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galaxy/scripts/tools/annotation_profiler/build_profile_indexes.py
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#!/usr/bin/env python
#Dan Blankenberg
VERSION = '1.0.0' # version of this script
from optparse import OptionParser
import os, gzip, struct, time
from ftplib import FTP #do we want a diff method than using FTP to determine Chrom Names, eg use local copy
#import md5 from hashlib; if python2.4 or less, use old md5
try:
from hashlib import md5
except ImportError:
from md5 import new as md5
#import BitSet from bx-python, try using eggs and package resources, fall back to any local installation
try:
from galaxy import eggs
import pkg_resources
pkg_resources.require( "bx-python" )
except: pass #Maybe there is a local installation available
from bx.bitset import BitSet
#Define constants
STRUCT_FMT = '<I'
STRUCT_SIZE = struct.calcsize( STRUCT_FMT )
DEFAULT_BITSET_SIZE = 300000000
CHUNK_SIZE = 1024
#Headers used to parse .sql files to determine column indexes for chromosome name, start and end
alias_spec = {
'chromCol' : [ 'chrom' , 'CHROMOSOME' , 'CHROM', 'Chromosome Name', 'tName' ],
'startCol' : [ 'start' , 'START', 'chromStart', 'txStart', 'Start Position (bp)', 'tStart', 'genoStart' ],
'endCol' : [ 'end' , 'END' , 'STOP', 'chromEnd', 'txEnd', 'End Position (bp)', 'tEnd', 'genoEnd' ],
}
#Headers used to parse trackDb.txt.gz
#TODO: these should be parsed directly from trackDb.sql
trackDb_headers = ["tableName", "shortLabel", "type", "longLabel", "visibility", "priority", "colorR", "colorG", "colorB", "altColorR", "altColorG", "altColorB", "useScore", "private", "restrictCount", "restrictList", "url", "html", "grp", "canPack", "settings"]
def get_columns( filename ):
input_sql = open( filename ).read()
input_sql = input_sql.split( 'CREATE TABLE ' )[1].split( ';' )[0]
input_sql = input_sql.split( ' (', 1 )
table_name = input_sql[0].strip().strip( '`' )
input_sql = [ split.strip().split( ' ' )[0].strip().strip( '`' ) for split in input_sql[1].rsplit( ')', 1 )[0].strip().split( '\n' ) ]
print input_sql
chrom_col = None
start_col = None
end_col = None
for col_name in alias_spec['chromCol']:
for i, header_name in enumerate( input_sql ):
if col_name == header_name:
chrom_col = i
break
if chrom_col is not None:
break
for col_name in alias_spec['startCol']:
for i, header_name in enumerate( input_sql ):
if col_name == header_name:
start_col = i
break
if start_col is not None:
break
for col_name in alias_spec['endCol']:
for i, header_name in enumerate( input_sql ):
if col_name == header_name:
end_col = i
break
if end_col is not None:
break
return table_name, chrom_col, start_col, end_col
def create_grouping_xml( input_dir, output_dir, dbkey ):
output_filename = os.path.join( output_dir, '%s_tables.xml' % dbkey )
def load_groups( file_name = 'grp.txt.gz' ):
groups = {}
for line in gzip.open( os.path.join( input_dir, file_name ) ):
fields = line.split( '\t' )
groups[fields[0]] = { 'desc': fields[1], 'priority': fields[2] }
return groups
f = gzip.open( os.path.join( input_dir, 'trackDb.txt.gz' ) )
out = open( output_filename, 'wb' )
tables = {}
cur_buf = ''
while True:
line = f.readline()
if not line: break
#remove new lines
line = line.rstrip( '\n\r' )
line = line.replace( '\\\t', ' ' ) #replace escaped tabs with space
cur_buf += "%s\n" % line.rstrip( '\\' )
if line.endswith( '\\' ):
continue #line is wrapped, next line
#all fields should be loaded now...
