[2] | 1 | import sys |
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| 2 | import string |
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| 3 | import tempfile |
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| 4 | import subprocess |
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| 5 | from os import path |
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| 6 | |
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| 7 | # ----------------------------------------------------------------------------------- |
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| 8 | |
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| 9 | def stop_err(msg): |
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| 10 | sys.stderr.write(msg) |
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| 11 | sys.exit() |
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| 12 | |
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| 13 | # ----------------------------------------------------------------------------------- |
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| 14 | def gi_name_to_sorted_list(file_name, gi_col, name_col): |
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| 15 | """ Suppose input file looks like this: |
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| 16 | a 2 |
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| 17 | b 4 |
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| 18 | c 5 |
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| 19 | d 5 |
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| 20 | where column 1 is gi_col and column 0 is name_col |
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| 21 | output of this function will look like this: |
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| 22 | [[2, 'a'], [4, 'b'], [5, 'c'], [5, 'd']] |
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| 23 | """ |
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| 24 | |
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| 25 | result = [] |
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| 26 | try: |
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| 27 | F = open( file_name, 'r' ) |
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| 28 | try: |
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| 29 | for line in F: |
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| 30 | file_cols = string.split(line.rstrip(), '\t') |
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| 31 | file_cols[gi_col] = int( file_cols[gi_col] ) |
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| 32 | result.append( [ file_cols[gi_col], file_cols[name_col] ] ) |
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| 33 | except: |
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| 34 | print >>sys.stderr, 'Non numeric GI field...skipping' |
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| 35 | |
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| 36 | except Exception, e: |
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| 37 | stop_err('%s\n' % e) |
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| 38 | F.close() |
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| 39 | result.sort() |
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| 40 | return result |
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| 41 | |
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| 42 | # ----------------------------------------------------------------------------------- |
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| 43 | |
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| 44 | def collapse_repeating_gis( L ): |
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| 45 | """ Accepts 2-d array of gi-key pairs such as this |
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| 46 | L = [ |
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| 47 | [gi1, 'key1'], |
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| 48 | [gi1, 'key2'], |
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| 49 | [gi2','key3'] |
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| 50 | ] |
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| 51 | |
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| 52 | Returns this: |
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| 53 | [ [gi1, 'key1', 'key2'], |
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| 54 | [gi2, 'key3' ] |
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| 55 | ] |
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| 56 | |
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| 57 | The first value in each sublist MUST be int |
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| 58 | """ |
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| 59 | gi = [] |
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| 60 | i = 0 |
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| 61 | result = [] |
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| 62 | |
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| 63 | try: |
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| 64 | for item in L: |
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| 65 | if i == 0: |
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| 66 | prev = item[0] |
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| 67 | |
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| 68 | if prev != item[0]: |
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| 69 | prev_L = [] |
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| 70 | prev_L.append( prev ) |
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| 71 | result.append( prev_L + gi ) |
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| 72 | prev = item[0] |
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| 73 | gi =[] |
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| 74 | |
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| 75 | gi.append( item[1] ) |
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| 76 | i += 1 |
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| 77 | |
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| 78 | except Exception, e: |
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| 79 | stop_err('%s\n' % e) |
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| 80 | |
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| 81 | prev_L = [] |
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| 82 | prev_L.append( prev ) |
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| 83 | result.append( prev_L + gi ) |
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| 84 | del(L) |
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| 85 | return result |
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| 86 | |
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| 87 | # ----------------------------------------------------------------------------------- |
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| 88 | |
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| 89 | def get_taxId( gi2tax_file, gi_name_list, out_file ): |
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| 90 | """ Maps GI numbers from gi_name_list to TaxId identifiers from gi2tax_file and |
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| 91 | prints result to out_file |
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| 92 | |
