Wrote code to map ids to sequence objects.

shailen · May 25, 2011 · 5bea51d · 5bea51d
1 parent 2bf05ed
commit 5bea51d
Show file tree

Hide file tree

Showing 5 changed files with 15 additions and 0 deletions.
diff --git a/README b/README
diff --git a/fc_rough.py b/fc_rough.py
@@ -1,4 +1,19 @@
 #!/usr/bin/python
 
+from Bio import Phylo, AlignIO
+
 tree_file = "sample_tree.ml"
 msa_file = "sample_alignment.msa"
+new_sequence_file = "new_sequence.fasta"
+
+tree = Phylo.read(tree_file, "newick")
+msa = AlignIO.read(msa_file, "fasta")
+
+# Note: the name of the tree leaf nodes is going to be the 
+# same as the id of each msa entry
+
+sequence_msa_map = {}
+for entry in msa:
+    sequence_msa_map[entry.id] = entry
+
+
diff --git a/new_sequence.fasta b/new_sequence.fasta
diff --git a/sample_alignment.msa b/sample_alignment.msa
diff --git a/sample_tree.ml b/sample_tree.ml