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1 #!/usr/bin/env python
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2
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3 """
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4 Split into windows.
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5
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6 usage: %prog input size out_file
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7 -l, --cols=N,N,N,N: Columns for chrom, start, end, strand in file
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8 """
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9
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10 import sys, re, os
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11
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12 from galaxy import eggs
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13 import pkg_resources; pkg_resources.require( "bx-python" )
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14 from bx.cookbook import doc_optparse
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15 from galaxy.tools.util.galaxyops import *
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16
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17 def stop_err( msg ):
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18 sys.stderr.write( msg )
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19 sys.exit()
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20
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21 def main():
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22 # Parsing Command Line here
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23 options, args = doc_optparse.parse( __doc__ )
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24
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25 try:
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26 chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols )
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27 inp_file, winsize, out_file, makesliding, offset = args
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28 winsize = int(winsize)
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29 offset = int(offset)
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30 makesliding = int(makesliding)
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31 if strand_col_1 <= 0:
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32 strand = "+" #if strand is not defined, default it to +
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33 except:
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34 stop_err( "Data issue, click the pencil icon in the history item to correct the metadata attributes of the input dataset." )
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35
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36 fo = open(out_file,'w')
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37
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38 skipped_lines = 0
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39 first_invalid_line = 0
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40 invalid_line = None
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41 if offset == 0:
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42 makesliding = 0
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43
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44 for i, line in enumerate( file( inp_file ) ):
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45 line = line.strip()
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46 if line and line[0:1] != "#":
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47 try:
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48 elems = line.split('\t')
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49 if strand_col_1 != -1:
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50 strand = elems[strand_col_1]
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51 start = int(elems[start_col_1])
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52 end = int(elems[end_col_1])
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53 if makesliding == 0:
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54 numwin = (end - start)/winsize
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55 else:
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56 numwin = (end - start)/offset
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57 if numwin > 0:
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58 for win in range(numwin):
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59 elems_1 = elems
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60 elems_1[start_col_1] = str(start)
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61 elems_1[end_col_1] = str(start + winsize)
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62 fo.write( "%s\n" % '\t'.join( elems_1 ) )
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63 if makesliding == 0:
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64 start = start + winsize
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65 else:
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66 start = start + offset
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67 if start+winsize > end:
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68 break
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69 except:
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70 skipped_lines += 1
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71 if not invalid_line:
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72 first_invalid_line = i + 1
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73 invalid_line = line
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74
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75 fo.close()
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76
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77 if makesliding == 1:
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78 print 'Window size=%d, Sliding=Yes, Offset=%d' %(winsize, offset)
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79 else:
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80 print 'Window size=%d, Sliding=No' %(winsize)
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81 if skipped_lines > 0:
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82 print 'Skipped %d invalid lines starting with #%d: "%s"' % ( skipped_lines, first_invalid_line, invalid_line )
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83
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84 if __name__ == "__main__":
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85 main()
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