gravatar for haasroni

3 hours ago by

Hi!
I am having an unexplained problem with the code I wrote, using SeqIO of Biopython.
I am doing several filtering steps for a fastq file using this code:

def extract_from_fastq(fq, output_fq):
    """
    Takes a fastq file, examines each read using all the above functions, and writes to a 
    new file the non-ambiguous reads
    :param fq: the fastq file
    :param output_fq: the output fastq file after filtering
    """
    input_iterator = SeqIO.parse(fq, "fastq")
    #goes over each record and tests if the read meets the requirements
    short_iterator = (rec for rec in input_iterator if filter_by_quality(rec.letter_annotations["phred_quality"]) 
        and filter_by_single_nucleotide_appearance(rec.seq) and filter_by_long_stretches_repeats(rec.seq))
    #writes to a new file after the conversion to a fastq format again
    SeqIO.write(short_iterator, output_fq, "fastq")

The problem is that the created file sometimes includes only the last record (the last 4 lines of the input fastq), so I assume it is overwritten in each iteration. However, sometimes it does work and I get all records in one file!

Any idea why is this and how to avoid it?

Thank you!!

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modified 3 hours ago

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3 hours ago
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haasroni0



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