Closed:How to get fasta by gene id

Question

[Xylanaser]

Hey, I'm tired with this... I'm trying to get fasta sequences(~1000) by gene id. And i wrote several scrips ( with selenium ) and all is ok but sometimes all scripts breaks because of error ( database sometimes not found record, but this record exist :/ after 5 minuts i check or page infinite loading) even scripts as efetch from eutiles are stuck.... Anyone have solution for me? please

i have problem with exception handling :/

def name_add_missedIDs(name):
    split_name = name.split('.') 
    new_name = split_name[0] + '_missedIDs' + '.txt'
    return new_name

def name_add_result(name):
    split_name = name.split('.') 
    new_name = split_name[0] + '_sequences' + '.txt'
    return new_name


name = 'names.txt'

with open(name,'r')as file:
    from selenium import webdriver
    import re
    import time
    from selenium.common.exceptions import TimeoutException

    sentences_list = []
    for sentence in file:
        sentences_list.append(sentence)


    browser = webdriver.Chrome()
    counter = 0
    for phrase in sentences_list:
        counter += 1
        print(counter, phrase)
        browser.implicitly_wait(60)
        browser.get('https://www.ncbi.nlm.nih.gov/protein/?term=' + phrase )
        try:
            try:
                print('    try-1')
                time.sleep(3)
                browser.implicitly_wait(60)
                browser.find_element_by_css_selector('div.rprt:nth-child(1) > div:nth-child(2) > p:nth-child(1) > a:nth-child(1)').click()
                browser.implicitly_wait(60)
                time.sleep(3)
                browser.find_element_by_css_selector('#EntrezSystem2\.PEntrez\.Protein\.Sequence_ResultsPanel\.Sequence_DisplayBar\.Display').click()
                time.sleep(3)
                browser.implicitly_wait(60)
                browser.find_element_by_css_selector('#display_settings_menu_report > fieldset > ul > li:nth-child(5) > label').click()
            except:
                try:
                    print('    except-a')
                    time.sleep(3)
                    browser.implicitly_wait(60)
                    browser.find_element_by_css_selector('#EntrezSystem2\.PEntrez\.Protein\.Sequence_ResultsPanel\.Sequence_DisplayBar\.Display').click()
                    time.sleep(3)
                    browser.implicitly_wait(60)
                    browser.find_element_by_css_selector('#display_settings_menu_report > fieldset > ul > li:nth-child(5) > label').click()
                except:
                    if browser.find_element_by_css_selector('#msgportlet > li:nth-child(1) > span').text == 'The following id was not found in Protein:' \
                    or browser.find_element_by_css_selector('#msgportlet > li:nth-child(1) > span').text == 'Search failed!' or \
                    browser.find_element_by_css_selector('#msgportlet > li > span').text == 'The requested page does not exist.':
                        print("reload")
                        time.sleep(60)
                        browser.refresh()
                        browser.implicitly_wait(60)
                        browser.get('https://www.ncbi.nlm.nih.gov/protein/')
                        browser.implicitly_wait(60)
                        browser.get('https://www.ncbi.nlm.nih.gov/protein/?term=' + phrase )
                        try:
                            print('    try-1b')
                            time.sleep(3)
                            browser.implicitly_wait(60)
                            browser.find_element_by_css_selector('div.rprt:nth-child(1) > div:nth-child(2) > p:nth-child(1) > a:nth-child(1)').click()
                            browser.implicitly_wait(60)
                            time.sleep(3)
                            browser.find_element_by_css_selector('#EntrezSystem2\.PEntrez\.Protein\.Sequence_ResultsPanel\.Sequence_DisplayBar\.Display').click()
                            time.sleep(3)
                            browser.implicitly_wait(60)
                            browser.find_element_by_css_selector('#display_settings_menu_report > fieldset > ul > li:nth-child(5) > label').click()
                        except:
                            print('    except-b')
                            time.sleep(3)
                            browser.implicitly_wait(60)
                            browser.find_element_by_css_selector('#EntrezSystem2\.PEntrez\.Protein\.Sequence_ResultsPanel\.Sequence_DisplayBar\.Display').click()
                            time.sleep(3)
                            browser.implicitly_wait(60)
                            browser.find_element_by_css_selector('#display_settings_menu_report > fieldset > ul > li:nth-child(5) > label').click()
                            browser.implicitly_wait(60)
    time.sleep(5)
    sequence = browser.find_element_by_css_selector('#viewercontent1').text
    adding_gene_name = '>' + phrase.strip() + ' '
    sequence_with_gene_id = re.sub('>', adding_gene_name, sequence )
    with open(name_add_result(name), "a") as f:
        f.write(sequence_with_gene_id + '\n')
with open(name_add_missedIDs(name),'a') as missedIDs:
    seqs = open(name_add_result(name),'r') 
    for row in sentences_list:
        if row not in seqs:
            missedIDs.write(row)
    seqs.close()