fields = cur_buf.split( '\t' )
cur_buf = '' #reset buffer
assert len( fields ) == len( trackDb_headers ), 'Failed Parsing trackDb.txt.gz; fields: %s' % fields
table_name = fields[ 0 ]
tables[ table_name ] = {}
for field_name, field_value in zip( trackDb_headers, fields ):
tables[ table_name ][ field_name ] = field_value
#split settings fields into dict
fields = fields[-1].split( '\n' )
tables[ table_name ][ 'settings' ] = {}
for field in fields:
setting_fields = field.split( ' ', 1 )
setting_name = setting_value = setting_fields[ 0 ]
if len( setting_fields ) > 1:
setting_value = setting_fields[ 1 ]
if setting_name or setting_value:
tables[ table_name ][ 'settings' ][ setting_name ] = setting_value
#Load Groups
groups = load_groups()
in_groups = {}
for table_name, values in tables.iteritems():
if os.path.exists( os.path.join( output_dir, table_name ) ):
group = values['grp']
if group not in in_groups:
in_groups[group]={}
#***NAME CHANGE***, 'subTrack' no longer exists as a setting...use 'parent' instead
#subTrack = values.get('settings', {} ).get( 'subTrack', table_name )
subTrack = values.get('settings', {} ).get( 'parent', table_name ).split( ' ' )[0] #need to split, because could be e.g. 'trackgroup on'
if subTrack not in in_groups[group]:
in_groups[group][subTrack]=[]
in_groups[group][subTrack].append( table_name )
assigned_tables = []
out.write( """<filter type="data_meta" data_ref="input1" meta_key="dbkey" value="%s">\n""" % ( dbkey ) )
out.write( " <options>\n" )
for group, subTracks in sorted( in_groups.iteritems() ):
out.write( """ <option name="%s" value="group-%s">\n""" % ( groups[group]['desc'], group ) )
for sub_name, sub_tracks in subTracks.iteritems():
if len( sub_tracks ) > 1:
out.write( """ <option name="%s" value="subtracks-%s">\n""" % ( sub_name, sub_name ) )
sub_tracks.sort()
for track in sub_tracks:
track_label = track
if "$" not in tables[track]['shortLabel']:
track_label = tables[track]['shortLabel']
out.write( """ <option name="%s" value="%s"/>\n""" % ( track_label, track ) )
assigned_tables.append( track )
out.write( " </option>\n" )
else:
track = sub_tracks[0]
track_label = track
if "$" not in tables[track]['shortLabel']:
track_label = tables[track]['shortLabel']
out.write( """ <option name="%s" value="%s"/>\n""" % ( track_label, track ) )
assigned_tables.append( track )
out.write( " </option>\n" )
unassigned_tables = list( sorted( [ table_dir for table_dir in os.listdir( output_dir ) if table_dir not in assigned_tables and os.path.isdir( os.path.join( output_dir, table_dir ) ) ] ) )
if unassigned_tables:
out.write( """ <option name="Uncategorized Tables" value="group-trackDbUnassigned">\n""" )
for table_name in unassigned_tables:
out.write( """ <option name="%s" value="%s"/>\n""" % ( table_name, table_name ) )
out.write( " </option>\n" )
out.write( " </options>\n" )
out.write( """</filter>\n""" )
out.close()
def write_database_dump_info( input_dir, output_dir, dbkey, chrom_lengths, default_bitset_size ):
#generate hash for profiled table directories
#sort directories off output root (files in output root not hashed, including the profiler_info.txt file)
#sort files in each directory and hash file contents
profiled_hash = md5()
for table_dir in sorted( [ table_dir for table_dir in os.listdir( output_dir ) if os.path.isdir( os.path.join( output_dir, table_dir ) ) ] ):
for filename in sorted( os.listdir( os.path.join( output_dir, table_dir ) ) ):
f = open( os.path.join( output_dir, table_dir, filename ), 'rb' )
