How to read in a fasta file (gene sequence) using dcc.Upload()

Dash Python
1

I copied the example and change function parse_contents() like this:

    def parse_contents(contents, filename, date):
        content_type, content_string, = contents.split(',')
        print(f'name:{type(filename)}\n{filename}\n')
        print(f'type:{type(content_type)}\n{content_type}\n')
        print(f'string:{type(content_string)}\n{content_string}\n')
        decoded = base64.b64decode(content_string)
        print(f'decoded:{decoded}\n')
        #seq1 = SeqIO.parse(decoded, "fasta")
        #print(f'seq parsed {seq1}')
        seq_str = str(decoded)
        print(f'seq_str: {seq_str}')
        #split into lines for output as P's
        seq_arr = seq_str.split('\n')
        #replace \n
        seq_arr = [x.replace("\n", " ") for x in seq_arr]
        print('seq_arr')
        for line in seq_arr:
            print(line)
        '''
        try:
            
            seq = SeqIO.read(decoded, "fasta")
            print(f'\n\nseq:{seq}')
        except Exception as e:
            print(e)
            return html.Div([
                'Error processing file upload'
            ])
        '''
        return html.Div([
            html.H5(filename),
            html.H6(datetime.datetime.fromtimestamp(date)),

            html.Div([
                html.P(line)
                for line in seq_arr
            ]),
            html.Hr(),

            #debugging content
            html.Div('Raw Content'),
            html.Pre(contents[0:100] + '...', style={
                'whiteSpace': 'pre-wrap',
                'wordBreak': 'break-all'
            })

        ])

But it won’t split on newline nor replace them in the above snippet.
fasta is a very common text format for sequences.
This is the output on stdout

string:<class 'str'>
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

decoded:b'>WP_011143314.1 L-lactate dehydrogenase [Gloeobacter violaceus]\nMQDRLFVSMEHPRALPETDLIKGAIVGAGAVGMAIAYSMLIQNTFDELVLVDIDRRKVEGEVMDLVHGIP\nFVEPSVVRAGTLADCRGVDVVVITAGARQREGETRLSLVQRNVEIFRGLIGEIMEHCPNAILLVVSNPVD\nVMTYVAMKLAGLPPSRVIGSGTVLDTARFRYLLAERLRVDPRSLHAYIIGEHGDSEVPVWSRANVAGAFL\nSEIEPAVGTPDDPAKMFEVFEHVKNAAYEIIERKGATSWAIGLATTQIVRAITRNQNRVLPVSVLMSGLH\nGIEEVCLAYPAVLNRQGIDRLVKFSLSPGEEEQLQRSARVMRQTLDGIQF\n\n'

seq_str: b'>WP_011143314.1 L-lactate dehydrogenase [Gloeobacter violaceus]\nMQDRLFVSMEHPRALPETDLIKGAIVGAGAVGMAIAYSMLIQNTFDELVLVDIDRRKVEGEVMDLVHGIP\nFVEPSVVRAGTLADCRGVDVVVITAGARQREGETRLSLVQRNVEIFRGLIGEIMEHCPNAILLVVSNPVD\nVMTYVAMKLAGLPPSRVIGSGTVLDTARFRYLLAERLRVDPRSLHAYIIGEHGDSEVPVWSRANVAGAFL\nSEIEPAVGTPDDPAKMFEVFEHVKNAAYEIIERKGATSWAIGLATTQIVRAITRNQNRVLPVSVLMSGLH\nGIEEVCLAYPAVLNRQGIDRLVKFSLSPGEEEQLQRSARVMRQTLDGIQF\n\n'
seq_arr
b'>WP_011143314.1 L-lactate dehydrogenase [Gloeobacter violaceus]\nMQDRLFVSMEHPRALPETDLIKGAIVGAGAVGMAIAYSMLIQNTFDELVLVDIDRRKVEGEVMDLVHGIP\nFVEPSVVRAGTLADCRGVDVVVITAGARQREGETRLSLVQRNVEIFRGLIGEIMEHCPNAILLVVSNPVD\nVMTYVAMKLAGLPPSRVIGSGTVLDTARFRYLLAERLRVDPRSLHAYIIGEHGDSEVPVWSRANVAGAFL\nSEIEPAVGTPDDPAKMFEVFEHVKNAAYEIIERKGATSWAIGLATTQIVRAITRNQNRVLPVSVLMSGLH\nGIEEVCLAYPAVLNRQGIDRLVKFSLSPGEEEQLQRSARVMRQTLDGIQF\n\n'

Newlines are there in the output div as well. How can I go from base64 to a Python string and then run strip and replace from a fasta file upload to dcc.Upload()?

Here is a raw sample that can be copy and pasted into a file called s.fasta to try:

>WP_011143314.1 L-lactate dehydrogenase [Gloeobacter violaceus]
MQDRLFVSMEHPRALPETDLIKGAIVGAGAVGMAIAYSMLIQNTFDELVLVDIDRRKVEGEVMDLVHGIP
FVEPSVVRAGTLADCRGVDVVVITAGARQREGETRLSLVQRNVEIFRGLIGEIMEHCPNAILLVVSNPVD
VMTYVAMKLAGLPPSRVIGSGTVLDTARFRYLLAERLRVDPRSLHAYIIGEHGDSEVPVWSRANVAGAFL
SEIEPAVGTPDDPAKMFEVFEHVKNAAYEIIERKGATSWAIGLATTQIVRAITRNQNRVLPVSVLMSGLH
GIEEVCLAYPAVLNRQGIDRLVKFSLSPGEEEQLQRSARVMRQTLDGIQF
2

You could try this:

def decode_file_content(file: str) -> str:
	"""
	Decode file content from base64 to ascii
	Parameters
	----------
	file: str, required
		A base64 encoded str

	Returns
	-------
	result:
		A decoded str
	"""
	return base64.b64decode(file.split(',')[-1].encode('ascii')).decode()
1 Like
3

Thanks! And for anyone else reading this the arrows next to functions (What does -> mean in Python function definitions? - Stack Overflow)