# HG changeset patch
# User drosofff
# Date 1446045913 14400
# Node ID 79cb7620843d401b820c403472a7c83f137305d1
# Parent  0bdc5a73c8d1fb2ab086c7bfecae6693b432ca64
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit e0a1114b735bf1af257456174f64e5ef8d205754-dirty

diff -r 0bdc5a73c8d1 -r 79cb7620843d retrieve_fasta_from_NCBI.py
--- 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
diff -r 0bdc5a73c8d1 -r 79cb7620843d retrieve_fasta_from_NCBI.xml
--- 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>