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