-
Notifications
You must be signed in to change notification settings - Fork 2
/
Create_Taxonomy_Database_1of3.pl
394 lines (341 loc) · 21.9 KB
/
Create_Taxonomy_Database_1of3.pl
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
#use warnings;
# PUT BUGS HERE TO WORK ON #
# Fix naming of metagenome/microbiome
# microbiome->environmental->teresstrial/aquatic->paludis/limnic/fluvial/marine
# microbiome->engineered->bioreactor/synthetic_community/man-made_habitat
# microbiome->host-associated->plant/animal/fungal/protozoa/algal->organ
# END OF BUG BIN #
#GET I/O FILES
qx{wget -O new_taxdump.tar.gz https://ftp.ncbi.nih.gov/pub/taxonomy/new_taxdump/new_taxdump.tar.gz};
my $indat = qx{tar -tzf new_taxdump.tar.gz | grep -P "^fullnamelineage.dmp"};
my $inlevs = qx{tar -tzf new_taxdump.tar.gz | grep -P "^nodes.dmp"};
my $inlin = qx{tar -tzf new_taxdump.tar.gz | grep -P "^taxidlineage.dmp"};
my $inmrg = qx{tar -tzf new_taxdump.tar.gz | grep -P "^merged.dmp"};
qx{tar --extract --occurrence=1 --file=new_taxdump.tar.gz $indat};
qx{tar --extract --occurrence=1 --file=new_taxdump.tar.gz $inlevs};
qx{tar --extract --occurrence=1 --file=new_taxdump.tar.gz $inlin};
qx{tar --extract --occurrence=1 --file=new_taxdump.tar.gz $inmrg};
$inictv = 'ICTV.txt';
$inimg = 'All_IMG_Genomes.txt';
$time = localtime;
$time = uc($time);
$time =~ /^[A-Z]+\s+([A-Z]+)\s+\S+\s+\S+\s+(\d\d\d\d)/;
$month = $1; $year = $2;
$version=$1."_".$2;
$output = "TAXONOMY_DB_".$version."_raw.txt";
open(INVIR, $inictv)||die;
open(INIMG, $inimg)||die;
open(INDAT, $indat)||die;
open(INLEV, $inlevs)||die;
open(INLIN, $inlin)||die;
open(OUTPUT, ">", $output)||die;
##########################################################################
### GET THE STRUCTURAL INFORMATION ABOUT VIRUSES (EG. SSRNA, DSDNA...) ###
##########################################################################
print "INPUT ICTV.TXT\n";
@ODDS=(1,3,5,7,9,11,13);
while(<INVIR>){
if($_ !~/^\d/){next;}
$_ = uc($_);
$_ =~ s/[\r\n]+//;
@stuff = split("\t", $_,-1);
$stuff[15]=""; #fixes problem with misid'd satellites
if(exists($VIRTYPE{$stuff[9]}) && exists($VIRTYPE{$stuff[11]}) && exists($VIRTYPE{$stuff[13]})){next;}
if($_ =~ /(SATELLIT|ALBETOVIRUS|AUMAIVIRUS|PAPANIVIRUS|VIRTOVIRUS|SARTHROVIRIDAE|MACRONOVIRUS)/){
foreach my $i (@ODDS){ if($stuff[$i] =~ /\w/){$VIRTYPE{$stuff[$i]} ="MONA;VIRUSES;SATELLITES";}}
next;}
if($_ =~ /(PHAGE|CAUDOVIRALES|ACKERMANNVIRIDAE|AUTOLYKIVIRIDAE|CORTICOVIRIDAE|CYSTOVIRIDAE|INOVIRIDAE)/){
