This is a test version of Biostars. For the public version, visit https://www.biostars.org.
extract list of positions from fasta file biopython

I have a list of positions of interest eg:

10
20
1000
4000000

I want to extract the base call at these positions from a fasta file using biopython. This is what I have tried:

query_dic ={}
with open(line) as pos_file:
                for x in pos_file:
                        for seq_record in SeqIO.parse(query_file, "fasta"):
                                nuc = seq_record[x] 
                                query_dic[x]=nuc
The error message says 'invalid index' - what is wrong?
biopython python
• 4,145 views • link
written by s.i.lipworth • s.i.lipworth

Steps:

  1. read the positions as list

  2. iterate FASTA records:

    for seq_record in SeqIO.parse(query_file, "fasta"):
       for x in positions:
              # get the base at position x
              seq_record.seq[x-1]
• 0 views • link
written by shenwei356 shenwei356

Firstly, you should get the right Chromosome; then extract the base from fasta sequence.

• 0 views • link
written by Ben Ben

Does you FASTA file have one sequence in it, or many?

If one, you only need to open the FASTA file once, and you should use SeqIO.read for that.

If many, you need to know which sequence each of the values x refers to. Perhaps SeqIO.index would be useful here for loading the relevant record from a multiple sequence FASTA file?

• 0 views • link
written by Peter Peter

0 answers

No answers yet.

Log in to answer this question.

More posts like this