diff --git a/sequence_extractor/exon_concatenation.py b/sequence_extractor/exon_concatenation.py index c5348ac1542304c2246ec4df4036a9fe99ac1d69..ccc01035fbd08236228178663c8a28b663c5213c 100644 --- a/sequence_extractor/exon_concatenation.py +++ b/sequence_extractor/exon_concatenation.py @@ -1,6 +1,7 @@ -def exon_concatenation: - fa = open("fasta.fa",'r') +def exon_concatenation(filename): + fa = open(filename,'r') lines = fa.readlines() + to_write_to_file = [] for x in range(int(len(lines)/2)): if x == 0: annotation = lines[0] @@ -9,5 +10,10 @@ def exon_concatenation: if lines[2*x] == lines[2*(x-1)]: read+= lines[(2*x)+1] else: + to_write_to_file.append(annotation) + to_write_to_file.append(read) annotation = lines[2*x] read = lines[(2*x)+1] + to_write_to_file.append(annotation) + to_write_to_file.append(read) + return to_write_to_file \ No newline at end of file