I have been using python 3.6 and biopython 1.72 to work with protein data files. I am using a protein sequence file (phylip format), for example:
14 678 Zebrafish LSSCGVVSGD LISVILPASS LEETQTSSAA AHQTHTDQQA GGSHVSSSSS Fugu LASCGIVSGD LIRVALIRAA LMAADAPDRA DDGGGHSEQA VAMATNQVS- Chicken LASCGIVSGD LIRVALIRAA LMAADAPDRA DDGGGHSEQA VAMATNQVS- Zebra LASYGIVPGD LICLLLEETD AKSSLPPPSS SSPPSLQNGR ETSTLTPKNQ
I want to manipulate the file in a way so that;
- I may get the number of columns which have all the same letters (amino acids)
- The number of columns which have at least 2 different amino acids (with no dashes).
- The number of columns which have any single dash.
I have iterated over the columns of the file with:
alignment = AlignIO.read(open("example.phy"), "phylip") def column(alignment): n = len(alignment.seq) for i in range(n): c =  for record in alignment: c.append(record.seq[i]) yield c
This returns the columns of the file, but I don't understand how I can manipulate them further.
Can I get some helpful suggestions?