~ubuntu-branches/ubuntu/oneiric/bioperl/oneiric

use enum qw(:all_bacends__ x matches misMatches repMatches nCount qNumInsert tNumInsert tBaseInsert strand qName qSize qStart qEnd tName tSize tStart tEnd blockCount blockSizes qStarts tStarts);

use enum qw(:all_est__ bin matches misMatches repMatches nCount qNumInsert qBaseInsert tNumInsert tBaseInsert strand qName qSize qStart qEnd tName tSize tStart tEnd blockCount blockSizes qStarts tStarts);

use enum qw(:all_mrna__ bin matches misMatches repMatches nCount qNumInsert qBaseInsert tNumInsert tBaseInsert strand qName qSize qStart qEnd tName tSize tStart tEnd blockCount blockSizes qStarts tStarts);

use enum qw(:all_sts_primer__ matches misMatches repMatches nCount qNumInsert qBaseInsert tNumInsert tBaseInsert strand qName qSize qStart qEnd tName tSize tStart tEnd blockCount blockSizes qStarts tStarts);

use enum qw(:all_sts_seq__ matches misMatches repMatches nCount qNumInsert qBaseInsert tNumInsert tBaseInsert strand qName qSize qStart qEnd tName tSize tStart tEnd blockCount blockSizes qStarts tStarts);

use enum qw(:bacEndPairs__ bin chrom chromStart chromEnd name score strand pslTable lfCount lfStarts lfSizes lfNames);

use enum qw(:blatFish__ bin matches misMatches repMatches nCount qNumInsert qBaseInsert tNumInsert tBaseInsert strand qName qSize qStart qEnd tName tSize tStart tEnd blockCount blockSizes qStarts tStarts);

use enum qw(:gap__ bin chrom chromStart chromEnd ix n size type bridge);

use enum qw(:gl__ bin frag start end strand);

use enum qw(:gold__ bin chrom chromStart chromEnd ix type frag fragStart fragEnd strand);

use enum qw(:intronEst__ bin matches misMatches repMatches nCount qNumInsert qBaseInsert tNumInsert tBaseInsert strand qName qSize qStart qEnd tName tSize tStart tEnd blockCount blockSizes qStarts tStarts);

use enum qw(:mrna__ bin matches misMatches repMatches nCount qNumInsert qBaseInsert tNumInsert tBaseInsert strand qName qSize qStart qEnd tName tSize tStart tEnd blockCount blockSizes qStarts tStarts);

use enum qw(:rmsk__ bin swScore milliDiv milliDel milliIns genoName genoStart genoEnd genoLeft strand repName repClass repFamily repStart repEnd repLeft id);

use enum qw(:clonePos__ name seqSize phase chrom chromStart chromEnd stage faFile);

use enum qw(:ctgPos__ contig size chrom chromStart chromEnd);

use enum qw(:cytoBand__ chrom chromStart chromEnd name gieStain);

use enum qw(:fishClones__ chrom chromStart chromEnd name score placeCount bandStarts bandEnds labs placeType accCount accNames stsCount stsNames beCount beNames);

use enum qw(:gcPercent__ chrom chromStart chromEnd name gcPpt);

use enum qw(:genscan__ name chrom strand txStart txEnd cdsStart cdsEnd exonCount exonStarts exonEnds);

use enum qw(:genscanSubopt__ bin chrom chromStart chromEnd name score strand);

use enum qw(:jaxOrtholog__ humanSymbol humanBand mgiId mouseSymbol mouseChr mouseCm mouseBand);

use enum qw(:refGene__ name chrom strand txStart txEnd cdsStart cdsEnd exonCount exonStarts exonEnds);

use enum qw(:refLink__ name product mrnaAcc protAcc geneName prodName locusLinkID omimId);

use enum qw(:refSeqAli__ bin matches misMatches repMatches nCount qNumInsert qBaseInsert tNumInsert tBaseInsert strand qName qSize qStart qEnd tName tSize tStart tEnd blockCount blockSizes qStarts tStarts);