while True:
hash_chunk = f.read( CHUNK_SIZE )
if not hash_chunk:
break
profiled_hash.update( hash_chunk )
profiled_hash = profiled_hash.hexdigest()
#generate hash for input dir
#sort directories off input root
#sort files in each directory and hash file contents
database_hash = md5()
for dirpath, dirnames, filenames in sorted( os.walk( input_dir ) ):
for filename in sorted( filenames ):
f = open( os.path.join( input_dir, dirpath, filename ), 'rb' )
while True:
hash_chunk = f.read( CHUNK_SIZE )
if not hash_chunk:
break
database_hash.update( hash_chunk )
database_hash = database_hash.hexdigest()
#write out info file
out = open( os.path.join( output_dir, 'profiler_info.txt' ), 'wb' )
out.write( 'dbkey\t%s\n' % ( dbkey ) )
out.write( 'chromosomes\t%s\n' % ( ','.join( [ '%s=%s' % ( chrom_name, chrom_len ) for chrom_name, chrom_len in chrom_lengths.iteritems() ] ) ) )
out.write( 'bitset_size\t%s\n' % ( default_bitset_size ) )
for line in open( os.path.join( input_dir, 'trackDb.sql' ) ):
line = line.strip()
if line.startswith( '-- Dump completed on ' ):
line = line[ len( '-- Dump completed on ' ): ]
out.write( 'dump_time\t%s\n' % ( line ) )
break
out.write( 'dump_hash\t%s\n' % ( database_hash ) )
out.write( 'profiler_time\t%s\n' % ( time.time() ) )
out.write( 'profiler_hash\t%s\n' % ( profiled_hash ) )
out.write( 'profiler_version\t%s\n' % ( VERSION ) )
out.write( 'profiler_struct_format\t%s\n' % ( STRUCT_FMT ) )
out.write( 'profiler_struct_size\t%s\n' % ( STRUCT_SIZE ) )
out.close()
def __main__():
usage = "usage: %prog options"
parser = OptionParser( usage=usage )
parser.add_option( '-d', '--dbkey', dest='dbkey', default='hg18', help='dbkey to process' )
parser.add_option( '-i', '--input_dir', dest='input_dir', default=os.path.join( 'golden_path','%s', 'database' ), help='Input Directory' )
parser.add_option( '-o', '--output_dir', dest='output_dir', default=os.path.join( 'profiled_annotations','%s' ), help='Output Directory' )
parser.add_option( '-c', '--chromosomes', dest='chromosomes', default='', help='Comma separated list of: ChromName1[=length],ChromName2[=length],...' )
parser.add_option( '-b', '--bitset_size', dest='bitset_size', default=DEFAULT_BITSET_SIZE, type='int', help='Default BitSet size; overridden by sizes specified in chromInfo.txt.gz or by --chromosomes' )
parser.add_option( '-f', '--ftp_site', dest='ftp_site', default='hgdownload.cse.ucsc.edu', help='FTP site; used for chromosome info when chromInfo.txt.gz method fails' )
parser.add_option( '-p', '--ftp_path', dest='ftp_path', default='/goldenPath/%s/chromosomes/', help='FTP Path; used for chromosome info when chromInfo.txt.gz method fails' )
( options, args ) = parser.parse_args()
input_dir = options.input_dir
if '%' in input_dir:
input_dir = input_dir % options.dbkey
assert os.path.exists( input_dir ), 'Input directory does not exist'
output_dir = options.output_dir
if '%' in output_dir:
output_dir = output_dir % options.dbkey
assert not os.path.exists( output_dir ), 'Output directory already exists'
os.makedirs( output_dir )
ftp_path = options.ftp_path
if '%' in ftp_path:
ftp_path = ftp_path % options.dbkey
#Get chromosome names and lengths
chrom_lengths = {}
if options.chromosomes:
for chrom in options.chromosomes.split( ',' ):
fields = chrom.split( '=' )
chrom = fields[0]
if len( fields ) > 1:
chrom_len = int( fields[1] )
else:
chrom_len = options.bitset_size
chrom_lengths[ chrom ] = chrom_len
chroms = chrom_lengths.keys()
print 'Chrom info taken from command line option.'
