Pairwise Alignment, Biopython : Bio.pairwise2

Question

[fareehakanwal90]

hello,

I am trying to do pairwise alignment of sequences in my data set. I am currently using Bio.pairwise2 module for this. My data set however, is saved in the files. Is there a way to pass files containing sequences to the paiwise2 as input argument? I know the longer way of reading it and then passing the value but it would really help if there is a direct way to pass file inputs to Bio.pairwise2.

[Kirill Tsyganov]

Can you post some of your python code that you have attempted? Also can give a bit more information on the file types and the data you are trying to compare.

[Kirill Tsyganov]

In python easiest way is to use sys.argv[1].

Answer 1

[Peter]

No, there isn't. You might be interested in calling out to something like EMBOSS needleall instead?

http://emboss.sourceforge.net/apps/release/6.6/emboss/apps/needleall.html