This is my first time to use Biopython to convert my fastq files to fasta, unfortunately, I am getting two lines of sequences instead of one, although in the original fastq file, there is only one sequence.
E.g.
@SRR222178.1 HWI-EAS382:4:1:8:1240/1
GAAAAACATTAAACACAGTGGGAATATNNNTNTTGATGAGATTGTCAACATT
+
BAACB?A?
Well i think, this is the way of fasta format. First line contains title and other information, and from the seccond line it contains sequences.
https://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml
I hope you can easily remove the newline characters.
Or, you can extract only the sequence with the following command:
print SeqIO.read('myfile.fasta','fasta').seq
What program you are trying to run with it?
Good luck.
The reason for that is quite simple: The Python script uses the "old" standard of 60 chars per line of output. In the "good old times" before the rise of FASTQ that was not a problem and made things better "readable". Still, most programs should be able to handle these line feeds.
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