fsa = open(fasta_file)
#read the files in, open files with csv
with open('watermelon.gff', 'r') as melon:
#create a csv reader object
csvreader = csv.reader(melon, delimiter=',')
for line in csvreader:
if not line:
continue
else:
for line in melon:
print(line)
for fsa in SeqIO.parser("watermelon.fsa", "fasta"):
print(seq_record.id)
print(repr(seq_record.seq))
print(len(seq_record))
#sequence, source, features, begin, end, length, strand, phase,
attributes = line.split('\t')
fields = line.split('\t')
print(fields[3], fields[4]
#extract the DNA sequence from the genome for this feature
substring = []
trimmed_dna = dna[0]
from Bio import SeqIO
count=0
for rec in SeqIO.parser("data/SRR567585.fastq", "fastq"):
count+=1
print("%i reads" % count)
good_reads=(rec for rec in \
SeqIO.parse("data/SRR567585.fastq","fastq") \
if min(rec.letter_annotations["phred_quality"])>=20)
count=seqIO.write(good_reads, "good_quality.fastq", "fastq")
print("Saved %i reads" % count)