jjohnson/gmap: gmap/lib/galaxy/datatypes/gmap.py annotate

annotate gmap/lib/galaxy/datatypes/gmap.py @ 2:52da588232b0

Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these.

author	Jim Johnson <jj@umn.edu>
date	Fri, 21 Oct 2011 11:38:55 -0500
parents	d58d272914e7
children	f4b4c1712e39

rev	line source
0 d58d272914e7 Uploaded jjohnson parents: diff changeset	1 """
d58d272914e7 Uploaded jjohnson parents: diff changeset	2 GMAP indexes
d58d272914e7 Uploaded jjohnson parents: diff changeset	3 """
d58d272914e7 Uploaded jjohnson parents: diff changeset	4 import logging
d58d272914e7 Uploaded jjohnson parents: diff changeset	5 import os,os.path,re
2 52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	6 import data
0 d58d272914e7 Uploaded jjohnson parents: diff changeset	7 from data import Text
2 52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	8 from galaxy import util
0 d58d272914e7 Uploaded jjohnson parents: diff changeset	9 from metadata import MetadataElement
d58d272914e7 Uploaded jjohnson parents: diff changeset	10
d58d272914e7 Uploaded jjohnson parents: diff changeset	11 log = logging.getLogger(__name__)
d58d272914e7 Uploaded jjohnson parents: diff changeset	12
d58d272914e7 Uploaded jjohnson parents: diff changeset	13 class GmapDB( Text ):
d58d272914e7 Uploaded jjohnson parents: diff changeset	14 """
d58d272914e7 Uploaded jjohnson parents: diff changeset	15 A GMAP DB for indexes
d58d272914e7 Uploaded jjohnson parents: diff changeset	16 """
d58d272914e7 Uploaded jjohnson parents: diff changeset	17 MetadataElement( name="db_name", desc="The db name for this index set", default='unknown', set_in_upload=True, readonly=True )
d58d272914e7 Uploaded jjohnson parents: diff changeset	18 MetadataElement( name="basesize", default="12", desc="The basesize for offsetscomp", visible=True, readonly=True )
d58d272914e7 Uploaded jjohnson parents: diff changeset	19 MetadataElement( name="kmers", default=[''], desc="The kmer sizes for indexes", visible=True, no_value=[''], readonly=True )
d58d272914e7 Uploaded jjohnson parents: diff changeset	20 MetadataElement( name="map_dir", desc="The maps directory", default='unknown', set_in_upload=True, readonly=True )
d58d272914e7 Uploaded jjohnson parents: diff changeset	21 MetadataElement( name="maps", default=[''], desc="The names of maps stored for this gmap gmapdb", visible=True, no_value=[''], readonly=True )
d58d272914e7 Uploaded jjohnson parents: diff changeset	22 MetadataElement( name="snps", default=[''], desc="The names of SNP indexes stored for this gmapdb", visible=True, no_value=[''], readonly=True )
d58d272914e7 Uploaded jjohnson parents: diff changeset	23 MetadataElement( name="cmet", default=False, desc="Has a cmet index", visible=True, readonly=True )
d58d272914e7 Uploaded jjohnson parents: diff changeset	24 MetadataElement( name="atoi", default=False, desc="Has a atoi index", visible=True, readonly=True )
d58d272914e7 Uploaded jjohnson parents: diff changeset	25
d58d272914e7 Uploaded jjohnson parents: diff changeset	26 file_ext = 'gmapdb'
d58d272914e7 Uploaded jjohnson parents: diff changeset	27 is_binary = True
d58d272914e7 Uploaded jjohnson parents: diff changeset	28 composite_type = 'auto_primary_file'
d58d272914e7 Uploaded jjohnson parents: diff changeset	29 allow_datatype_change = False
d58d272914e7 Uploaded jjohnson parents: diff changeset	30
d58d272914e7 Uploaded jjohnson parents: diff changeset	31 def generate_primary_file( self, dataset = None ):
d58d272914e7 Uploaded jjohnson parents: diff changeset	32 """
d58d272914e7 Uploaded jjohnson parents: diff changeset	33 This is called only at upload to write the html file
d58d272914e7 Uploaded jjohnson parents: diff changeset	34 cannot rename the datasets here - they come with the default unfortunately
d58d272914e7 Uploaded jjohnson parents: diff changeset	35 """
d58d272914e7 Uploaded jjohnson parents: diff changeset	36 return '<html><head></head><body>AutoGenerated Primary File for Composite Dataset</body></html>'
d58d272914e7 Uploaded jjohnson parents: diff changeset	37
d58d272914e7 Uploaded jjohnson parents: diff changeset	38 def regenerate_primary_file(self,dataset):
d58d272914e7 Uploaded jjohnson parents: diff changeset	39 """
d58d272914e7 Uploaded jjohnson parents: diff changeset	40 cannot do this until we are setting metadata
d58d272914e7 Uploaded jjohnson parents: diff changeset	41 """
