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| """ | |
| Helper function | |
| """ | |
| def get_sequence_example(example): | |
| print(example) | |
| if example.startswith("Amino Acid Long Sequence"): | |
| return """\ | |
| >CCP45025.1|FEATURES|hmdarg|isoniazid|kasA | |
| GARAGVMTPVSACSSGSEAIAHAWRQIVMGDADVAVCGGVEGPIEALPIAAFSMMRAMST | |
| RNDEPERASRPFDKDRDGFVFGEAGALMLIETEEHAKARGAKPLARLLGAGITSDAFHMV | |
| APAADGVRAGRAMTRSLELAGLSPADIDHVNAHGTATPIGDAAEANAIRVAGCDQAAVYA | |
| PKSALGHSIGAVGALESVLTVLTLRDGVIPPTLNYETPDPEIDLDVVAGEPRYGDYRYAV | |
| NNSFGFGGHN | |
| >gi:505065763:ref:WP_015252865.1:|FEATURES|deeparg|tunicamycin|tmrB | |
| GSFGSGKTQTAFELHRRLNPSYVYDPEKMGFALRSMVPQEIAKDDFQSYPLWRAFNYSLL""" | |
| elif example.startswith("Amino Acid Short Sequence"): | |
| return """\ | |
| >gi:505065763:ref:WP_015252865.1:|FEATURES|deeparg|tunicamycin|tmrB_0 | |
| RGIIIVPMTIVYPEYFNEIIGRLRQEGRIV | |
| >AGQ48857.1|FEATURES|hmdarg|pleuromutilin|eatAv_0 | |
| GNFSIYEEQKKLRDEFEMAQNEKLKKEVSR""" | |
| elif example.startswith("Nucleotide Long Sequence"): | |
| return """\ | |
| >AJ635405|FEATURES|resfinder|beta-lactam|blaLEN9 | |
| GGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGCTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGTCGACGGGATGACGATCGGCGAACTCTGTGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGT""" | |
| elif example.startswith("Nucleotide Short Sequence"): | |
| return """\ | |
| >S60108|FEATURES|resfinder|aminoglycoside|kgmB_0 | |
| CCGCACCCGGCTCCCGGACCCGGCGATCCCGAGGACCCGAGGCTGGCGGAGGTCGTCGACGCGGTCCGGTCCAGCAGGCGCTACCAGAGCGTCGCGCCCG | |
| >APOK01000044|FEATURES|resfinder|beta-lactam|blaOXA-290_0 | |
| ACATATGATGGGCAAACATTTCAAGAATATGGCAATGCGTTGAGTCGATCGAATACGGCTTATATTCCAGCCTCAACCTTCAAGATGTTAAATGCTCTGA""" | |
| def classify_sequence(sequence): | |
| nucleotide_chars = set("ATGC-") | |
| if all(char in nucleotide_chars for char in sequence): | |
| return "nt" # "Nucleotide" | |
| else: | |
| return "aa" # "Amino Acid | |
| def count_length_sequences(sequence): | |
| count_length_sequences = [] | |
| for i in sequence: | |
| count_length_sequences.append(len(i)) | |
| max_sequence_length = max(count_length_sequences) | |
| return max_sequence_length | |
| def classify_sequence_type_length(sequence): | |
| sequence_type = classify_sequence(sequence[0]) | |
| sequence_length = count_length_sequences(sequence) | |
| if sequence_type == "nt": # nucleotide | |
| if sequence_length > 150: | |
| sequence_length_type = "l" # "long" | |
| else: | |
| sequence_length_type = "s" # "short" | |
| else: # amino acid | |
| if sequence_length > 50 : | |
| sequence_length_type = "l" | |
| else: | |
| sequence_length_type = "s" | |
| return (sequence_type, sequence_length_type) | |