diff tools/filters/axt_to_concat_fasta.py @ 0:9071e359b9a3

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/filters/axt_to_concat_fasta.py	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,51 @@
+#!/usr/bin/env python
+"""
+Adapted from bx/scripts/axt_to_concat_fasta.py
+"""
+from galaxy import eggs
+import pkg_resources
+pkg_resources.require( "bx-python" )
+
+import sys
+import bx.align.axt
+
+def usage(s=None):
+	message = """
+axt_to_fasta species1 species2 < axt_file > fasta_file
+"""
+	if (s == None): sys.exit (message)
+	else:           sys.exit ("%s\n%s" % (s,message))
+
+
+def main():
+
+	# check the command line
+	species1 = sys.argv[1]
+	species2 = sys.argv[2]
+
+	# convert the alignment blocks
+
+	reader = bx.align.axt.Reader(sys.stdin,support_ids=True,\
+	                             species1=species1,species2=species2)
+	sp1text = list()
+	sp2text = list()
+	for a in reader:
+		sp1text.append(a.components[0].text)
+		sp2text.append(a.components[1].text)
+	sp1seq = "".join(sp1text)
+	sp2seq = "".join(sp2text)
+	print_component_as_fasta(sp1seq,species1)
+	print_component_as_fasta(sp2seq,species2)
+		
+
+
+# $$$ this should be moved to a bx.align.fasta module
+
+def print_component_as_fasta(text,src):
+	header = ">" + src
+	print header
+	print text
+
+
+if __name__ == "__main__": main()
+