d58d272914e7 Uploaded jjohnson parents: diff changeset	42 bn = dataset.metadata.db_name
d58d272914e7 Uploaded jjohnson parents: diff changeset	43 log.info( "GmapDB regenerate_primary_file %s" % (bn))
d58d272914e7 Uploaded jjohnson parents: diff changeset	44 rval = ['<html><head><title>GMAPDB %s</title></head><p/><H3>GMAPDB %s</H3><p/>cmet %s<br>atoi %s<H4>Maps:</H4><ul>' % (bn,bn,dataset.metadata.cmet,dataset.metadata.atoi)]
d58d272914e7 Uploaded jjohnson parents: diff changeset	45 for i,name in enumerate(dataset.metadata.maps):
d58d272914e7 Uploaded jjohnson parents: diff changeset	46 rval.append( '<li>%s' % name)
d58d272914e7 Uploaded jjohnson parents: diff changeset	47 rval.append( '</ul></html>' )
d58d272914e7 Uploaded jjohnson parents: diff changeset	48 f = file(dataset.file_name,'w')
d58d272914e7 Uploaded jjohnson parents: diff changeset	49 f.write("\n".join( rval ))
d58d272914e7 Uploaded jjohnson parents: diff changeset	50 f.write('\n')
d58d272914e7 Uploaded jjohnson parents: diff changeset	51 f.close()
d58d272914e7 Uploaded jjohnson parents: diff changeset	52
d58d272914e7 Uploaded jjohnson parents: diff changeset	53 def set_peek( self, dataset, is_multi_byte=False ):
d58d272914e7 Uploaded jjohnson parents: diff changeset	54 log.info( "GmapDB set_peek %s" % (dataset))
d58d272914e7 Uploaded jjohnson parents: diff changeset	55 if not dataset.dataset.purged:
d58d272914e7 Uploaded jjohnson parents: diff changeset	56 dataset.peek = "GMAPDB index %s\n cmet %s\n atoi %s\n maps %s" % ( dataset.metadata.db_name,dataset.metadata.cmet,dataset.metadata.atoi,dataset.metadata.maps )
d58d272914e7 Uploaded jjohnson parents: diff changeset	57 dataset.blurb = "GMAPDB %s" % ( dataset.metadata.db_name )
d58d272914e7 Uploaded jjohnson parents: diff changeset	58 else:
d58d272914e7 Uploaded jjohnson parents: diff changeset	59 dataset.peek = 'file does not exist'
d58d272914e7 Uploaded jjohnson parents: diff changeset	60 dataset.blurb = 'file purged from disk'
d58d272914e7 Uploaded jjohnson parents: diff changeset	61 def display_peek( self, dataset ):
d58d272914e7 Uploaded jjohnson parents: diff changeset	62 try:
d58d272914e7 Uploaded jjohnson parents: diff changeset	63 return dataset.peek
d58d272914e7 Uploaded jjohnson parents: diff changeset	64 except:
d58d272914e7 Uploaded jjohnson parents: diff changeset	65 return "GMAP index file"
2 52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	66
0 d58d272914e7 Uploaded jjohnson parents: diff changeset	67 def sniff( self, filename ):
d58d272914e7 Uploaded jjohnson parents: diff changeset	68 return False
d58d272914e7 Uploaded jjohnson parents: diff changeset	69 def set_meta( self, dataset, overwrite = True, **kwd ):
d58d272914e7 Uploaded jjohnson parents: diff changeset	70 """
d58d272914e7 Uploaded jjohnson parents: diff changeset	71 Expecting:
d58d272914e7 Uploaded jjohnson parents: diff changeset	72 extra_files_path/<db_name>/db_name>.ref<basesize><kmer>3<index>
d58d272914e7 Uploaded jjohnson parents: diff changeset	73 extra_files_path/db_name/db_name.ref1[2345]1[2345]3offsetscomp
d58d272914e7 Uploaded jjohnson parents: diff changeset	74 extra_files_path/db_name/db_name.ref1[2345]1[2345]3positions
d58d272914e7 Uploaded jjohnson parents: diff changeset	75 extra_files_path/db_name/db_name.ref1[2345]1[2345]3gammaptrs
d58d272914e7 Uploaded jjohnson parents: diff changeset	76 index maps:
d58d272914e7 Uploaded jjohnson parents: diff changeset	77 extra_files_path/db_name/db_name.maps/*.iit
d58d272914e7 Uploaded jjohnson parents: diff changeset	78 """
d58d272914e7 Uploaded jjohnson parents: diff changeset	79 log.info( "GmapDB set_meta %s %s" % (dataset,dataset.extra_files_path))
d58d272914e7 Uploaded jjohnson parents: diff changeset	80 pat = '(.*)\.((ref)\|(met)[atgc][atgc]\|(a2i)[atgc][atgc])((\d\d)(\d\d))?3positions(\.(.+))?'
d58d272914e7 Uploaded jjohnson parents: diff changeset	81 efp = dataset.extra_files_path
d58d272914e7 Uploaded jjohnson parents: diff changeset	82 flist = os.listdir(efp)
d58d272914e7 Uploaded jjohnson parents: diff changeset	83 for i,fname in enumerate(flist):
d58d272914e7 Uploaded jjohnson parents: diff changeset	84 log.info( "GmapDB set_meta %s %s" % (i,fname))
d58d272914e7 Uploaded jjohnson parents: diff changeset	85 fpath = os.path.join(efp,fname)
d58d272914e7 Uploaded jjohnson parents: diff changeset	86 if os.path.isdir(fpath):
d58d272914e7 Uploaded jjohnson parents: diff changeset	87 ilist = os.listdir(fpath)
