parsing a fastq file using biopython
I am trying to store reads from a fastq file into a text file (tab delimited). I use the following code which just stores the read_id and sequence from the fastq file. What should I add to store the third and fourth rows of each entry? Thanks
def parsing_readid(input_file):
f_read = open ('read1.txt','a')
for record in SeqIO.parse(open(input_file,"rU"),"fastq"):
f_read.write("%s\t%s\n" %record.id,record.seq))
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Usually I work with FastqGeneralIterator to parse fastq files but... Have you tried record.qual to print out the read quality?
For other hand, the third line in fq format usually is only a "+" or a "+" followed by the read_id, so, you can just print it like this:
f_read.write("@%s\t%s\t+\t%s\n" % record.id,record.seq, record.qual))
Hope it helps.
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