Question

I have a FASTA-format file containing my assembled transcripts called asm.fasta. My instructions are to create a python script that will leave my file containing only the assembled transcripts that are 300 base pairs or longer.

Answer 1

You want to parse the FASTA sequence into python,you can do it this way:

def fasta_reader(filename):
  from Bio.SeqIO.FastaIO import FastaIterator
  with open(filename) as handle:
    for record in FastaIterator(handle):
      yield record

for entry in fasta_reader("file.fasta"):
  print strentry.id) #This is header of fasta entry
  print str(entry.seq) #This is sequence of specific fasta entry