hello!
I'm using pyrosetta and biopython to write a code that folds proteins. I want to make the protein name a variable because I use it to label intput/output files throughout the code.
for fastafile in fastafiles:
for record in SeqIO.parse(fastafile, 'fasta'):
protein = record.id
sequence = str(record.seq)
pose = pose_from_sequence(sequence)
pose.pdb_info().name('%s' % protein)
dump_pdb(pose, '%s_input_518.pdb' % protein)
input_pose = pose_from_pdb('%s_input_518.pdb' % protein)
but when I run this, the record.id comes out like this
print(record.id)
>6Q21_1|Chains
the same thing happens when I try record.name. how do I fix it so that it doesn't include the "_1|Chains" part?
I'm new to biopython and coding in general so any tips are greatly appreciate!
1 answer
If all of your IDs have a uniform format, you could address it by splitting the string, and removing the ">" character. For instance, this gives you the first element of the fasta header:
protein = ">6Q21_1|Chains"
# split the string by pipe char and take only the first element
protein = protein.split("|")[0]
protein = protein.replace(">","")
# get rid of the underscore
protein = protein.split("_")[0]
print(protein)
If all your IDs have underscores, you could split on that in the first place.
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