Converting fasta file into list with names and sequences
1
0
Entering edit mode
4.0 years ago
anme • 0
 def ReadFastaFile(filename):
  fileObj = open(filename, 'r')
  sequences = []
  seqFragments = []
  for line in fileObj:
    if line.startswith('>'):
      if seqFragments:
        sequence = ''.join(seqFragments)
        sequences.append(sequence)
      seqFragments = []
    else:
      seq = line.rstrip()
      seqFragments.append(seq)
  if seqFragments:
    sequence = ''.join(seqFragments)
    sequences.append(sequence)
  fileObj.close()
  return sequences

I want to get list with name and sequence This code gives me a list with only the sequence, because i first thought i would not need the name for what I want to do. But now i realized that it would be good to also include the names. Maybe if possible also in a dictionary form, so that it is like: dict = {'name':sequence}. Does somebody have I idea how to alter the code to achieve this?

python fasta list dictionary • 6.1k views
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can you post the example output format you want?

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0
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example output (would be happy about one of both): list = [['name1','sequence1'],['name2'],['sequence2'].....]

or

dictionary = {'name1':'sequence1','name2':['sequence2'.....} (but i am not sure right no if you can have both elements as strings in a dictionary?)

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1
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not sure about python...but in perl i would create a hash

list = [['name1','sequence1'],['name2'],['sequence2'].....] hash = [['key1','value1'],['key2'],['value2'].....]

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3
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4.0 years ago

Could also be a oneliner:

from Bio import SeqIO
seq_dict = {rec.id : rec.seq for rec in SeqIO.parse("myfile.fasta", "fasta")}

If you want to learn more about what's going on in this line, read about biopython, and list and dict comprehensions

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thank you very much, it worked! :)

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Glad to help.

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