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1 #!/usr/bin/env python
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2 """
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3 add_plant_tribes_scaffold.py - A script for adding a scaffold to the Galaxy PlantTribes
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4 database efficiently by bypassing the Galaxy model and operating directly on the database.
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5 PostgreSQL 9.1 or greater is required.
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6 """
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7 import argparse
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8 import glob
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9 import os
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10 import sys
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11
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12 import psycopg2
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13 from sqlalchemy.engine.url import make_url
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14
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15
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16 class AddScaffold(object):
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17 def __init__(self):
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18 self.args = None
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19 self.clustering_methods = []
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20 self.conn = None
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21 self.gene_sequences_dict = {}
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22 self.scaffold_genes_dict = {}
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23 self.scaffold_recs = []
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24 self.species_genes_dict = {}
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25 self.species_ids_dict = {}
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26 self.taxa_lineage_config = None
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3
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27 self.parse_args()
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28 self.fh = open(self.args.output, "w")
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29 self.connect_db()
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30
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3
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31 def parse_args(self):
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32 parser = argparse.ArgumentParser()
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33 parser.add_argument('--database_connection_string', dest='database_connection_string', help='Postgres database connection string'),
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34 parser.add_argument('--output', dest='output', help='Output dataset'),
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35 parser.add_argument('--scaffold_path', dest='scaffold_path', help='Full path to PlantTribes scaffold directory')
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36 self.args = parser.parse_args()
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37
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5
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38 def stop_err(self, msg):
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39 sys.stderr.write(msg)
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3
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40 self.fh.flush()
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41 self.fh.close()
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42 sys.exit(1)
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43
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3
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44 def connect_db(self):
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45 url = make_url(self.args.database_connection_string)
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46 self.fh.write('Connecting to database with URL: %s' % url)
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47 args = url.translate_connect_args(username='user')
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48 args.update(url.query)
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49 assert url.get_dialect().name == 'postgresql', 'This script can only be used with PostgreSQL.'
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50 self.conn = psycopg2.connect(**args)
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51
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3
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52 def flush(self):
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53 self.conn.commit()
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54
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3
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55 def shutdown(self):
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56 self.conn.close()
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57
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3
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58 def update(self, sql, args):
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59 try:
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60 cur = self.conn.cursor()
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61 cur.execute(sql, args)
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62 except Exception as e:
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4
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63 msg = "Caught exception executing SQL:\n%s\nException:\n%s\n" % (sql.format(args), e)
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64 self.stop_err(msg)
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65 return cur
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66
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6
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67 @property
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68 def can_add_scaffold(self):
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69 """
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70 Make sure the scaffold has not already been added.
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71 """
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72 scaffold_id = os.path.basename(self.args.scaffold_path)
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73 sql = "SELECT id FROM plant_tribes_scaffold WHERE scaffold_id = '%s';" % scaffold_id
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74 cur = self.conn.cursor()
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75 cur.execute(sql)
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76 try:
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77 cur.fetchone()[0]
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78 # The scaffold has been added to the database.
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79 return False
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80 except:
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81 # The scaffold has not yet been added.
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82 return True
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83
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3
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84 def run(self):
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85 if self.can_add_scaffold:
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86 self.process_annot_dir()
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87 self.process_scaffold_config_files()
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88 self.process_orthogroup_fasta_files()
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89 self.fh.flush()
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90 self.fh.close()
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91 else:
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92 self.stop_err("The scaffold %s has already been added to the database." % os.path.basename(self.args.scaffold_path))
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93
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94 def process_annot_dir(self):
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95 """
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96 First, parse all of the *.min_evalue.summary files in the
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97 ~/<scaffold_id>/annot directory (e.g., ~/22Gv1.1/annot) to populate
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98 both the plant_tribes_scaffold and the plant_tribes_orthogroup tables.
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99 Next, parse all of the *.list files in the same directory to populate
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100 self.scaffold_genes_dict.
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101 """
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102 scaffold_id = os.path.basename(self.args.scaffold_path)
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103 file_dir = os.path.join(self.args.scaffold_path, 'annot')
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104 # The scaffol naming convention must follow this pattern:
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105 # <integer1>Gv<integer2>.<integer3>
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106 # where integer 1 is the number of genomes in the scaffold_id. For example:
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107 # 22Gv1.1 -> 22 genomes
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108 # 12Gv1.0 -> 12 genomes
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109 # 26Gv2.0 -> 26 genomes, etc.
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110 num_genomes = int(scaffold_id.split("Gv")[0])
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111 super_ortho_start_index = num_genomes + 1
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112 for file_name in glob.glob(os.path.join(file_dir, "*min_evalue.summary")):
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113 items = os.path.basename(file_name).split(".")
