'Extrude Acc (Gene ID or accession number) from a fasta file

What does ".gb\\|(.*)\\|.*","\\1 in the function gsub mean?

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regexbioinformaticsgsubfasta


Solution 1:[1]

If you have a single FASTA sequence in the file you can solve the problem by reading the first line of the file and then split it by the pipe character |.

If you have multiple sequences then you can read the first character for each line and look for the > character.

Here is a code example in Python. If you need another ID then you can change the index.

with open('AE004437.faa') as fh:
    header_line = fh.readline()
    ids = header_line.split('|')
    gene_ids = ids[3]

Sources

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Source: Stack Overflow

Solution Source
Solution 1 liveware

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