d58d272914e7 Uploaded jjohnson parents: diff changeset	88 kmers = {'':'default'} # HACK '' empty key added so user has default choice when selecting kmer from metadata
d58d272914e7 Uploaded jjohnson parents: diff changeset	89 for j,iname in enumerate(ilist):
d58d272914e7 Uploaded jjohnson parents: diff changeset	90 log.info( "GmapDB set_meta file %s %s" % (j,iname))
d58d272914e7 Uploaded jjohnson parents: diff changeset	91 ipath = os.path.join(fpath,iname)
d58d272914e7 Uploaded jjohnson parents: diff changeset	92 if os.path.isdir(ipath): # find maps
d58d272914e7 Uploaded jjohnson parents: diff changeset	93 dataset.metadata.map_dir = iname
d58d272914e7 Uploaded jjohnson parents: diff changeset	94 for mapfile in os.listdir(ipath):
d58d272914e7 Uploaded jjohnson parents: diff changeset	95 mapname = mapfile.replace('.iit','')
d58d272914e7 Uploaded jjohnson parents: diff changeset	96 log.info( "GmapDB set_meta map %s %s" % (mapname,mapfile))
d58d272914e7 Uploaded jjohnson parents: diff changeset	97 dataset.metadata.maps.append(mapname)
d58d272914e7 Uploaded jjohnson parents: diff changeset	98 else:
d58d272914e7 Uploaded jjohnson parents: diff changeset	99 m = re.match(pat,iname)
d58d272914e7 Uploaded jjohnson parents: diff changeset	100 if m:
d58d272914e7 Uploaded jjohnson parents: diff changeset	101 log.info( "GmapDB set_meta m %s %s " % (iname, m))
d58d272914e7 Uploaded jjohnson parents: diff changeset	102 assert len(m.groups()) == 10
d58d272914e7 Uploaded jjohnson parents: diff changeset	103 dataset.metadata.db_name = fname
d58d272914e7 Uploaded jjohnson parents: diff changeset	104 if m.groups()[2] == 'ref':
d58d272914e7 Uploaded jjohnson parents: diff changeset	105 if m.groups()[-1] != None:
d58d272914e7 Uploaded jjohnson parents: diff changeset	106 dataset.metadata.snps.append(m.groups()[-1])
d58d272914e7 Uploaded jjohnson parents: diff changeset	107 else:
d58d272914e7 Uploaded jjohnson parents: diff changeset	108 if m.groups()[-3] != None:
d58d272914e7 Uploaded jjohnson parents: diff changeset	109 k = int(m.groups()[-3])
d58d272914e7 Uploaded jjohnson parents: diff changeset	110 kmers[k] = k
d58d272914e7 Uploaded jjohnson parents: diff changeset	111 if m.groups()[-4] != None:
d58d272914e7 Uploaded jjohnson parents: diff changeset	112 dataset.metadata.basesize = int( m.groups()[-4])
d58d272914e7 Uploaded jjohnson parents: diff changeset	113 elif m.groups()[3] == 'met':
d58d272914e7 Uploaded jjohnson parents: diff changeset	114 dataset.metadata.cmet = True
d58d272914e7 Uploaded jjohnson parents: diff changeset	115 elif m.groups()[4] == 'a2i':
d58d272914e7 Uploaded jjohnson parents: diff changeset	116 dataset.metadata.atoi = True
d58d272914e7 Uploaded jjohnson parents: diff changeset	117 dataset.metadata.kmers = kmers.keys()
d58d272914e7 Uploaded jjohnson parents: diff changeset	118
2 52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	119 class GmapSnpIndex( Text ):
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	120 """
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	121 A GMAP SNP index created by snpindex
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	122 """
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	123 MetadataElement( name="db_name", desc="The db name for this index set", default='unknown', set_in_upload=True, readonly=True )
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	124 MetadataElement( name="snps_name", default='snps', desc="The name of SNP index", visible=True, no_value='', readonly=True )
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	125
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	126 file_ext = 'gmapsnpindex'
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	127 is_binary = True
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	128 composite_type = 'auto_primary_file'
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	129 allow_datatype_change = False
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	130
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	131 def generate_primary_file( self, dataset = None ):
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	132 """
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	133 This is called only at upload to write the html file
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	134 cannot rename the datasets here - they come with the default unfortunately
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	135 """