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114 clustering_method = items[0]
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115 # Save all clustering methods for later processing.
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116 if clustering_method not in self.clustering_methods:
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117 self.clustering_methods.append(clustering_method)
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118 # Insert a row in to the plant_tribes_scaffold table.
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119 self.fh.write("Inserting a row into the plant_tribes_scaffold table for scaffold %s and clustering method %s..." % (scaffold_id, clustering_method))
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120 args = [scaffold_id, clustering_method]
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121 sql = """
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122 INSERT INTO plant_tribes_scaffold
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123 VALUES (nextval('plant_tribes_scaffold_id_seq'), %s, %s)
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124 RETURNING id;
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125 """
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126 cur = self.update(sql, tuple(args))
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127 self.flush()
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128 scaffold_id_db = cur.fetchone()[0]
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129 self.scaffold_recs.append([scaffold_id_db, scaffold_id, clustering_method])
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130 with open(file_name, "r") as fh:
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131 for i, line in enumerate(fh):
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132 if i == 0:
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133 # Skip first line.
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134 continue
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135 num_genes = 0
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136 num_species = 0
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137 items = line.split("\t")
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138 orthogroup_id = int(items[0])
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139 # Zero based items 1 to num_genomes consists of the
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140 # number of species classified in the orthogroup (i.e.,
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141 # species with at least 1 gene in the orthogroup).
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142 for j in range(1, num_genomes):
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143 j_int = int(items[j])
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144 if j_int > 0:
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145 # The species has at least 1 gene
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146 num_species += 1
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147 num_genes += j_int
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148 # Insert a row into the plant_tribes_orthogroup table.
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149 self.fh.write("Inserting a row into the plant_tribes_orthogroup table...")
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150 args = [orthogroup_id, scaffold_id_db, num_species, num_genes]
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151 for k in range(super_ortho_start_index, len(items)):
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152 args.append('%s' % str(items[k]))
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153 sql = """
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154 INSERT INTO plant_tribes_orthogroup
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155 VALUES (nextval('plant_tribes_orthogroup_id_seq'), %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s);
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156 """
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157 cur = self.update(sql, tuple(args))
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158 self.flush()
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159 for file_name in glob.glob(os.path.join(file_dir, "*list")):
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160 items = os.path.basename(file_name).split(".")
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161 clustering_method = items[0]
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162 with open(file_name, "r") as fh:
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163 for i, line in enumerate(fh):
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164 items = line.split("\t")
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165 # The key will be a combination of clustering_method and
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166 # orthogroup_id separated by "^^" for easy splitting later.
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167 key = "%s^^%s" % (clustering_method, items[0])
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168 # The value is the gen_id with all white space replaced by "_".
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169 val = items[1].replace("|", "_")
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170 if key in self.scaffold_genes_dict:
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171 self.scaffold_genes_dict[key].append(val)
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172 else:
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173 self.scaffold_genes_dict[key] = [val]
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174
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175 def process_scaffold_config_files(self):
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176 """
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177 1. Parse ~/<scaffold_id>/<scaffold_id>/.rootingOrder.config
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178 (e.g., ~/22Gv1.1/22Gv1.1..rootingOrder.config) to populate.
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179 2. Calculate the number of genes found
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180 for each species and add the number to self.species_genes_dict.
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181 3. Parse ~/<scaffold_id>/<scaffold_id>.taxaLineage.config to
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182 populate the plant_tribes_taxon table.
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183 """
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184 scaffold_id = os.path.basename(self.args.scaffold_path)
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185 file_name = os.path.join(self.args.scaffold_path, '%s.rootingOrder.config' % scaffold_id)
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186 self.fh.write("Processing rooting order config: %s" % str(file_name))
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187 # Populate self.species_ids_dict.
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188 with open(file_name, "r") as fh:
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189 for i, line in enumerate(fh):
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190 line = line.strip()
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191 if len(line) == 0 or line.startswith("#") or line.startswith("["):
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192 # Skip blank lines, comments and section headers.
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193 continue
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194 # Example line:
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195 # Physcomitrella patens=Phypa
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196 items = line.split("=")
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197 self.species_ids_dict[items[1]] = items[0]
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198 # Get lineage information for orthogrpoup taxa.
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199 for scaffold_genes_dict_key in sorted(self.scaffold_genes_dict.keys()):
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200 # The format of key is <clustering_method>^^<orthogroup_id>.
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201 # For example: {"gfam^^1" : "gnl_Musac1.0_GSMUA_Achr1T11000_001"
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202 scaffold_genes_dict_key_items = scaffold_genes_dict_key.split("^^")
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203 clustering_method = scaffold_genes_dict_key_items[0]
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204 # Get the list of genes for the current scaffold_genes_dict_key.
