names) st.dataframe(df) tmp.close() os.unlink(tmp.name) uploaded_file = st.file_uploader("or upload your fasta file here")if uploaded_file is not None: bytes_data = uploaded_file.getvalue() #print(type(bytes_data)) #st.write(bytes_data) tmp = tempfile.NamedTemporaryFile(suffix=".fasta",delete=False) st.write(tmp.name) try: tmp.write(bytes_data) tmp.seek(0) with open(tmp.name,'r') as fr: for line in fr: if line.startswith(">"): st.write("input seq id is: %s"%(line.strip().replace(">",""))) cmd = [blastn,'-db',db,'-query',tmp.name,'-evalue','0.0001','-outfmt','6'] process = subprocess.Popen(cmd,stdout=subprocess.PIPE, stderr=subprocess.PIPE, universal_newlines=True) stdout,stderr = process.communicate() # for record in NCBIXML.parse(io.StringIO(stdout)): # st.write(record.query) df = pd.read_csv(io.StringIO(stdout),sep="\t",header=None,names=names) st.dataframe(df) finally: tmp.close() os.unlink(tmp.name)运行代码
streamlit run main.py怎样摆设呢？
在查资料吧
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