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Question: can not get the alignment result from needle alignment
0
gravatar for Medhat
3.5 years ago by
Medhat ♦ 8.2k
Texas
Medhat ♦ 8.2k wrote:

I am using this script to compare to sequence and parse the result:

 

from Bio.Emboss.Applications import NeedleCommandline
from Bio import AlignIO

needle_cline = NeedleCommandline(asequence="a.fa",
                bsequence="b.fa",
                gapopen=10, gapextend=0.5, outfile="needle.txt")

filename= "needle.txt"
format = "emboss"


alignments = list(AlignIO.parse(filename, format))

 

when i try to print the results in the alignments list it gives me only part of the last line 

like that

 

SingleLetterAlphabet() alignment with 2 rows and 2258 columns
TTGATGAGTGGGCACCATGATTGCCCGACTGTTATTACCGTCAA...TCT ref
TGGATGAGTGGGCACCATGATTGCCCGACTGTTATTACCGTCAA...T-- corr

 

any Idea?
alignment sequence • 851 views
ADD COMMENT • link •
modified 3.5 years ago by Kamil • 1.9k • written 3.5 years ago by Medhat ♦ 8.2k
0
gravatar for Kamil
3.5 years ago by
Kamil • 1.9k
Boston
Kamil • 1.9k wrote:

Consider checking the examples in the documentation for the MultipleSeqAlignment class returned by AlignIO.

I guess this might do what you want:

print alignments[:,:]
ADD COMMENT • link written 3.5 years ago by Kamil • 1.9k
1

I figured it I need to add another loop to get the sequence

 

for alignment in AlignIO.parse(filename, format):
  for sequence in alignment:
   print(sequence.seq)

ADD REPLY • link modified 3.5 years ago • written 3.5 years ago by Medhat ♦ 8.2k

I changed the method from parse to read like this 

alignments = AlignIO.read(filename, format)
print alignments[:,:]

 

but, the result is the same 

SingleLetterAlphabet() alignment with 2 rows and 2258 columns
TTGATGAGTGGGCACCATGATTGCCCGACTGTTATTACCGTCAA...TCT ref
TGGATGAGTGGGCACCATGATTGCCCGACTGTTATTACCGTCAA...T-- corr

any Idea?

ADD REPLY • link written 3.5 years ago by Medhat ♦ 8.2k
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