foreach my $i (@ODDS){ if($stuff[$i] =~ /\w/){$VIRTYPE{$stuff[$i]} ="MONA;VIRUSES;PHAGE";}}
next;}
if($_ =~ /(LEVIVIRIDAE|MICROVIRIDAE|SPHAEROLIPOVIRIDAE|MYOVIRIDAE|PODOVIRIDAE|SIPHOVIRIDAE|TECTIVIRIDAE)/){
foreach my $i (@ODDS){ if($stuff[$i] =~ /\w/){$VIRTYPE{$stuff[$i]} ="MONA;VIRUSES;PHAGE";}}
next;}
#CLEAN UP STRUCTURAL CLASS NAMING
$stuff[16]=~/([DS]*.NA)/; $type = $1;
$stuff[16]=~/[DS]*.NA.*[DS]*(.NA)/; $type = $1;
if($type !~ /\w/){ $type = ""; }
elsif($stuff[16]=~/RT|RETRO/){ $type .= "_RT";}
elsif($stuff[16]=~/\+|POS/){ $type .= "_POS";}
elsif($stuff[16]=~/\-|NEG/){ $type .= "_NEG";}
elsif($stuff[16]=~/([\+\-]).*([\+\-])/){$type .= "_BOTH";}
else{$type=$type;} #KEEP AN EYE ON THIS IN CASE ICTV ADDS CATEGORY
#NAME WITH STRUCTURAL CLASS
$stuff[16]=$type;
foreach my $i (@ODDS){
if($stuff[$i] =~ /\w/){ $VIRTYPE{$stuff[$i]} ="MONA;VIRUSES;$stuff[16]";
#print "i $i stuffi $stuff[$i] type $type lin $VIRTYPE{$stuff[$i]}\n";
}}
}
#############################
### INPUT IMG GENOMES ###
#############################
print "INPUT IMG GENOMES\n";
while(<INIMG>){
if($_ !~/^\d/){next;}
$_ = uc($_);
$_ =~ s/[\r\n]+//;
@stuff = split('\t', $_,-1);
@NOW=();
$oid = shift(@stuff);
$tid = shift(@stuff);
#FIX NAME AND FILL MISSING
if($stuff[7] =~ /^0$/){$stuff[7]="";}
if($_ =~ /\bPLASMID\b/ && $stuff[6] !~ /PLASMID/ && $stuff[7] !~/PLASMID/){
if($stuff[7]=~/\w/){$stuff[7].="_PLASMID";}
else{$stuff[6].="_PLASMID";}
}
@TMP = @stuff[0..8]; # 0:Domain 1:Phylum 2:Class 3:Order 4:Family 5:Genus 6:Species 7:Strain 8:Genome/Sample
if($TMP[0]=~/UNKNOWN/ && $_ =~ /ARCHAEON/){ $TMP[0] = "ARCHAEA";} #FIX IMG UNKNOWN ARCHAEON ISSUE
for my $y (0..8){ $TMP[$y] = fix_names($TMP[$y]); } #GENERAL NAME CLEAN-UP
if($TMP[8] !~ /$TMP[7]/ && $TMP[7]=~/\w/){ $TMP[8].="_".$TMP[7];} #FILL IN STRAIN INFO FROM COL 9
if($TMP[8]=~/\w/){$TMP[7]=$TMP[8];} #REPLACE WITH FULL STRAIN NAME FROM COL 9
if($TMP[6] !~ /\w/ && $TMP[5] =~ /\w/){ #FILL IN SPECIES WITH GENUS - NEED FOR LATER
if($TMP[0] =~ /VIRUS/){$TMP[6]=$TMP[5];}
else{$TMP[6]=$TMP[5]."_SP";}
}
if($TMP[6] !~ /\w/){ $TMP[6] = $TMP[8];} #IF STILL NO SPECIES, FILL WITH GENOME/SAMPLE
#GET THE HIGHEST MICROBIOME INFO THAT ISN'T TOO SPECIFIC NOR UNCLASSIFIED
if($TMP[0]=~/MICROBIOME/){ for my $x (2..5){ if($TMP[$x] ne "UNCLASSIFIED" && $TMP[$x] ne ""){ $NOW[2]=$TMP[$x]; }} }
$line = join(";",@TMP);
#SET NAMES
if( $TMP[0] =~ /^(BACTERIA|EUKARYOTA|ARCHAEA)$/ ){ @NOW=@TMP[0..7]; }
else{ #GET THE MONA AND MICROBIOMES
#first sort the microbiome/metagenome