use enum qw(:simpleRepeat__ bin chrom chromStart chromEnd name period copyNum consensusSize perMatch perIndel score A C G T entropy sequence);

use enum qw(:stsAlias__ alias identNo trueName);

use enum qw(:stsInfo__ identNo name gbCount genbank gdbCount gdb nameCount otherNames dbSTSid otherDbstsCount otherDbSTS leftPrimer rightPrimer distance organism sequence otherUCSCcount otherUCSC mergeUCSCcount mergeUCSC genethonName genethonChr genethonPos genethonLOD marshfieldName marshfieldChr marshfieldPos marshfieldLOD wiyacName wiyacChr wiyacPos wiyacLOD wirhName wirhChr wirhPos wirhLOD gm99gb4Name gm99gb4Chr gm99gb4Pos gm99gb4LOD gm99g3Name gm99g3Chr gm99g3Pos gm99g3LOD tngName tngChr tngPos tngLOD);

use enum qw(:stsMap__ chrom chromStart chromEnd name score identNo ctgAcc otherAcc genethonChrom genethonPos marshfieldChrom marshfieldPos gm99Gb4Chrom gm99Gb4Pos shgcTngChrom shgcTngPos shgcG3Chrom shgcG3Pos wiYacChrom wiYacPos wiRhChrom wiRhPos fishChrom beginBand endBand lab);

use enum qw(:uniGene_2__ bin chrom chromStart chromEnd name score strand txStart txEnd reserved exonCount exonStarts exonEnds);

###############################################

# end enum

###############################################

my %parentpos;

my %nolandmark = map {$_=>1} qw(gap cpgIsland recombRate_decode recombRate_marshfield recombRate_genethon

humMusL zoom1_humMusL zoom50_humMusL zoom2500_humMusL

genscanSubopt simpleRepeat snpNih snpTsc

);

foreach my $filename (@ARGV){

my $newfilename = $filename;

$newfilename =~ s/txt\.gz/gff/;

open(my $fhi, "zcat $filename |");

open(my $fho, ">$newfilename");

while(my $line = <$fhi>){

#these three should work the same way as unigene, but the fields are different order

# $filename =~ /affyRatio/ ? toGFF($line,$fho,['affyRatio', '', 3, 0, 1, 2, 4, 5,-1,-1,-1,10,11]) :

# $filename =~ /nci60/ ? toGFF($line,$fho,['nci60', '', 3, 0, 1, 2, 4, 5,-1,-1,-1,10,11]) :

# $filename =~ /rnaCluster/ ? toGFF($line,$fho,['rnaCluster', '', 4, 1, 2, 3, 5, 6,-1, 7, 8,11,12]) :

#these two are not yet handled

# $filename =~ /cpgIsland/ ? toGFF($line,$fho,['cpgIsland', '', 3, 0, 1, 2,-1,-1,-1]) :

# $filename =~ /estOrientInfo/ ? toGFF($line,$fho,['estOrientInfo', '',]) :

$filename =~ /uniGene_2/ ? toGFF($line,$fho,['uniGene_2', '', 4, 1, 2, 3, 5, 6,-1,-1,-1,11,12]) :

$filename =~ /all_bacends/ ? toGFF($line,$fho,['bacends', '', 9,13,15,16,-1, 8,-1,11,12,18,20]) :

$filename =~ /all_est/ ? toGFF($line,$fho,['est', '',10,14,16,17,-1, 9,-1,12,13,19,21]) :

$filename =~ /all_mrna/ ? toGFF($line,$fho,['mrna', '',10,14,16,17,-1, 9,-1,12,13,19,21]) :

$filename =~ /all_sts_primer/ ? toGFF($line,$fho,['sts_primer', '', 9,13,15,16,-1, 8,-1,11,12,18,20]) :

$filename =~ /all_sts_seq/ ? toGFF($line,$fho,['sts_seq', '', 9,13,15,16,-1, 8,-1,11,12,18,20]) :

