Mercurial > repos > drosofff > fetch_fasta_from_ncbi
changeset 1:79cb7620843d draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit e0a1114b735bf1af257456174f64e5ef8d205754-dirty
| author | drosofff |
|---|---|
| date | Wed, 28 Oct 2015 11:25:13 -0400 |
| parents | 0bdc5a73c8d1 |
| children | befdb392fece |
| files | retrieve_fasta_from_NCBI.py retrieve_fasta_from_NCBI.xml |
| diffstat | 2 files changed, 2 insertions(+), 5 deletions(-) [+] |
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--- a/retrieve_fasta_from_NCBI.py Sun Jun 21 14:29:45 2015 -0400 +++ b/retrieve_fasta_from_NCBI.py Wed Oct 28 11:25:13 2015 -0400 @@ -166,7 +166,7 @@ try: response = urllib2.urlopen(req) fasta = response.read() - if "Resource temporarily unavailable" in fasta: + if ("Resource temporarily unavailable" in fasta) or (not fasta.startswith(">") ): serverTransaction = False else: serverTransaction = True @@ -176,8 +176,6 @@ except httplib.IncompleteRead as e: serverTransaction = False self.logger.info("IncompleteRead error: %s" % ( e.partial ) ) - if self.dbname != "pubmed": - assert fasta.startswith(">"), fasta fasta = self.sanitiser(self.dbname, fasta) # time.sleep(1) return fasta
--- a/retrieve_fasta_from_NCBI.xml Sun Jun 21 14:29:45 2015 -0400 +++ b/retrieve_fasta_from_NCBI.xml Wed Oct 28 11:25:13 2015 -0400 @@ -1,4 +1,4 @@ -<tool id="retrieve_fasta_from_NCBI" name="Retrieve FASTA from NCBI" version="0.9.2"> +<tool id="retrieve_fasta_from_NCBI" name="Retrieve FASTA from NCBI" version="0.9.3"> <description></description> <command interpreter="python">retrieve_fasta_from_NCBI.py -i "$queryString" -d $dbname -o $outfilename -l $logfile </command> @@ -18,7 +18,6 @@ <param name="dbname" type="select" label="NCBI database"> <option value="nuccore">Nucleotide</option> <option value="protein">Protein</option> -<!-- <option value="pubmed">Pubmed (experimental)</option> --> </param> </inputs> <outputs>