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	136 return '<html><head></head><body>AutoGenerated Primary File for Composite Dataset</body></html>'
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	137
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	138 def regenerate_primary_file(self,dataset):
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	139 """
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	140 cannot do this until we are setting metadata
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	141 """
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	142 bn = dataset.metadata.db_name
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	143 log.info( "GmapDB regenerate_primary_file %s" % (bn))
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	144 rval = ['<html><head><title>GMAPDB %s</title></head><p/><H3>GMAPDB %s</H3><p/>cmet %s<br>atoi %s<H4>Maps:</H4><ul>' % (bn,bn,dataset.metadata.cmet,dataset.metadata.atoi)]
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	145 for i,name in enumerate(dataset.metadata.maps):
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	146 rval.append( '<li>%s' % name)
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	147 rval.append( '</ul></html>' )
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	148 f = file(dataset.file_name,'w')
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	149 f.write("\n".join( rval ))
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	150 f.write('\n')
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	151 f.close()
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	152 def set_peek( self, dataset, is_multi_byte=False ):
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	153 log.info( "GmapSnpIndex set_peek %s" % (dataset))
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	154 if not dataset.dataset.purged:
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	155 dataset.peek = "GMAP SNPindex %s on %s\n" % ( dataset.metadata.snps_name,dataset.metadata.db_name)
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	156 dataset.blurb = "GMAP SNPindex %s on %s\n" % ( dataset.metadata.snps_name,dataset.metadata.db_name)
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	157 else:
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	158 dataset.peek = 'file does not exist'
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	159 dataset.blurb = 'file purged from disk'
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	160 def display_peek( self, dataset ):
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	161 try:
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	162 return dataset.peek
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	163 except:
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	164 return "GMAP SNP index"
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	165
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	166 def sniff( self, filename ):
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	167 return False
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	168 def set_meta( self, dataset, overwrite = True, **kwd ):
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	169 """
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	170 Expecting:
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	171 extra_files_path/snp_name.iit
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	172 extra_files_path/db_name/db_name.ref1[2345]1[2345]3offsetscomp.snp_name
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	173 extra_files_path/db_name/db_name.ref1[2345]1[2345]3positions.snp_name
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	174 extra_files_path/db_name/db_name.ref1[2345]1[2345]3gammaptrs.snp_name
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	175 """
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	176 log.info( "GmapSnpIndex set_meta %s %s" % (dataset,dataset.extra_files_path))
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	177 pat = '(.*)\.(ref((\d\d)(\d\d))?3positions)\.(.+)?'
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	178 efp = dataset.extra_files_path
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	179 flist = os.listdir(efp)
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	180 for i,fname in enumerate(flist):
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	181 m = re.match(pat,fname)
