On Jun 11, 3:39 am, Elfine Peterson Tjio <[EMAIL PROTECTED]> wrote: > I'm trying to make a program that reads Fasta file and print it out. I used > the SeqIO module and the results is: > > 'ATGGTCAT....SingleAlphabet()' > > For this purpose, should I use SeqIO or Fasta? > > for example: > > from Bio import SeqIO > > or > > from Bio import Fasta > > I want it to print every letter. Can anyone point me to the right direction. > The newest biopython tutorial or book recommendation will be appreciated, too.
As I understand it, a "Fasta" file is a text file, correct? If so, this should be trivial with Python. I created a file with the following data from http://en.wikipedia.org/wiki/Fasta_format: >gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus] LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV EWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLG LLILILLLLLLALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVIL GLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX IENY Then I did the following to read it: >>> fil = open(r'c:\test\fasta.txt') >>> for f in fil.readlines(): if '>' in f: print f else: for letter in f: print letter That seemed to work for me. You probably don't want to print the first line, but that's easily fixed. Hope that helps. Mike -- http://mail.python.org/mailman/listinfo/python-list