$filename =~ /blastzBestMouse/ ? toGFF($line,$fho,['blastzBestMouse', '',10,14,16,17,-1, 9,-1,12,13,19,21]) :

$filename =~ /blastzMm2/ ? toGFF($line,$fho,['blastzMm2', '',10,14,16,17,-1, 9,-1,12,13,19,21]) :

$filename =~ /blastzTightMouse/ ? toGFF($line,$fho,['blastzTightMouse', '',10,14,16,17,-1, 9,-1,12,13,19,21]) :

$filename =~ /blatFish/ ? toGFF($line,$fho,['blatFish', '',10,14,16,17,-1, 9,-1,12,13,19,21]) :

$filename =~ /chimpBac/ ? toGFF($line,$fho,['chimpBac', '',10,14,16,17,-1, 9,-1,12,13,19,21]) :

$filename =~ /chimpBlat/ ? toGFF($line,$fho,['chimpBlat', '',10,14,16,17,-1, 9,-1,12,13,19,21]) :

$filename =~ /clonePos/ ? toGFF($line,$fho,['clonePos', '', 0, 3, 4, 5,-1,-1, 2]) :

$filename =~ /ctgPos/ ? toGFF($line,$fho,['ctgPos', '', 0, 2, 3, 4,-1,-1,-1]) :

$filename =~ /cytoBand/ ? toGFF($line,$fho,['cytoBand', '', 3, 0, 1, 2,-1,-1,-1]) :

$filename =~ /est/ ? toGFF($line,$fho,['est', '',10,14,16,17,-1,9,-1,12,13,19,21]) :

$filename =~ /fishClones/ ? toGFF($line,$fho,['fishClones', '', 3, 0, 1, 2, 4,-1,-1]) :

$filename =~ /gap/ ? toGFF($line,$fho,['gap', '', 7, 1, 2, 3,-1,-1,-1]) :

$filename =~ /gcPercent/ ? toGFF($line,$fho,['gcPercent', '', 3, 0, 1, 2, 4,-1,-1]) :

$filename =~ /genMapDb/ ? toGFF($line,$fho,['genMapDb', '', 3, 0, 1, 2, 4, 5,-1]) :

$filename =~ /genscanSubopt/ ? toGFF($line,$fho,['genscanSubopt', '', 4, 1, 2, 3, 5, 6,-1]) :

$filename =~ /gold/ ? toGFF($line,$fho,['gold', '', 6, 1, 2, 3,-1, 9,-1, 7, 8]) :

$filename =~ /intronEst/ ? toGFF($line,$fho,['intron_est', '',10,14,16,17,-1, 9,-1,12,13,19,21]) :

$filename =~ /recombRate/ ? eval { toGFF($line,$fho,['recombRate_decode', '', 3, 0, 1, 2, 4,-1,-1]);

toGFF($line,$fho,['recombRate_marshfield', '', 3, 0, 1, 2, 7,-1,-1]);

toGFF($line,$fho,['recombRate_genethon', '', 3, 0, 1, 2,10,-1,-1]); } :

$filename =~ /refSeqAli/ ? toGFF($line,$fho,['refSeqAli', '',10,14,16,17,-1, 9,-1,12,13,19,21]) :

$filename =~ /rmsk/ ? toGFF($line,$fho,['rmsk', '',10, 5, 6, 7,-1, 9,-1,13,14]) :

$filename =~ /simpleRepeat/ ? toGFF($line,$fho,['simpleRepeat', '', 4, 1, 2, 3,10,-1,-1]) :

$filename =~ /snpNih/ ? toGFF($line,$fho,['snpNih', '', 4, 1, 2, 3]) :

$filename =~ /snpTsc/ ? toGFF($line,$fho,['snpTsc', '', 4, 1, 2, 3]) :

$filename =~ /stsMap/ ? toGFF($line,$fho,['stsMap', '', 3, 0, 1, 2, 4,-1,-1]) :

