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afrendeiro/getChrSizesFromFasta.py

Last active January 4, 2016 21:09
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Make tab-delimited chromossome size file from fasta genome
Raw
getChrSizesFromFasta.py
import csv
from Bio import SeqIO
fastagenome = "data/oikopleura/assembly/Oikopleura_reference_unmasked_v3.0.fa"
output = "data/oikopleura/assembly/Oikopleura_reference_chrSizes.tsv"
myfile = open(output, "wb")
spamwriter = csv.writer(myfile, delimiter='\t', quoting=csv.QUOTE_MINIMAL)
for seq_record in SeqIO.parse(fastagenome, "fasta"):
spamwriter.writerow([str(seq_record.id) , str(len(seq_record))])
myfile.close()
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