Example #1
0
    def create(self):
        """POST /fastas: Create a new item."""
        # url_for('fastas')

        uploadfile = request.POST['uploadfile']
        fasta_file = open(os.path.join(permanent_store,
                                           uploadfile.filename.lstrip(os.sep)),
                                           'w')

        shutil.copyfileobj(uploadfile.file, fasta_file)
        uploadfile.file.close()
        fasta_file.close()
        handle = open( fasta_file.name )
#        if false:
        it = Bio.Fasta.Iterator(handle, Bio.Fasta.SequenceParser())
        seq = it.next()
        c.sequences = [] 
        output_string = "" 
        while seq:
            c.sequences.append(seq) 
            output_string += seq.description 
            output_string += "<br /> " 
            log.debug("seq : %s" ,  seq.description) 
            seq = it.next()

        handle.close()
        fastafile.formatdb(fasta_file.name) 

        log.debug('Hello Kenglish' )
        print "Hello Kenglish" 

        return render('/fastas/created_fasta.mako')
        return 'Successfully uploaded: %s, description: %s, <br /> results: <br /> %s ' % \
            (uploadfile.filename, request.POST['description'], output_string)
Example #2
0
def blast_2_files(input_filename,input_db):
    blast_db = fastafile.PERMANENT_STORE + input_db
    blast_file = fastafile.PERMANENT_STORE + input_filename
    if not os.path.exists(blast_db + ".nin"):
        fastafile.formatdb(blast_db)

    blast_out, error_handle = NCBIStandalone.blastall(BLAST_EXE, BLAST_PROGRAM, blast_db, blast_file)
    return blast_out 
Example #3
0
    def upload(self):
        message = "They called file upload " + request.POST["Filedata"].filename
        log.debug(message)
        uploadfile = request.POST["Filedata"]
        fasta_file = open(os.path.join(permanent_store,
                                           uploadfile.filename.lstrip(os.sep)),
                                           'w')

        shutil.copyfileobj(uploadfile.file, fasta_file)    
        uploadfile.file.close()
        fasta_file.close()
        fastafile.formatdb(fasta_file.name)
Example #4
0
    def create(self):
        """POST /flexfastas: Create a new item."""
        # url_for('flexfastas')
        message = "They called file upload " + request.POST["Filedata"].filename
        log.debug(message)
        uploadfile = request.POST["Filedata"]
        fasta_file = open(os.path.join(permanent_store,
                                           uploadfile.filename.lstrip(os.sep)),
                                           'w')

        shutil.copyfileobj(uploadfile.file, fasta_file)    
        uploadfile.file.close()
        fasta_file.close()
        fastafile.formatdb(fasta_file.name)