Question: Trouble with sliding window for FASTA file in python
gravatar for asidhu
10 days ago by
asidhu10 wrote:

I'm struggling to create a sliding window that will loop through sequences (first 30 nucleotides) and identify the forward primer to later trim the primer from the sequences. The file being used as a FASTA file with around 3400 sequences.

filename = "paired.fasta"

min_length = 150
mismatches = 3

fprimer = np.asarray(list("GTGCCAGCMGCCGCGGTAA"))
f_len = len(fprimer)

rprimer = np.asarray(list(reverse_complement(rprimer)))
r_len = len(rprimer)

forward_region = sequences[0:30]
reverse_region = sequences[-30]
winSizeF = len(forward_region) - len(fprimer) + 1
winSizeR = len(reverse_region) - len(rprimer) + 1

for header, sequence in good_reads.items():
    for i in range(winSizeF):
        start = i
        end = i + len(fprimer)
        target = forward_region[start:end]
        distance = hamming(fprimer, winSizeF)
        if distance == 0:

When I run the for loop I get the following error:

line 103
    """ for header, data in sequences.items():
SyntaxError: invalid syntax

Any help with this sliding window would be appreciated.

python • 117 views
ADD COMMENTlink written 10 days ago by asidhu10

The code with the error is not shown.

line 103
    """ for header, data in sequences.items():
SyntaxError: invalid syntax
ADD REPLYlink written 10 days ago by WouterDeCoster35k

Your line 103 is not in your example, maybe you missed a paranthesis or a braket before line 103

ADD REPLYlink written 9 days ago by Bastien Hervé2.7k
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