def export( self ):
print( "Exporting..." )
# Get all transcript IDs
results = db_session.query( Transcript.id ).all()
n = 0
target_filepath = settings.data_folder + "/transcripts.fasta"
output_handle = open( target_filepath, "w" )
for result in results:
transcript_id = result[ 0 ]
seq_record = Transcript( transcript_id ).get_sequence()
if seq_record is None:
print( "Missing sequence for [" + transcript_id + "]" )
continue
seq_record.id = transcript_id
SeqIO.write( seq_record, output_handle, "fasta" )
n += 1
if n % 100 == 0:
print( "[{}] sequences written".format( n ) )
output_handle.close()
print( "...Saved transcripts to [{}]".format( target_filepath ) )
def export(self):
print("Exporting...")
from Bio import SeqIO
from database import db_session
from models import Transcript
import settings
# Get all transcript IDs
results = db_session \
.query(Transcript.id) \
.all()
n = 0
target_filepath = settings.data_folder+"/transcripts.fasta"
output_handle = open(target_filepath, "w")
for result in results:
transcript_id = result[0]
seq_record = Transcript(transcript_id).get_sequence()
if seq_record == None:
print ("Missing sequence for ["+transcript_id+"]")
continue
seq_record.id = transcript_id
SeqIO.write(seq_record, output_handle, "fasta")
n += 1
if n % 100 == 0:
print("["+str(n)+"] sequences written")
output_handle.close()
print("...Saved transcripts to ["+target_filepath+"]")