Append only sequence itself to list, no metadata
1
1
Entering edit mode
2.8 years ago

when doing this:

from Bio.Alphabet import generic_protein
from Bio.Seq import Seq

    seq_records = SeqIO.parse(filename, 'fasta', alphabet=generic_protein)
    for record in seq_records:
        total.append(record.seq)
    print(total)

I get the output

[Seq('SRTRMKLDNKTQVGVHDQGVDGMSKQLMPKYTYVLKIILWCVAPYREDARFWMC...HLL', ProteinAlphabet()), Seq('YMQGCKKQRMRRRCNKYHATIIMNIMHDYQDVSWFTIQDSPLQYPNYQPWSCTI...IDM', ProteinAlphabet()), Seq('RLLFDEVVFTITPRYFYQLEDLYFNGLAYQIWARFARAINTLIRYHGCMQQHIK...CGQ', ProteinAlphabet()), Seq('RWPMDQFGCFMAGNWEAYGGSIFFCMHHFFLNYMNISSQTVWLGNTKWVDTYSC...DCA', ProteinAlphabet()), Seq('NFPGLFRDRPQTEDRTVKYLEGIAHLEINDAQVWLWFSDKDTCRRPEYNQYIFV...KVD', ProteinAlphabet()), Seq('TGVFYSWGWFADEVLVDTWQNTSEYEDPPHWDFYVFTCYNVLRNWWGESSWPGL...NHP', ProteinAlphabet()), Seq('HFYIGLFEMLSFEGMTDTIITMTQNVNQSNVTDADYWDKGIARHGSQRWAWYAD...HKN', ProteinAlphabet()), Seq('NMKVGPYWGCYACWQFPYFDNCFEPKNDMILEECDAYHPLLRRRCHWYFFALKP...SMV', ProteinAlphabet()), Seq('VEQWVLTHPVDPVCACDTPHSQQNQEGIANHAGLHAKYNVPFERIYWWCTSYLG...TSN', ProteinAlphabet()),...

Why don't I just get a list of the sequences themself? If I just use print(record.seq) for each record individually I just get the sequences themselves. I want a list of only the sequences.

python biopython fasta • 551 views
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2
Entering edit mode
2.8 years ago

Replace total.append(record.seq) with total.append(str(record.seq)).

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