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

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi commit 1a90ac7cdeb35399011207ab43c78043fd5c7287

5:706fe8139955

                self.logger.debug("Going to read, de code was : %s",
                                  str(response_code))
                fasta = response.read()
                self.logger.debug("Did all that")
                response.close()
                if((response_code != 200) or
                   (b"Resource temporarily unavailable" in fasta) or
                   (b"Error" in fasta) or (not fasta.startswith(b">"))):
                    serverTransaction = False
                    if (response_code != 200):
                        self.logger.info("urlopen error: Response code is not\

        response.close()
        time.sleep(1)
        return querylog

    def sanitiser(self, db, fastaseq):
        if(db not in "nuccore protein"):
            return fastaseq
        regex = re.compile(r"[ACDEFGHIKLMNPQRSTVWYBZ]{49,}")
        sane_seqlist = []
        seqlist = fastaseq.split('\n\n')
        for seq in seqlist[:-1]:

6:4af77e1af12a

                self.logger.debug("Going to read, de code was : %s",
                                  str(response_code))
                fasta = response.read()
                self.logger.debug("Did all that")
                response.close()
                if ((response_code != 200) or
                   (b"Resource temporarily unavailable" in fasta) or
                   (b"Error" in fasta) or (not fasta.startswith(b">"))):
                    serverTransaction = False
                    if (response_code != 200):
                        self.logger.info("urlopen error: Response code is not\

        response.close()
        time.sleep(1)
        return querylog

    def sanitiser(self, db, fastaseq):
        if (db not in "nuccore protein"):
            return fastaseq
        regex = re.compile(r"[ACDEFGHIKLMNPQRSTVWYBZ]{49,}")
        sane_seqlist = []
        seqlist = fastaseq.split('\n\n')
        for seq in seqlist[:-1]: