Mercurial > repos > xuebing > sharplabtool
comparison tools/new_operations/get_flanks.py @ 0:9071e359b9a3
Uploaded
| author | xuebing |
|---|---|
| date | Fri, 09 Mar 2012 19:37:19 -0500 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:9071e359b9a3 |
|---|---|
| 1 #!/usr/bin/env python | |
| 2 #Done by: Guru | |
| 3 | |
| 4 """ | |
| 5 Get Flanking regions. | |
| 6 | |
| 7 usage: %prog input out_file size direction region | |
| 8 -l, --cols=N,N,N,N: Columns for chrom, start, end, strand in file | |
| 9 -o, --off=N: Offset | |
| 10 """ | |
| 11 | |
| 12 import sys, re, os | |
| 13 from galaxy import eggs | |
| 14 import pkg_resources; pkg_resources.require( "bx-python" ) | |
| 15 from bx.cookbook import doc_optparse | |
| 16 from galaxy.tools.util.galaxyops import * | |
| 17 | |
| 18 def stop_err( msg ): | |
| 19 sys.stderr.write( msg ) | |
| 20 sys.exit() | |
| 21 | |
| 22 def main(): | |
| 23 try: | |
| 24 if int( sys.argv[3] ) < 0: | |
| 25 raise Exception | |
| 26 except: | |
| 27 stop_err( "Length of flanking region(s) must be a non-negative integer." ) | |
| 28 | |
| 29 # Parsing Command Line here | |
| 30 options, args = doc_optparse.parse( __doc__ ) | |
| 31 try: | |
| 32 chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols ) | |
| 33 inp_file, out_file, size, direction, region = args | |
| 34 if strand_col_1 <= 0: | |
| 35 strand = "+" #if strand is not defined, default it to + | |
| 36 except: | |
| 37 stop_err( "Metadata issue, correct the metadata attributes by clicking on the pencil icon in the history item." ) | |
| 38 try: | |
| 39 offset = int(options.off) | |
| 40 size = int(size) | |
| 41 except: | |
| 42 stop_err( "Invalid offset or length entered. Try again by entering valid integer values." ) | |
| 43 | |
| 44 fo = open(out_file,'w') | |
| 45 | |
| 46 skipped_lines = 0 | |
| 47 first_invalid_line = 0 | |
| 48 invalid_line = None | |
| 49 elems = [] | |
| 50 j=0 | |
| 51 for i, line in enumerate( file( inp_file ) ): | |
| 52 line = line.strip() | |
| 53 if line and (not line.startswith( '#' )) and line != '': | |
| 54 j+=1 | |
| 55 try: | |
| 56 elems = line.split('\t') | |
| 57 #if the start and/or end columns are not numbers, skip that line. | |
| 58 assert int(elems[start_col_1]) | |
| 59 assert int(elems[end_col_1]) | |
| 60 if strand_col_1 != -1: | |
| 61 strand = elems[strand_col_1] | |
| 62 #if the stand value is not + or -, skip that line. | |
| 63 assert strand in ['+', '-'] | |
| 64 if direction == 'Upstream': | |
| 65 if strand == '+': | |
| 66 if region == 'end': | |
| 67 elems[end_col_1] = str(int(elems[end_col_1]) + offset) | |
| 68 elems[start_col_1] = str( int(elems[end_col_1]) - size ) | |
| 69 else: | |
| 70 elems[end_col_1] = str(int(elems[start_col_1]) + offset) | |
| 71 elems[start_col_1] = str( int(elems[end_col_1]) - size ) | |
| 72 elif strand == '-': | |
| 73 if region == 'end': | |
| 74 elems[start_col_1] = str(int(elems[start_col_1]) - offset) | |
| 75 elems[end_col_1] = str(int(elems[start_col_1]) + size) | |
| 76 else: | |
| 77 elems[start_col_1] = str(int(elems[end_col_1]) - offset) | |
| 78 elems[end_col_1] = str(int(elems[start_col_1]) + size) | |
| 79 assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0 | |
| 80 fo.write( "%s\n" % '\t'.join( elems ) ) | |
| 81 | |
| 82 elif direction == 'Downstream': | |
| 83 if strand == '-': | |
| 84 if region == 'start': | |
| 85 elems[end_col_1] = str(int(elems[end_col_1]) - offset) | |
| 86 elems[start_col_1] = str( int(elems[end_col_1]) - size ) | |
| 87 else: | |
| 88 elems[end_col_1] = str(int(elems[start_col_1]) - offset) | |
| 89 elems[start_col_1] = str( int(elems[end_col_1]) - size ) | |
| 90 elif strand == '+': | |
| 91 if region == 'start': | |
| 92 elems[start_col_1] = str(int(elems[start_col_1]) + offset) | |
| 93 elems[end_col_1] = str(int(elems[start_col_1]) + size) | |
| 94 else: | |
| 95 elems[start_col_1] = str(int(elems[end_col_1]) + offset) | |
| 96 elems[end_col_1] = str(int(elems[start_col_1]) + size) | |
| 97 assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0 | |
| 98 fo.write( "%s\n" % '\t'.join( elems ) ) | |
| 99 | |
| 100 elif direction == 'Both': | |
| 101 if strand == '-': | |
| 102 if region == 'start': | |
| 103 start = str(int(elems[end_col_1]) - offset) | |
| 104 end1 = str(int(start) + size) | |
| 105 end2 = str(int(start) - size) | |
| 106 elems[start_col_1]=start | |
| 107 elems[end_col_1]=end1 | |
| 108 assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0 | |
| 109 fo.write( "%s\n" % '\t'.join( elems ) ) | |
| 110 elems[start_col_1]=end2 | |
| 111 elems[end_col_1]=start | |
| 112 assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0 | |
| 113 fo.write( "%s\n" % '\t'.join( elems ) ) | |
| 114 elif region == 'end': | |
| 115 start = str(int(elems[start_col_1]) - offset) | |
| 116 end1 = str(int(start) + size) | |
| 117 end2 = str(int(start) - size) | |
| 118 elems[start_col_1]=start | |
| 119 elems[end_col_1]=end1 | |
| 120 assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0 | |
| 121 fo.write( "%s\n" % '\t'.join( elems ) ) | |
| 122 elems[start_col_1]=end2 | |
| 123 elems[end_col_1]=start | |
| 124 assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0 | |
| 125 fo.write( "%s\n" % '\t'.join( elems ) ) | |
| 126 else: | |
| 127 start1 = str(int(elems[end_col_1]) - offset) | |
| 128 end1 = str(int(start1) + size) | |
| 129 start2 = str(int(elems[start_col_1]) - offset) | |
| 130 end2 = str(int(start2) - size) | |
| 131 elems[start_col_1]=start1 | |
| 132 elems[end_col_1]=end1 | |
| 133 assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0 | |
| 134 fo.write( "%s\n" % '\t'.join( elems ) ) | |
| 135 elems[start_col_1]=end2 | |
| 136 elems[end_col_1]=start2 | |
| 137 assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0 | |
| 138 fo.write( "%s\n" % '\t'.join( elems ) ) | |
| 139 elif strand == '+': | |
| 140 if region == 'start': | |
| 141 start = str(int(elems[start_col_1]) + offset) | |
| 142 end1 = str(int(start) - size) | |
| 143 end2 = str(int(start) + size) | |
| 144 elems[start_col_1]=end1 | |
| 145 elems[end_col_1]=start | |
| 146 assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0 | |
| 147 fo.write( "%s\n" % '\t'.join( elems ) ) | |
| 148 elems[start_col_1]=start | |
| 149 elems[end_col_1]=end2 | |
| 150 assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0 | |
| 151 fo.write( "%s\n" % '\t'.join( elems ) ) | |
| 152 elif region == 'end': | |
| 153 start = str(int(elems[end_col_1]) + offset) | |
| 154 end1 = str(int(start) - size) | |
| 155 end2 = str(int(start) + size) | |
| 156 elems[start_col_1]=end1 | |
| 157 elems[end_col_1]=start | |
| 158 assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0 | |
| 159 fo.write( "%s\n" % '\t'.join( elems ) ) | |
| 160 elems[start_col_1]=start | |
| 161 elems[end_col_1]=end2 | |
| 162 assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0 | |
| 163 fo.write( "%s\n" % '\t'.join( elems ) ) | |
| 164 else: | |
| 165 start1 = str(int(elems[start_col_1]) + offset) | |
| 166 end1 = str(int(start1) - size) | |
| 167 start2 = str(int(elems[end_col_1]) + offset) | |
| 168 end2 = str(int(start2) + size) | |
| 169 elems[start_col_1]=end1 | |
| 170 elems[end_col_1]=start1 | |
| 171 assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0 | |
| 172 fo.write( "%s\n" % '\t'.join( elems ) ) | |
| 173 elems[start_col_1]=start2 | |
| 174 elems[end_col_1]=end2 | |
| 175 assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0 | |
| 176 fo.write( "%s\n" % '\t'.join( elems ) ) | |
| 177 except: | |
| 178 skipped_lines += 1 | |
| 179 if not invalid_line: | |
| 180 first_invalid_line = i + 1 | |
| 181 invalid_line = line | |
| 182 fo.close() | |
| 183 | |
| 184 if skipped_lines == j: | |
| 185 stop_err( "Data issue: click the pencil icon in the history item to correct the metadata attributes." ) | |
| 186 if skipped_lines > 0: | |
| 187 print 'Skipped %d invalid lines starting with #%dL "%s"' % ( skipped_lines, first_invalid_line, invalid_line ) | |
| 188 print 'Location: %s, Region: %s, Flank-length: %d, Offset: %d ' %( direction, region, size, offset ) | |
| 189 | |
| 190 if __name__ == "__main__": | |
| 191 main() |