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205 gene_list = self.scaffold_genes_dict[scaffold_genes_dict_key]
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206 for gene_id in gene_list:
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207 # Example species_code: Musac1.0, where
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208 # species_name is Musac and version is 1.0.
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209 species_code = gene_id.split("_")[1]
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210 # Strip the version from the species_code.
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211 species_code = species_code[0:5]
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212 # Get the species_name from self.species_ids_dict.
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213 species_name = self.species_ids_dict[species_code]
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214 # Create a key for self.species_genes_dict, with the format:
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215 # <clustering_method>^^<species_code>
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216 species_genes_dict_key = "%s^^%s" % (clustering_method, species_code)
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217 # Add an entry to self.species_genes_dict, where the value
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218 # is a list containing species_name and num_genes.
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219 if species_genes_dict_key in self.species_genes_dict:
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220 tup = self.species_genes_dict[species_genes_dict_key]
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221 tup[1] += 1
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222 self.species_genes_dict[species_genes_dict_key] = tup
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223 else:
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224 self.species_genes_dict[species_genes_dict_key] = [species_name, 1]
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225 # Populate the plant_tribes_taxon table.
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226 file_name = os.path.join(self.args.scaffold_path, '%s.taxaLineage.config' % scaffold_id)
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227 self.fh.write("Processing taxa lineage config: %s" % str(file_name))
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228 with open(file_name, "r") as fh:
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229 for i, line in enumerate(fh):
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230 line = line.strip()
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231 if len(line) == 0 or line.startswith("#") or line.startswith("Species"):
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232 # Skip blank lines, comments and section headers.
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233 continue
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234 # Example line: Populus trichocarpa\tSalicaceae\tMalpighiales\tRosids\tCore Eudicots
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235 items = line.split("\t")
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236 species_name = items[0]
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237 self.fh.write("Calculating the number of genes for species_name: %s" % str(species_name))
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238 for species_genes_dict_key in sorted(self.species_genes_dict.keys()):
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239 # The format of species_genes_dict_key is <clustering_method>^^<species_code>.
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240 species_genes_dict_key_items = species_genes_dict_key.split("^^")
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241 clustering_method = species_genes_dict_key_items[0]
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242 species_code = species_genes_dict_key_items[1]
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243 # Get the scaffold_rec for the current scaffold_id and clustering_method.
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244 # The list is [<scaffold_id_db>, <scaffold_id>, <clustering_method>]
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245 for scaffold_rec in self.scaffold_recs:
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246 if scaffold_id in scaffold_rec and clustering_method in scaffold_rec:
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247 scaffold_id_db = scaffold_rec[0]
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248 # The value is a list containing species_name and num_genes.
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249 val = self.species_genes_dict[species_genes_dict_key]
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250 if species_name == val[0]:
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251 num_genes = val[1]
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252 else:
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253 num_genes = 0
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254 # Insert a row in to the plant_tribes_scaffold table.
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255 args = [species_name, scaffold_id_db, num_genes, items[1], items[2], items[3], items[4]]
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256 sql = """
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257 INSERT INTO plant_tribes_taxon
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258 VALUES (nextval('plant_tribes_taxon_id_seq'), %s, %s, %s, %s, %s, %s, %s);
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259 """
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260 self.update(sql, tuple(args))
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261 self.flush()
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262
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263 def process_orthogroup_fasta_files(self):
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264 scaffold_id = os.path.basename(self.args.scaffold_path)
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265 aa_dict = {}
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266 dna_dict = {}
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267 # Populate aa_dict and dna_dict.
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268 for clustering_method in self.clustering_methods:
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269 file_dir = os.path.join(self.args.scaffold_path, 'fasta', clustering_method)
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270 for file_name in os.listdir(file_dir):
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271 items = file_name.split(".")
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272 orthogroup_id = items[0]
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273 file_extension = items[1]
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274 if file_extension == "fna":
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275 adict = dna_dict
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276 else:
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277 adict = aa_dict
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278 file_path = os.path.join(file_dir, file_name)
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279 with open(file_path, "r") as fh:
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280 for i, line in enumerate(fh):
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281 line = line.strip()
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282 if len(line) == 0:
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283 # Skip blank lines (shoudn't happen).
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284 continue
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285 if line.startswith(">"):
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286 # Example line:
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287 # >gnl_Ambtr1.0.27_AmTr_v1.0_scaffold00001.110
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288 gene_id = line.lstrip(">")
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289 # The dictionary keys will combine the orthogroup_id,
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290 # clustering method and gene id using the format
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291 # ,orthogroup_id>^^<clustering_method>^^<gene_id>.