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| 93 | gi2tax_file MUST be sorted on GI column |
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| 94 | |
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| 95 | gi_name_list is a list that look slike this: |
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| 96 | [[1,'a'], [2,'b','x'], [7,'c'], [10,'d'], [90,'f']] |
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| 97 | where the first element of each sublist is a GI number |
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| 98 | this list MUST also be sorted on GI |
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| 99 | |
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| 100 | This function searches through 117,000,000 rows of gi2taxId file from NCBI |
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| 101 | in approximately 4 minutes. This time is not dependent on the length of |
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| 102 | gi_name_list |
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| 103 | """ |
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| 104 | |
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| 105 | L = gi_name_list.pop(0) |
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| 106 | my_gi = L[0] |
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| 107 | F = open( out_file, 'w' ) |
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| 108 | gi = 0 |
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| 109 | for line in file( gi2tax_file ): |
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| 110 | line = line.rstrip() |
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| 111 | gi, taxId = string.split( line, '\t' ) |
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| 112 | gi = int( gi ) |
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| 113 | |
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| 114 | if gi > my_gi: |
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| 115 | try: |
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| 116 | while ( my_gi < gi ): |
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| 117 | L = gi_name_list.pop(0) |
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| 118 | my_gi = L[0] |
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| 119 | except: |
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| 120 | break |
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| 121 | |
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| 122 | if gi == my_gi: |
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| 123 | for i in range( 1,len( L ) ): |
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| 124 | print >>F, '%s\t%s\t%d' % (L[i], taxId, gi) |
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| 125 | try: |
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| 126 | L = gi_name_list.pop(0) |
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| 127 | my_gi = L[0] |
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| 128 | except: |
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| 129 | break |
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| 130 | |
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| 131 | # ----------------------------------------------------------------------------------- |
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| 132 | |
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| 133 | |
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| 134 | try: |
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| 135 | in_f = sys.argv[1] # input file with GIs |
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| 136 | gi_col = int( sys.argv[2] ) - 1 # column in input containing GIs |
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| 137 | name_col = int( sys.argv[3] ) - 1 # column containing sequence names |
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| 138 | out_f = sys.argv[4] # output file |
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| 139 | tool_data = sys.argv[5] |
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| 140 | except: |
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| 141 | stop_err('Check arguments\n') |
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| 142 | |
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| 143 | # GI2TAX point to a file produced by concatenation of: |
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| 144 | # ftp://ftp.ncbi.nih.gov/pub/taxonomy/gi_taxid_nucl.zip |
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| 145 | # and |
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| 146 | # ftp://ftp.ncbi.nih.gov/pub/taxonomy/gi_taxid_prot.zip |
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| 147 | # a sorting using this command: |
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| 148 | # sort -n -k 1 |
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| 149 | |
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| 150 | GI2TAX = path.join( tool_data, 'taxonomy', 'gi_taxid_sorted.txt' ) |
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| 151 | |
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| 152 | # NAME_FILE and NODE_FILE point to names.dmg and nodes.dmg |
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| 153 | # files contained within: |
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| 154 | # ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz |
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| 155 | |
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| 156 | NAME_FILE = path.join( tool_data, 'taxonomy', 'names.dmp' ) |
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| 157 | NODE_FILE = path.join( tool_data, 'taxonomy', 'nodes.dmp' ) |
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| 158 | |
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| 159 | g2n = gi_name_to_sorted_list(in_f, gi_col, name_col) |
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| 160 | |
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| 161 | if len(g2n) == 0: |
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| 162 | stop_err('No valid GI-containing fields. Please, check your column assignments.\n') |
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| 163 | |
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| 164 | tb_F = tempfile.NamedTemporaryFile('w') |
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| 165 | |
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| 166 | get_taxId( GI2TAX, collapse_repeating_gis( g2n ), tb_F.name ) |
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| 167 | |
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| 168 | try: |
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| 169 | tb_cmd = 'taxBuilder %s %s %s %s' % ( NAME_FILE, NODE_FILE, tb_F.name, out_f ) |
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| 170 | retcode = subprocess.call( tb_cmd, shell=True ) |
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| 171 | if retcode < 0: |
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| 172 | print >>sys.stderr, "Execution of taxBuilder terminated by signal", -retcode |
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| 173 | except OSError, e: |
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| 174 | print >>sys.stderr, "Execution of taxBuilder2tree failed:", e |
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