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	182 if m:
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	183 assert len(m.groups()) == 6
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	184 dataset.metadata.db_name = m.groups()[0]
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	185 dataset.metadata.snps_name = m.groups()[-1]
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	186
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	187
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	188
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	189
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	190 class IntervalIndexTree( Text ):
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	191 """
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	192 A GMAP Interval Index Tree Map
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	193 created by iit_store
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	194 (/path/to/map)/(mapname).iit
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	195 """
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	196 file_ext = 'iit'
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	197 is_binary = True
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	198
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	199 class SpliceSitesIntervalIndexTree( IntervalIndexTree ):
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	200 """
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	201 A GMAP Interval Index Tree Map
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	202 created by iit_store
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	203 """
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	204 file_ext = 'splicesites.iit'
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	205
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	206 class IntronsIntervalIndexTree( IntervalIndexTree ):
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	207 """
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	208 A GMAP Interval Index Tree Map
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	209 created by iit_store
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	210 """
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	211 file_ext = 'introns.iit'
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	212
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	213 class SNPsIntervalIndexTree( IntervalIndexTree ):
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	214 """
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	215 A GMAP Interval Index Tree Map
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	216 created by iit_store
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	217 """
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	218 file_ext = 'snps.iit'
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	219
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	220 class IntervalAnnotation( Text ):
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	221 """
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	222 Class describing a GMAP Interval format:
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	223 >label coords optional_tag
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	224 optional_annotation (which may be zero, one, or multiple lines)
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	225 The coords should be of the form:
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	226 chr:position
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	227 chr:startposition..endposition
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	228 """
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	229 file_ext = 'gmap_annotation'
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	230 """Add metadata elements"""
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	231 MetadataElement( name="annotations", default=0, desc="Number of interval annotations", readonly=True, optional=True, visible=False, no_value=0 )
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	232
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	233 def set_meta( self, dataset, **kwd ):
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	234 """
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	235 Set the number of annotations and the number of data lines in dataset.
