1 | #!/usr/bin/env python |
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2 | |
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3 | from __future__ import division |
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4 | |
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5 | import sys |
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6 | from galaxy import eggs |
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7 | import pkg_resources; pkg_resources.require( "pysam" ) |
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8 | |
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9 | from pysam import csamtools |
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10 | from galaxy.visualization.tracks.summary import * |
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11 | |
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12 | def main(): |
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13 | |
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14 | input_fname = sys.argv[1] |
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15 | index_fname = sys.argv[2] |
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16 | out_fname = sys.argv[3] |
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17 | |
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18 | bamfile = csamtools.Samfile( filename=input_fname, mode='rb', index_filename=index_fname ) |
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19 | |
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20 | st = SummaryTree(block_size=25, levels=6, draw_cutoff=150, detail_cutoff=30) |
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21 | for read in bamfile.fetch(): |
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22 | st.insert_range(bamfile.getrname(read.rname), read.pos, read.pos + read.rlen) |
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23 | |
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24 | st.write(out_fname) |
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25 | |
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26 | if __name__ == "__main__": |
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27 | main() |
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