/tools/filters/axt_to_fasta.py

 1#!/usr/bin/env python
 2"""
 3Adapted from bx/scripts/axt_to_fasta.py
 4"""
 5from galaxy import eggs
 6import pkg_resources
 7pkg_resources.require( "bx-python" )
 8
 9import sys
10import bx.align.axt
11
12def usage(s=None):
13	message = """
14axt_to_fasta species1 species2 < axt_file > fasta_file
15"""
16	if (s == None): sys.exit (message)
17	else:           sys.exit ("%s\n%s" % (s,message))
18
19
20def main():
21
22	# check the command line
23	species1 = sys.argv[1]
24	species2 = sys.argv[2]
25
26	# convert the alignment blocks
27
28	reader = bx.align.axt.Reader(sys.stdin,support_ids=True,\
29	                             species1=species1,species2=species2)
30
31	for a in reader:
32		if ("id" in a.attributes): id = a.attributes["id"]
33		else:                      id = None
34		print_component_as_fasta(a.components[0],id)
35		print_component_as_fasta(a.components[1],id)
36		print
37
38
39# $$$ this should be moved to a bx.align.fasta module
40
41def print_component_as_fasta(c,id=None):
42	header = ">%s_%s_%s" % (c.src,c.start,c.start+c.size)
43	if (id != None): header += " " + id
44	print header
45	print c.text
46
47
48if __name__ == "__main__": main()
49