$filename =~ /xenoEst/ ? toGFF($line,$fho,['xenoEst', '',10,14,16,17,-1, 9,-1,12,13,19,21]) :

100

$filename =~ /xenoMrna/ ? toGFF($line,$fho,['xenoMrna', '',10,14,16,17,-1, 9,-1,12,13,19,21]) :

101

$filename =~ /zoom1_humMusL/ ? toGFF($line,$fho,['zoom1_humMusL', '', 4, 1, 2, 3, 5, 6,-1]) :

102

$filename =~ /zoom2500_humMusL/ ? toGFF($line,$fho,['zoom2500_humMusL', '', 4, 1, 2, 3, 5, 6,-1]) :

103

$filename =~ /zoom50_humMusL/ ? toGFF($line,$fho,['zoom50_humMusL', '', 4, 1, 2, 3, 5, 6,-1]) :

104

$filename =~ /humMusL/ ? toGFF($line,$fho,['humMusL', '', 4, 1, 2, 3, 5, 6,-1]) :

105

106

$filename =~ /refGene/ ? toGFF2($line,$fho,['refGene', '', 0, 1, 2,-1,-1, 3, 4, 5, 6, 8, 9]) :

107

$filename =~ /genscan/ ? toGFF2($line,$fho,['genscan', '', 0, 1, 2,-1,-1, 3, 4, 5, 6, 8, 9]) :

108

$filename =~ /acembly/ ? toGFF2($line,$fho,['acembly', '', 0, 1, 2,-1,-1, 3, 4, 5, 6, 8, 9]) :

109

$filename =~ /ensGene/ ? toGFF2($line,$fho,['ensGene', '', 0, 1, 2,-1,-1, 3, 4, 5, 6, 8, 9]) :

110

$filename =~ /refFlat/ ? toGFF2($line,$fho,['refFlat', '', 0, 1, 2,-1,-1, 3, 4, 5, 6, 8, 9]) :

111

$filename =~ /sanger22pseudo/ ? toGFF2($line,$fho,['sanger22pseudo', '', 0, 1, 2,-1,-1, 3, 4, 5, 6, 8, 9]) :

112

$filename =~ /sanger22/ ? toGFF2($line,$fho,['sanger22', '', 0, 1, 2,-1,-1, 3, 4, 5, 6, 8, 9]) :

113

$filename =~ /softberryGene/ ? toGFF2($line,$fho,['softberryGene', '', 0, 1, 2,-1,-1, 3, 4, 5, 6, 8, 9]) :

114

$filename =~ /twinscan/ ? toGFF2($line,$fho,['twinscan', '', 0, 1, 2,-1,-1, 3, 4, 5, 6, 8, 9]) :

115

116

117

}

118

119

close($fhi);

120

close($fho);

121

}

122

123

###############################################

124

# begin filetype-specific subroutines

125

###############################################

126

127

sub toGFF2 {

128

my($line,$fho,$maps) = @_;

129

130

chomp $line; my @fields = split /\t/, $line;

131

132

if(!$nolandmark{render($maps->[v_refmethod],\@fields)}){

133

print join "\t", map {render($maps->[$_],\@fields)} (v_refseq,

134

v_refsource,

135

v_refmethod,

136

v_txstart,

137

v_txstop,

138

u_refscore,

139

v_refstrand,

140

v_refphase,);

141

print "\t";

142

print "Sequence " . render($maps->[v_refgroup],\@fields);

143

print "\n";

144

}

145

146

if(!$nolandmark{render($maps->[v_refmethod],\@fields)}){

147

print join "\t", map {render($maps->[$_],\@fields)} (v_refseq,

148

v_refsource,

149

v_refmethod,

150

v_cdsstart,

151

v_cdsstop,

152

u_refscore,

153

v_refstrand,

154

v_refphase,);

155

print "\t";

156

print "CDS " . render($maps->[v_refgroup],\@fields);

157

print "\n";

