[2] | 1 | #!/usr/bin/env python |
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| 2 | |
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| 3 | """ |
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| 4 | tax_read_grouping.py <file in taxonomy format> <id column> <taxonomic ranks> <output format> <output file> |
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| 5 | finds reads that only hit one taxonomic group. For example, consider the folliowing example: |
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| 6 | |
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| 7 | read1 mammalia |
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| 8 | read1 insecta |
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| 9 | read2 insecta |
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| 10 | |
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| 11 | in this case only read2 will be selected becuase it stays within insecta |
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| 12 | |
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| 13 | This program takes the following options: |
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| 14 | |
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| 15 | file in taxonomy format - dataset that complies with Galaxy's taxonomy format |
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| 16 | id column - integer specifying the number of column containing seq id (starting with 1) |
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| 17 | taxonomic ranks - a comma separated list of ranks from this list: |
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| 18 | |
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| 19 | superkingdom |
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| 20 | kingdom |
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| 21 | subkingdom |
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| 22 | superphylum |
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| 23 | phylum |
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| 24 | subphylum |
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| 25 | superclass |
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| 26 | class |
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| 27 | subclass |
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| 28 | superorder |
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| 29 | order |
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| 30 | suborder |
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| 31 | superfamily |
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| 32 | family |
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| 33 | subfamily |
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| 34 | tribe |
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| 35 | subtribe |
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| 36 | genus |
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| 37 | subgenus |
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| 38 | species |
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| 39 | subspecies |
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| 40 | |
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| 41 | output format - reads or counts |
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| 42 | |
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| 43 | """ |
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| 44 | |
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| 45 | from galaxy import eggs |
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| 46 | import pkg_resources |
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| 47 | pkg_resources.require( 'pysqlite' ) |
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| 48 | from pysqlite2 import dbapi2 as sqlite |
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| 49 | import string, sys, tempfile |
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| 50 | |
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| 51 | # This dictionary maps taxonomic ranks to fields of Taxonomy file |
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| 52 | taxRank = { |
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| 53 | 'root' :2, |
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| 54 | 'superkingdom':3, |
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| 55 | 'kingdom' :4, |
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| 56 | 'subkingdom' :5, |
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| 57 | 'superphylum' :6, |
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| 58 | 'phylum' :7, |
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| 59 | 'subphylum' :8, |
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| 60 | 'superclass' :9, |
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| 61 | 'class' :10, |
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| 62 | 'subclass' :11, |
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| 63 | 'superorder' :12, |
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| 64 | 'ord' :13, |
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| 65 | 'suborder' :14, |
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| 66 | 'superfamily' :15, |
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| 67 | 'family' :16, |
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| 68 | 'subfamily' :17, |
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| 69 | 'tribe' :18, |
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| 70 | 'subtribe' :19, |
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| 71 | 'genus' :20, |
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| 72 | 'subgenus' :21, |
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| 73 | 'species' :22, |
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| 74 | 'subspecies' :23, |
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| 75 | 'order' :13 |
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| 76 | } |
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| 77 | |
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| 78 | |
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| 79 | def stop_err(msg): |
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| 80 | sys.stderr.write(msg) |
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| 81 | sys.exit() |
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| 82 | |
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| 83 | |
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| 84 | db = tempfile.NamedTemporaryFile('w') |
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| 85 | |
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| 86 | try: |
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| 87 | con = sqlite.connect(db.name) |
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| 88 | cur = con.cursor() |
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| 89 | except: |
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| 90 | stop_err('Cannot connect to %s\n') % db.name |
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| 91 | |
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| 92 | try: |
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| 93 | tax_file = open(sys.argv[1], 'r') |
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| 94 | id_col = int(sys.argv[2]) - 1 |
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| 95 | taxa = string.split(sys.argv[3].rstrip(),',') |
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| 96 | |
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| 97 | if sys.argv[4] == 'reads': |
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| 98 | out_format = True |
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| 99 | elif sys.argv[4] == 'counts': |
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| 100 | out_format = False |
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| 101 | else: |
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| 102 | stop_err('Please specify "reads" or "counts" for output format\n') |
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| 103 | out_file = open(sys.argv[5], 'w') |
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| 104 | |
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| 105 | except: |
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| 106 | stop_err('Check arguments\n') |
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| 107 | |
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| 108 | if taxa[0] == 'None': stop_err('Please, use checkboxes to specify taxonomic ranks.\n') |
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| 109 | |
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| 110 | sql = "" |
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| 111 | for i in range(len(taxa)): |
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| 112 | if taxa[i] == 'order': taxa[i] = 'ord' # SQL does not like fields to be named 'order' |
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| 113 | sql += '%s text, ' % taxa[i] |
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| 114 | |
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| 115 | sql = sql.strip(', ') |
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| 116 | sql = 'create table tax (name varchar(50) not null, ' + sql + ')' |
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| 117 | |
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| 118 | |
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| 119 | cur.execute(sql) |
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| 120 | |
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| 121 | invalid_line_number = 0 |
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| 122 | |
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| 123 | try: |
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| 124 | for line in tax_file: |
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| 125 | fields = string.split(line.rstrip(), '\t') |
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| 126 | if len(fields) < 24: |
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| 127 | invalid_line_number += 1 |
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| 128 | continue # Skipping malformed taxonomy lines |
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| 129 | |
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| 130 | val_string = '"' + fields[id_col] + '", ' |
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| 131 | |
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| 132 | for rank in taxa: |
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| 133 | taxon = fields[taxRank[rank]] |
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| 134 | val_string += '"%s", ' % taxon |
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| 135 | |
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| 136 | val_string = val_string.strip(', ') |
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| 137 | val_string = "insert into tax values(" + val_string + ")" |
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| 138 | cur.execute(val_string) |
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| 139 | except Exception, e: |
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| 140 | stop_err('%s\n' % e) |
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| 141 | |
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| 142 | tax_file.close() |
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| 143 | |
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| 144 | try: |
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| 145 | for rank in taxa: |
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| 146 | cur.execute('create temporary table %s (name varchar(50), id text, rank text)' % rank ) |
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| 147 | cur.execute('insert into %s select name, name || %s as id, %s from tax group by id' % ( rank, rank, rank ) ) |
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| 148 | cur.execute('create temporary table %s_count(name varchar(50), id text, rank text, N int)' % rank) |
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| 149 | cur.execute('insert into %s_count select name, id, rank, count(*) from %s group by name' % ( rank, rank) ) |
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| 150 | |
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| 151 | if rank == 'ord': |
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| 152 | rankName = 'order' |
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| 153 | else: |
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| 154 | rankName = rank |
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| 155 | |
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| 156 | if out_format: |
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| 157 | cur.execute('select name,rank from %s_count where N = 1 and length(rank)>1' % rank) |
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| 158 | for item in cur.fetchall(): |
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| 159 | out_string = '%s\t%s\t' % ( item[0], item[1] ) |
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| 160 | out_string += rankName |
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| 161 | print >>out_file, out_string |
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| 162 | else: |
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| 163 | cur.execute('select rank, count(*) from %s_count where N = 1 and length(rank)>1 group by rank' % rank) |
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| 164 | for item in cur.fetchall(): |
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| 165 | out_string = '%s\t%s\t' % ( item[0], item[1] ) |
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| 166 | out_string += rankName |
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| 167 | print >>out_file, out_string |
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| 168 | except Exception, e: |
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| 169 | stop_err("%s\n" % e) |
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| 170 | |
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