Mercurial > repos > artbio > fetch_fasta_from_ncbi

comparison fetch_fasta_from_NCBI.py @ 6:4af77e1af12a draft default tip

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi commit 1a90ac7cdeb35399011207ab43c78043fd5c7287
author artbio
date Sat, 14 Oct 2023 22:34:56 +0000
parents 706fe8139955
children
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5:706fe8139955 6:4af77e1af12a
203 self.logger.debug("Going to read, de code was : %s", 203 self.logger.debug("Going to read, de code was : %s",
204 str(response_code)) 204 str(response_code))
205 fasta = response.read() 205 fasta = response.read()
206 self.logger.debug("Did all that") 206 self.logger.debug("Did all that")
207 response.close() 207 response.close()
208 if((response_code != 200) or 208 if ((response_code != 200) or
209 (b"Resource temporarily unavailable" in fasta) or 209 (b"Resource temporarily unavailable" in fasta) or
210 (b"Error" in fasta) or (not fasta.startswith(b">"))): 210 (b"Error" in fasta) or (not fasta.startswith(b">"))):
211 serverTransaction = False 211 serverTransaction = False
212 if (response_code != 200): 212 if (response_code != 200):
213 self.logger.info("urlopen error: Response code is not\ 213 self.logger.info("urlopen error: Response code is not\
258 response.close() 258 response.close()
259 time.sleep(1) 259 time.sleep(1)
260 return querylog 260 return querylog
261 261
262 def sanitiser(self, db, fastaseq): 262 def sanitiser(self, db, fastaseq):
263 if(db not in "nuccore protein"): 263 if (db not in "nuccore protein"):
264 return fastaseq 264 return fastaseq
265 regex = re.compile(r"[ACDEFGHIKLMNPQRSTVWYBZ]{49,}") 265 regex = re.compile(r"[ACDEFGHIKLMNPQRSTVWYBZ]{49,}")
266 sane_seqlist = [] 266 sane_seqlist = []
267 seqlist = fastaseq.split('\n\n') 267 seqlist = fastaseq.split('\n\n')
268 for seq in seqlist[:-1]: 268 for seq in seqlist[:-1]: