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+"]")