else:
try:
for line in gzip.open( os.path.join( input_dir, 'chromInfo.txt.gz' ) ):
fields = line.strip().split( '\t' )
chrom_lengths[ fields[0] ] = int( fields[ 1 ] )
chroms = chrom_lengths.keys()
print 'Chrom info taken from chromInfo.txt.gz.'
except Exception, e:
print 'Error loading chrom info from chromInfo.txt.gz, trying FTP method.'
chrom_lengths = {} #zero out chrom_lengths
chroms = []
ftp = FTP( options.ftp_site )
ftp.login()
for name in ftp.nlst( ftp_path ):
if name.endswith( '.fa.gz' ):
chroms.append( name.split( '/' )[-1][ :-len( '.fa.gz' ) ] )
ftp.close()
for chrom in chroms:
chrom_lengths[ chrom ] = options.bitset_size
#sort chroms by length of name, decending; necessary for when table names start with chrom name
chroms = list( reversed( [ chrom for chrom_len, chrom in sorted( [ ( len( chrom ), chrom ) for chrom in chroms ] ) ] ) )
#parse tables from local files
#loop through directory contents, if file ends in '.sql', process table
for filename in os.listdir( input_dir ):
if filename.endswith ( '.sql' ):
base_filename = filename[ 0:-len( '.sql' ) ]
table_out_dir = os.path.join( output_dir, base_filename )
#some tables are chromosome specific, lets strip off the chrom name
for chrom in chroms:
if base_filename.startswith( "%s_" % chrom ):
#found chromosome
table_out_dir = os.path.join( output_dir, base_filename[len( "%s_" % chrom ):] )
break
#create table dir
if not os.path.exists( table_out_dir ):
os.mkdir( table_out_dir ) #table dir may already exist in the case of single chrom tables
print "Created table dir (%s)." % table_out_dir
else:
print "Table dir (%s) already exists." % table_out_dir
#find column assignments
table_name, chrom_col, start_col, end_col = get_columns( "%s.sql" % os.path.join( input_dir, base_filename ) )
if chrom_col is None or start_col is None or end_col is None:
print "Table %s (%s) does not appear to have a chromosome, a start, or a stop." % ( table_name, "%s.sql" % os.path.join( input_dir, base_filename ) )
if not os.listdir( table_out_dir ):
print "Removing empty table (%s) directory (%s)." % ( table_name, table_out_dir )
os.rmdir( table_out_dir )
continue
#build bitsets from table
bitset_dict = {}
for line in gzip.open( '%s.txt.gz' % os.path.join( input_dir, base_filename ) ):
fields = line.strip().split( '\t' )
chrom = fields[ chrom_col ]
start = int( fields[ start_col ] )
end = int( fields[ end_col ] )
if chrom not in bitset_dict:
bitset_dict[ chrom ] = BitSet( chrom_lengths.get( chrom, options.bitset_size ) )
bitset_dict[ chrom ].set_range( start, end - start )
#write bitsets as profiled annotations
for chrom_name, chrom_bits in bitset_dict.iteritems():
out = open( os.path.join( table_out_dir, '%s.covered' % chrom_name ), 'wb' )
end = 0
total_regions = 0
total_coverage = 0
max_size = chrom_lengths.get( chrom_name, options.bitset_size )
while True:
start = chrom_bits.next_set( end )
if start >= max_size:
break
end = chrom_bits.next_clear( start )
out.write( struct.pack( STRUCT_FMT, start ) )
out.write( struct.pack( STRUCT_FMT, end ) )
total_regions += 1
total_coverage += end - start
if end >= max_size:
break
out.close()
open( os.path.join( table_out_dir, '%s.total_regions' % chrom_name ), 'wb' ).write( str( total_regions ) )
open( os.path.join( table_out_dir, '%s.total_coverage' % chrom_name ), 'wb' ).write( str( total_coverage ) )
#create xml
create_grouping_xml( input_dir, output_dir, options.dbkey )
#create database dump info file, for database version control
write_database_dump_info( input_dir, output_dir, options.dbkey, chrom_lengths, options.bitset_size )
if __name__ == "__main__": __main__()
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