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	236 """
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	237 data_lines = 0
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	238 annotations = 0
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	239 for line in file( dataset.file_name ):
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	240 line = line.strip()
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	241 if line and line.startswith( '>' ):
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	242 annotations += 1
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	243 data_lines +=1
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	244 else:
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	245 data_lines += 1
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	246 dataset.metadata.data_lines = data_lines
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	247 dataset.metadata.annotations = annotations
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	248 def set_peek( self, dataset, is_multi_byte=False ):
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	249 if not dataset.dataset.purged:
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	250 dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	251 if dataset.metadata.annotations:
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	252 dataset.blurb = "%s annotations" % util.commaify( str( dataset.metadata.annotations ) )
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	253 else:
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	254 dataset.blurb = data.nice_size( dataset.get_size() )
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	255 else:
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	256 dataset.peek = 'file does not exist'
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	257 dataset.blurb = 'file purged from disk'
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	258
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	259 def sniff( self, filename ):
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	260 """
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	261 Determines whether the file is a gmap annotation file
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	262 Format:
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	263 >label coords optional_tag
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	264 optional_annotation (which may be zero, one, or multiple lines)
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	265 For example, the label may be an EST accession, with the coords
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	266 representing its genomic position. Labels may be duplicated if
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	267 necessary.
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	268 The coords should be of the form
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	269 chr:position
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	270 chr:startposition..endposition
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	271 The term "chr:position" is equivalent to "chr:position..position". If
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	272 you want to indicate that the interval is on the minus strand or
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	273 reverse direction, then <endposition> may be less than <startposition>.
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	274 """
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	275 try:
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	276 pat = '>(\S+)\s((\S+):(\d+)(\.\.(\d+))?(\s.(.+))?$' #>label chr:position[..endposition][ optional_tag]
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	277 fh = open( filename )
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	278 count = 0
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	279 while True and count < 10:
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	280 line = fh.readline()
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	281 if not line:
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	282 break #EOF
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	283 line = line.strip()
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	284 if line: #first non-empty line
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	285 if line.startswith( '>' ):
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	286 count += 1
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	287 if re.match(pat,line) == None: # Failed to match
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	288 return False
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	289 finally:
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	290 fh.close()
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	291 return False
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	292
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	293 class SpliceSiteAnnotation(IntervalAnnotation):
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	294 file_ext = 'gmap_splicesites'
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	295 """
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	296 Example:
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	297 >NM_004448.ERBB2.exon1 17:35110090..35110091 donor 6678
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	298 >NM_004448.ERBB2.exon2 17:35116768..35116769 acceptor 6678
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	299 >NM_004448.ERBB2.exon2 17:35116920..35116921 donor 1179
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	300 >NM_004448.ERBB2.exon3 17:35118099..35118100 acceptor 1179
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	301 >NM_004449.ERG.exon1 21:38955452..38955451 donor 783
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	302 >NM_004449.ERG.exon2 21:38878740..38878739 acceptor 783
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	303 >NM_004449.ERG.exon2 21:38878638..38878637 donor 360
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	304 >NM_004449.ERG.exon3 21:38869542..38869541 acceptor 360
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	305 Each line must start with a ">" character, then be followed by an
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	306 identifier, which may have duplicates and can have any format, with
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	307 the gene name or exon number shown here only as a suggestion. Then
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	308 there should be the chromosomal coordinates which straddle the
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	309 exon-intron boundary, so one coordinate is on the exon and one is on
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	310 the intron. (Coordinates are all 1-based, so the first character of a
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	311 chromosome is number 1.) Finally, there should be the splice type:
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	312 "donor" or "acceptor". You may optionally store the intron distance
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	313 at the end. GSNAP can use this intron distance, if it is longer than
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	314 its value for --localsplicedist, to look for long introns at that
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	315 splice site. The same splice site may have different intron distances
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	316 in the database; GSNAP will use the longest intron distance reported
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	317 in searching for long introns.