158

}

159

160

if(defined($maps->[v_exonstarts]) and defined($maps->[v_exonstops])){

161

my @starts = split /,/, render($maps->[v_exonstarts],\@fields);

162

my @stops = split /,/, render($maps->[v_exonstops],\@fields);

163

164

while(my $start = shift @starts){

165

my $stop = shift @stops;

166

print join "\t", (render($maps->[v_refseq],\@fields),

167

render($maps->[v_refsource],\@fields),

168

render($maps->[v_refmethod],\@fields),

169

$start,

170

$stop,

171

render($maps->[v_refscore],\@fields),

172

render($maps->[v_refstrand],\@fields),

173

render($maps->[v_refphase],\@fields),

174

render($maps->[v_refmethod],\@fields) . " " . render($maps->[v_refgroup],\@fields)

175

), "\n";

176

}

177

}

178

179

}

180

181

sub toGFF {

182

my($line,$fho,$maps) = @_;

183

184

chomp $line; my @fields = split /\t/, $line;

185

186

if(!$maps->[u_qrystart] and !$nolandmark{render($maps->[u_refmethod],\@fields)}){

187

print join "\t", map {render($maps->[$_],\@fields)} (u_refseq,

188

u_refsource,

189

u_refmethod,

190

u_refstart,

191

u_refstop,

192

u_refscore,

193

u_refstrand,

194

u_refphase);

195

print "\t";

196

print "Sequence " . render($maps->[u_refgroup],\@fields);

197

print "\n";

198

}

199

print join "\t", map {render($maps->[$_],\@fields)} (u_refseq,

200

u_refsource,

201

u_refmethod,

202

u_refstart,

203

u_refstop,

204

u_refscore,

205

u_refstrand,

206

u_refphase);

207

print "\t";

208

if($maps->[u_qrystart] >= 0){

209

print "Target:" . render($maps->[u_refmethod],\@fields) . " ";

210

print render($maps->[u_refgroup],\@fields) . " " .

211

render($maps->[u_qrystart],\@fields) . " " .

212

render($maps->[u_qrystop], \@fields);

213

} else {

214

print "Sequence " . render($maps->[u_refgroup],\@fields) . " ";

215

}

216

print "\n";

217

218

if(defined($maps->[u_starts]) and defined($maps->[u_sizes])){

219

my @starts = split /,/, render($maps->[u_starts],\@fields);

220

my @sizes = split /,/, render($maps->[u_sizes],\@fields);

221

222

my $start;

223

while(defined($start = shift @starts)){

224

my $size = shift @sizes;

225

226

if($maps->[u_qrystart] < 1 and $maps->[u_qrystop] < 1){

227

print join "\t", (render($maps->[u_refseq],\@fields),

228

render($maps->[u_refsource],\@fields),

229

render($maps->[u_refmethod],\@fields),

230

render($maps->[u_refstart],\@fields) + $start,

231

render($maps->[u_refstart],\@fields) + $start + $size,

232

render($maps->[u_refscore],\@fields),

233

render($maps->[u_refstrand],\@fields),

234

render($maps->[u_refphase],\@fields),

235

render($maps->[u_refmethod],\@fields) . " " . render($maps->[u_refgroup],\@fields)

236

), "\n";

237

} else {

238

print join "\t", (render($maps->[u_refseq],\@fields),

239

render($maps->[u_refsource],\@fields),

240

render($maps->[u_refmethod],\@fields),

241

$start,

242

$start + $size,

243

render($maps->[u_refscore],\@fields),

244

render($maps->[u_refstrand],\@fields),

245

render($maps->[u_refphase],\@fields),

246

render($maps->[u_refmethod],\@fields) . " " . render($maps->[u_refgroup],\@fields)

247

), "\n";

248

}

249

}

250

}

251

}

252

253

sub render {

254

my($index,$fields) = @_;

255

return '.' if $index == -1;

256

return $index unless $index =~ /^\d+$/;

257

return $fields->[$index];

258

}

Older »