bioinformatics Common File Formats Sequence Writing In fasta Format
Example
This a python example function for sequence writing in fasta format.
Parameters:
- filename(String) - A file name for writing sequence in fasta format.
- seq(String) - A DNA or RNA sequence.
- id(String) - The ID of the given sequence.
- desc(String) - A short description of the given sequence.
import math
def save_fsta(filename,seq,id,desc):
fo = open(filename+'.fa',"a")
header= str(id)+' <'+desc+'> \n'
fo.write(header)
count=math.floor(len(seq)/80+1)
iteration = range(count)
for i in iteration:
fo.write(seq[80*(i):80*(i+1)]+'\n')
fo.write('\n \n')
fo.close()
Another way is using textwrap
import textwrap
def save_fasta(filename,seq, id, desc):
filename+='.fa'
with open(filename, 'w') as f:
f.write('>'+id+' <'+desc+'>\n');
text = textwrap.wrap(seq,80);
for x in text:
f.write(x+'\n');