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	318 """
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	319 def sniff( self, filename ): # TODO
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	320 """
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	321 Determines whether the file is a gmap splice site annotation file
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	322 """
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	323 try:
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	324 pat = '>(\S+\.intron\d+)\s((\S+):(\d+)\.\.(\d+))\s(donor\|acceptor)(\s(\d+))?$' #>label chr:position..position donor\|acceptor[ intron_dist]
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	325 fh = open( filename )
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	326 count = 0
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	327 while True and count < 10:
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	328 line = fh.readline()
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	329 if not line:
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	330 break #EOF
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	331 line = line.strip()
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	332 if line: #first non-empty line
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	333 count += 1
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	334 if re.match(pat,line) == None: # Failed to match
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	335 return False
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	336 finally:
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	337 fh.close()
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	338 return False
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	339
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	340 class IntronAnnotation(IntervalAnnotation):
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	341 file_ext = 'gmap_introns'
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	342 """
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	343 Example:
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	344 >NM_004448.ERBB2.intron1 17:35110090..35116769
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	345 >NM_004448.ERBB2.intron2 17:35116920..35118100
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	346 >NM_004449.ERG.intron1 21:38955452..38878739
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	347 >NM_004449.ERG.intron2 21:38878638..38869541
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	348 The coordinates are 1-based, and specify the exon coordinates
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	349 surrounding the intron, with the first coordinate being from the donor
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	350 exon and the second one being from the acceptor exon.
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	351 """
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	352 def sniff( self, filename ): # TODO
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	353 """
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	354 Determines whether the file is a gmap Intron annotation file
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	355 """
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	356 try:
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	357 pat = '>(\S+\.intron\d+)\s((\S+):(\d+)\.\.(\d+)(\s(.)+)?$' #>label chr:position
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	358 fh = open( filename )
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	359 count = 0
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	360 while True and count < 10:
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	361 line = fh.readline()
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	362 if not line:
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	363 break #EOF
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	364 line = line.strip()
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	365 if line: #first non-empty line
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	366 count += 1
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	367 if re.match(pat,line) == None: # Failed to match
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	368 return False
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	369 finally:
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	370 fh.close()
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	371 return False
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	372
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	373 class SNPAnnotation(IntervalAnnotation):
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	374 file_ext = 'gmap_snps'
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	375 """
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	376 Example:
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	377 >rs62211261 21:14379270 CG
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	378 >rs62211262 21:14379281 AT
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	379 >rs62211263 21:14379298 WN
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	380 Each line must start with a ">" character, then be followed by an
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	381 identifier (which may have duplicates). Then there should be the
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	382 chromosomal coordinate of the SNP. (Coordinates are all 1-based, so
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	383 the first character of a chromosome is number 1.) Finally, there
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	384 should be the two possible alleles. (Previous versions required that
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	385 these be in alphabetical order: "AC", "AG", "AT", "CG", "CT", or "GT",
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	386 but that is no longer a requirement.) These alleles must correspond
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	387 to the possible nucleotides on the plus strand of the genome. If the
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	388 one of these two letters does not match the allele in the reference
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	389 sequence, that SNP will be ignored in subsequent processing as a
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	390 probable error.
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	391
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	392 GSNAP also supports the idea of a wildcard SNP. A wildcard SNP allows
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	393 all nucleotides to match at that position, not just a given reference
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	394 and alternate allele. It is essentially as if an "N" were recorded at
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	395 that genomic location, although the index files still keep track of
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	396 the reference allele. To indicate that a position has a wildcard SNP,
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	397 you can indicate the genotype as "WN", where "W" is the reference
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	398 allele. Another indication of a wildcard SNP is to provide two
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	399 separate lines at that position with the genotypes "WX" and "WY",
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	400 where "W" is the reference allele and "X" and "Y" are two different
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	401 alternate alleles.
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	402 """
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	403 def sniff( self, filename ):
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	404 """
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	405 Determines whether the file is a gmap SNP annotation file
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	406 """
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	407 try:
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	408 pat = '>(\S+)\s((\S+):(\d+)\s([TACGW][TACGN])$' #>label chr:position ATCG
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	409 fh = open( filename )
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	410 count = 0
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	411 while True and count < 10:
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	412 line = fh.readline()
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	413 if not line:
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	414 break #EOF
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	415 line = line.strip()
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	416 if line: #first non-empty line
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	417 count += 1
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	418 if re.match(pat,line) == None: # Failed to match
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	419 return False
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	420 finally:
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	421 fh.close()
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	422 return False
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	423
52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these. Jim Johnson <jj@umn.edu> parents: 0 diff changeset	424

Mercurial > repos > jjohnson > gmap

annotate gmap/lib/galaxy/datatypes/gmap.py @ 2:52da588232b0