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1 #!/usr/bin/env python
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2 import os, sys, tempfile
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3
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4 assert sys.version_info[:2] >= ( 2, 4 )
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5
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6 def __main__():
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7 # Read parms.
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8 input_name = sys.argv[1]
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9 output_name = sys.argv[2]
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10 attribute_name = sys.argv[3]
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11
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12 # Create temp files.
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13 tmp_name1 = tempfile.NamedTemporaryFile().name
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14 tmp_name2 = tempfile.NamedTemporaryFile().name
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15
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16 # Do conversion.
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17 skipped_lines = 0
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18 first_skipped_line = 0
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19 out = open( tmp_name1, 'w' )
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20
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21 # Write track data to temporary file.
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22 i = 0
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23 for i, line in enumerate( file( input_name ) ):
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24 line = line.rstrip( '\r\n' )
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25
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26 if line and not line.startswith( '#' ):
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27 try:
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28 elems = line.split( '\t' )
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29 start = str( int( elems[3] ) - 1 ) # GTF coordinates are 1-based, BedGraph are 0-based.
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30 strand = elems[6]
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31 if strand not in ['+', '-']:
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32 strand = '+'
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33 attributes_list = elems[8].split(";")
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34 attributes = {}
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35 for name_value_pair in attributes_list:
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36 pair = name_value_pair.strip().split(" ")
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37 name = pair[0].strip()
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38 if name == '':
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39 continue
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40 # Need to strip double quote from values
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41 value = pair[1].strip(" \"")
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42 attributes[name] = value
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43 value = attributes[ attribute_name ]
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44 # GTF format: chrom source, name, chromStart, chromEnd, score, strand, frame, attributes.
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45 # BedGraph format: chrom, chromStart, chromEnd, value
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46 out.write( "%s\t%s\t%s\t%s\n" %( elems[0], start, elems[4], value ) )
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47 except:
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48 skipped_lines += 1
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49 if not first_skipped_line:
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50 first_skipped_line = i + 1
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51 else:
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52 skipped_lines += 1
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53 if not first_skipped_line:
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54 first_skipped_line = i + 1
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55 out.close()
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56
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57 # Sort tmp file by chromosome name and chromosome start to create ordered track data.
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58 cmd = "sort -k1,1 -k2,2n < %s > %s" % ( tmp_name1, tmp_name2 )
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59 try:
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60 os.system(cmd)
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61 os.remove(tmp_name1)
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62 except Exception, ex:
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63 sys.stderr.write( "%s\n" % ex )
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64 sys.exit(1)
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65
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66 # Create bedgraph file by combining track definition with ordered track data.
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67 cmd = "echo 'track type=bedGraph' | cat - %s > %s " % ( tmp_name2, output_name )
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68 try:
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69 os.system(cmd)
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70 os.remove(tmp_name2)
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71 except Exception, ex:
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72 sys.stderr.write( "%s\n" % ex )
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73 sys.exit(1)
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74
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75 info_msg = "%i lines converted to BEDGraph. " % ( i + 1 - skipped_lines )
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76 if skipped_lines > 0:
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77 info_msg += "Skipped %d blank/comment/invalid lines starting with line #%d." %( skipped_lines, first_skipped_line )
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78 print info_msg
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79
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80 if __name__ == "__main__": __main__()
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