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wormbase.py
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import urllib.request as request
import bs4
import json
import pandas as pd
import time
import numpy as np
import itertools
#this one is for intron only not the total one
def wormbase_crawler(transcript,version):
'''
input : transcript --str ，為輸入的transcript 名稱
output: exon_intron --df，以dataframe形式儲存unspliced情況的各區域資料
SequenceLength --int,儲存spliced情況的sequence長度
'''
url = 'https://wormbase.org/rest/widget/transcript/'+transcript+'/sequences'
req = request.Request(url,headers ={"User-Agent":"Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/103.0.0.0 Safari/537.36"})
with request.urlopen(req) as response:
sequence = response.read().decode("utf-8")
# sequence = json.loads(sequence)
with open(f'mRNA_json_{version}/{transcript}.json','w') as f:
f.write(sequence)
# try:
# strand = sequence['fields']['unspliced_sequence_context']['data']['strand']
# except:
# strand = sequence['fields']['unspliced_sequence_context']['data']['strand']
# #辨別正反股
# if strand =='+':
# try:
# exon_intron = pd.DataFrame(sequence['fields']['unspliced_sequence_context']['data']['positive_strand']['features'])
# SequenceLength =len(sequence['fields']['spliced_sequence_context']['data']['positive_strand']['sequence'])
# except:
# exon_intron = pd.DataFrame(sequence['fields']['unspliced_sequence_context_with_padding']['data']['positive_strand']['features'])
# SequenceLength =len(sequence['fields']['spliced_sequence_context_with_padding']['data']['positive_strand']['sequence'])
# elif strand =='-':
# try:
# exon_intron = pd.DataFrame(sequence['fields']['unspliced_sequence_context']['data']['negative_strand']['features'])
# SequenceLength =len(sequence['fields']['spliced_sequence_context']['data']['negative_strand']['sequence'])
# except:
# exon_intron = pd.DataFrame(sequence['fields']['unspliced_sequence_context_with_padding']['data']['negative_strand']['features'])
# SequenceLength =len(sequence['fields']['spliced_sequence_context_with_padding']['data']['negative_strand']['sequence'])
return("", "")
## 用來爬歸類在cds的transcript （不確定分類方式，但有多此種類別）
def wormbase_crawler_cds(transcript,version):
'''
input : transcript --str ，為輸入的transcript 名稱
output: exon_intron --df，以dataframe形式儲存unspliced情況的各區域資料
SequenceLength --int,儲存spliced情況的sequence長度
'''
url = 'https://wormbase.org/rest/widget/cds/'+transcript+'/sequences'
req = request.Request(url,headers ={"User-Agent":"Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/103.0.0.0 Safari/537.36"})
with request.urlopen(req) as response:
sequence = response.read().decode("utf-8")
# sequence = json.loads(sequence)
# print("this")
with open(f'mRNA_json_{version}/{transcript}.json','w') as f:
f.write(sequence)
# print("that")
# #print(sequence)
# strand = sequence['fields']['cds_sequence']['data']['strand']
# if strand =='+':
# exon_intron = pd.DataFrame(sequence['fields']['cds_sequence']['data']['positive_strand']['features'])
# SequenceLength = len(sequence['fields']['cds_sequence']['data']['positive_strand']['sequence'])
# elif strand =='-':
# exon_intron = pd.DataFrame(sequence['fields']['cds_sequence']['data']['negative_strand']['features'])
# SequenceLength = len(sequence['fields']['cds_sequence']['data']['negative_strand']['sequence'])
return("", "")
# def (transcript):
# '''
# input : transcript --str ，為輸入的transcript 名稱
# output: exon_intron --df，以dataframe形式儲存unspliced情況的各區域資料
# SequenceLength --int,儲存spliced情況的sequence長度
# '''
# url = 'https://wormbase.org/rest/widget/transcript/'+transcript+'/sequences'
# req = request.Request(url,headers ={"User-Agent":"Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/103.0.0.0 Safari/537.36"})
# with request.urlopen(req) as response:
# sequence = response.read().decode("utf-8")
# sequence = json.loads(sequence)
if __name__ =='__main__':
ExonIntron,SequenceLength = wormbase_crawler(transcript='C05C12.6.1',version = 285)
# ExonIntron,SequenceLength= wormbase_crawler_cds(transcript= 'B0213.1')
# print(ExonIntron)
# print(SequenceLength)
# IntronCount =(ExonIntron.type == 'exon').sum()-1
# FivePrimeNumber = 0
# try:
# FivePrime_df = ExonIntron[ExonIntron['type']=='five_prime_UTR']
# for j in range(len(FivePrime_df)):
# FivePrimeNumber += FivePrime_df.iloc[j]['stop'] - FivePrime_df.iloc[j]['start'] + 1
# except:
# FivePrimeNumber = 0