streamlit的參考資料

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 調(diào)用blastn钥屈，blastn輸出結(jié)果不保存到文件里窃祝，而是輸出到屏幕，輸出到屏幕的內(nèi)容需要用io.StringIO轉(zhuǎn)化一下才能被NCBIXML解析

https://janakiev.com/blog/python-shell-commands/

這個(gè)鏈接主要介紹的是python subprocess 調(diào)用blastn晶渠，blastn輸出結(jié)果不保存到文件里吼旧，而是輸出到屏幕 畜眨，然后如何將輸出到屏幕的內(nèi)容保存到一個(gè)python 對(duì)象里

https://stackabuse.com/the-python-tempfile-module/

這個(gè)鏈接主要介紹了如何生成臨時(shí)文件（用于存儲(chǔ)用戶(hù)上傳的fasta文件）

https://stackoverflow.com/questions/23212435/permission-denied-to-write-to-my-temporary-file

臨時(shí)文件寫(xiě)入內(nèi)容的時(shí)候不知道為啥總是提示沒(méi)有權(quán)限乘陪，這個(gè)鏈接里稍微有點(diǎn)介紹

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 的表頭

st.file_uploader https://docs.streamlit.io/library/api-reference/widgets/st.file_uploader

完整代碼

(還很不完善，只是勉強(qiáng)可以運(yùn)行)

import streamlit as st
import tempfile
import os
import io
from Bio import SeqIO
import subprocess
from Bio.Blast import NCBIXML
import pandas as pd

st.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 own
blastn = "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)

運(yùn)行代碼

streamlit run main.py

如何部署呢奄容？

在查資料吧

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小明的數(shù)據(jù)分析筆記本

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