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292 combined_id = "%s^^%s^^%s" % (orthogroup_id, clustering_method, gene_id)
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293 if combined_id not in adict:
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294 # The value will be the dna sequence string..
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295 adict[combined_id] = ""
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296 else:
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297 # Example line:
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298 # ATGGAGAAGGACTTT
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299 # Here combined_id is set because the fasta format specifies
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300 # that all lines following the gene id defined in the if block
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301 # above will be the sequence associated with that gene until
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302 # the next gene id line is encountered.
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303 sequence = adict[combined_id]
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304 sequence = "%s%s" % (sequence, line)
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305 adict[combined_id] = sequence
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306 # Populate the plant_tribes_gene and gen_scaffold_association tables
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307 # from the contents of aa_dict and dna_dict.
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308 for combined_id in sorted(dna_dict.keys()):
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309 # The dictionary keys combine the orthogroup_id, clustering method and
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310 # gene id using the format <orthogroup_id>^^<clustering_method>^^<gene_id>.
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311 items = combined_id.split("^^")
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312 orthogroup_id = items[0]
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313 clustering_method = items[1]
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314 gene_id = items[2]
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315 self.fh.write("Populating the plant_tribes_gene and gene_scaffold_orthogroup_association tables with gene %s, scaffold %s and orthogroup %s..." % (gene_id, scaffold_id, orthogroup_id))
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316 # The value will be a list containing both
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317 # clustering_method and the dna string.
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318 dna_sequence = dna_dict[combined_id]
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319 aa_sequence = aa_dict[combined_id]
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320 # Get the species_code from the gene_id.
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321 species_code = gene_id.split("_")[1]
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322 # Strip the version from the species_code.
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323 species_code = species_code[0:5]
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324 # Get the species_name from self.species_ids_dict.
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325 species_name = self.species_ids_dict[species_code]
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326 # Get the plant_tribes_orthogroup primary key id for
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327 # the orthogroup_id from the plant_tribes_orthogroup table.
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328 sql = "SELECT id FROM plant_tribes_orthogroup WHERE orthogroup_id = '%s';" % orthogroup_id
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329 cur = self.conn.cursor()
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330 cur.execute(sql)
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331 orthogroup_id_db = cur.fetchone()[0]
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332 # If the plant_tribes_gene table contains a row that has the gene_id,
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333 # then we'll add a row only to the gene_scaffold_orthogroup_association table.
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334 # Get the taxon_id for the species_name from the plant_tribes_taxon table.
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335 sql = "SELECT id FROM plant_tribes_taxon WHERE species_name = '%s';" % species_name
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336 cur = self.conn.cursor()
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337 cur.execute(sql)
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338 taxon_id = cur.fetchone()[0]
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339 # If the plant_tribes_gene table contains a row that has the gene_id,
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340 # then we'll add a row only to the gene_scaffold_orthogroup_association table.
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341 sql = "SELECT id FROM plant_tribes_gene WHERE gene_id = '%s';" % gene_id
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342 cur = self.conn.cursor()
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343 cur.execute(sql)
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344 try:
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345 gene_id_db = cur.fetchone()[0]
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346 except:
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347 # Insert a row into the plant_tribes_gene table.
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348 args = [gene_id, taxon_id, dna_sequence, aa_sequence]
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349 sql = """
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350 INSERT INTO plant_tribes_gene
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351 VALUES (nextval('plant_tribes_gene_id_seq'), %s, %s, %s, %s)
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352 RETURNING id;
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353 """
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3
|
354 cur = self.update(sql, tuple(args))
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355 self.flush()
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0
|
356 gene_id_db = cur.fetchone()[0]
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357 # Insert a row into the gene_scaffold_orthogroup_association table.
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358 # Get the scaffold_rec for the current scaffold_id and clustering_method.
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359 # The list is [<scaffold_id_db>, <scaffold_id>, <clustering_method>]
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360 for scaffold_rec in self.scaffold_recs:
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|
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361 if scaffold_id in scaffold_rec and clustering_method in scaffold_rec:
|
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362 scaffold_id_db = scaffold_rec[0]
|
|
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363 args = [gene_id_db, scaffold_id_db, orthogroup_id_db]
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364 sql = """
|
|
|
365 INSERT INTO gene_scaffold_orthogroup_association
|
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366 VALUES (nextval('gene_scaffold_orthogroup_association_id_seq'), %s, %s, %s);
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|
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367 """
|
|
3
|
368 cur = self.update(sql, tuple(args))
|
|
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369 self.flush()
|
|
0
|
370
|
|
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371
|
|
|
372 if __name__ == '__main__':
|
|
|
373 add_scaffold = AddScaffold()
|
|
3
|
374 add_scaffold.run()
|
|
|
375 add_scaffold.shutdown()
|
