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#!/usr/bin/python3
"""
Application to convert AXT file to FASTA file. Reads an AXT file from standard
input and writes a FASTA file to standard out.
usage: %prog < axt_file > fasta_file
"""
__author__ = "Bob Harris (rsharris@bx.psu.edu)"
import sys
import bx.align.axt
def usage(s=None):
message = """
axt_to_fasta < axt_file > fasta_file
"""
if s is None:
sys.exit(message)
else:
sys.exit(f"{s}\n{message}")
def main():
# check the command line
if len(sys.argv) > 1:
usage("give me no arguments")
# convert the alignment blocks
reader = bx.align.axt.Reader(sys.stdin, support_ids=True, species1="", species2="")
for a in reader:
if "id" in a.attributes:
id = a.attributes["id"]
else:
id = None
print_component_as_fasta(a.components[0], id)
print_component_as_fasta(a.components[1], id)
print()
# $$$ this should be moved to a bx.align.fasta module
def print_component_as_fasta(c, id=None):
header = f">{c.src}_{c.start}_{c.start + c.size}"
if id is not None:
header += " " + id
print(header)
print(c.text)
if __name__ == "__main__":
main()
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