Edit Seq object with Biopython
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Entering edit mode
7.5 years ago
joreamayarom ▴ 140

I am using SeqIO to load a fasta file and play my sequences. For the sake of my analysis, I want to eliminate a fixed number of bases to the left and right of my sequences. Nevertheless, whenever I try to eliminate the last ten bases I get an error saying

sequences = list (SeqIO.parse(file("myfile.fasta"), "fasta")
for sequence in sequences:
            del sequence.seq[-10:]

TypeError: 'Seq' object doesn't support item deletion

I assume trimming borders and doing other edits are very basic functionalities in bioinformatics (the same can be done in Perl in a couple of lines) but I am bit surprised I can't find a method to do such things in Python because the Seq objects are immutable. Is there a way to trim a Seq object?

python biopython • 2.0k views
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1
Entering edit mode
7.5 years ago
Sanjar ▴ 140
for sequence in sequences:
    sequence.seq = sequence.seq[10:-10]
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