#then sort the vectors (plasmids, artificial constructs, IS)
#then grab the unknown/other - quiddam
#then deal with satellites, phages, and all other viruses
if($line=~/(ECOLOGICAL|ENVIRONMENTAL)/ && $line =~ /(METAGENOME|MICROBIOME)/){ @NOW[0..1]=split(";", "MICROBIOME;ENVIRONMENTAL",-1);}
elsif($line=~/(ORGANISMAL|HOST)/ && $line =~ /(METAGENOME|MICROBIOME)/){ @NOW[0..1]=split(";", "MICROBIOME;HOST-ASSOCIATED",-1);}
elsif($line=~/(ENGINEERED|SYNTHETIC|ARTIFICIAL)/ && $line =~ /(METAGENOME|MICROBIOME)/){ @NOW[0..1]=split(";", "MICROBIOME;ENGINEERED",-1);}
elsif($line=~/(METAGENOME|MICROBIOME)/){ @NOW[0..1]=split(";", "MICROBIOME;UNCLASSIFIED_MICROBIOME",-1);}
elsif($line=~/(ARTIFICIAL|SYNTHETIC|VECTOR|COSMID|CONSTRUCT)/){ @NOW[0..1]=split(";", "MONA;CONSTRUCTS",-1); $NOW[6]=$TMP[7];}
elsif($line=~/(INSERTION.SEQUENCE|TRANSPOSON|INTEGRON)/){ @NOW[0..1]=split(";", "MONA;TRANSPOSONS",-1);$NOW[6]=$TMP[7];}
elsif($line=~/([^A-Z]PLASMID|PLASMID[^A-Z]|MINICHROMOSOME)/ || $TMP[0]=~/PLASMID/){ @NOW[0..1]=split(";", "MONA;PLASMIDS",-1); $NOW[6]=$TMP[7];}
elsif($line=~/(UNCLASSIFIED.ENTRIES|OTHER.SEQUENCES)/ || $TMP[0]!~/\w/){ @NOW[0..1]=split(";", "QUIDDAM;$TMP[7]",-1);}
elsif($line=~/(SATELLITE|VIRUS.*SATELLIT)/){ @NOW[0..2]=split(";", "MONA;VIRUSES;SATELLITES",-1); @NOW[3..7]=@TMP[3..7];}
elsif($line=~/(ALBETOVIRUS|AUMAIVIRUS|PAPANIVIRUS|VIRTOVIRUS|SARTHROVIRIDAE|MACRONOVIRUS)/){ @NOW[0..2]=split(";", "MONA;VIRUSES;SATELLITES",-1); @NOW[3..7]=@TMP[3..7];}
elsif($line=~/PHAGE/ && $line=~/VIRUS/){ @NOW[0..2]=split(";", "MONA;VIRUSES;PHAGE",-1); @NOW[3..7]=@TMP[3..7];}
elsif($line=~/(CAUDOVIRALES|ACKERMANNVIRIDAE|AUTOLYKIVIRIDAE|CORTICOVIRIDAE|CYSTOVIRIDAE|INOVIRIDAE)/){ @NOW[0..2]=split(";", "MONA;VIRUSES;PHAGE",-1); @NOW[3..7]=@TMP[3..7];}
elsif($line=~/(LEVIVIRIDAE|MICROVIRIDAE|SPHAEROLIPOVIRIDAE|MYOVIRIDAE|PODOVIRIDAE|SIPHOVIRIDAE|TECTIVIRIDAE)/){ @NOW[0..2]=split(";", "MONA;VIRUSES;PHAGE",-1); @NOW[3..7]=@TMP[3..7];}
elsif($line=~/VIRUSES|VIRUS[\_\b]/){
@NOW[3..7]=@TMP[3..7];
foreach my $lev (@TMP){ if(exists($VIRTYPE{$lev})){ @NOW[0..2]=split(";", $VIRTYPE{$lev},-1); last;}}
if($NOW[0] !~ /MONA/){
$stuff[1]=~/([DS]*.NA)/; $type = $1;
$stuff[1]=~/[DS]*.NA.*[DS]*(.NA)/; $type = $1;
if($type !~ /\w/){ $type = ""; }
elsif($stuff[1]=~/RT|RETRO/){ $type .= "_RT";}
elsif($stuff[1]=~/\+|POS/){ $type .= "_POS";}
elsif($stuff[1]=~/\-|NEG/){ $type .= "_NEG";}
elsif($stuff[1]=~/([\+\-]).*([\+\-])/){ $type .= "_BOTH";}
else{$type=$type;}
$NOW[0]="MONA"; $NOW[1]="VIRUSES"; $NOW[2]=$type;
}
}
else{ @NOW[0..1]=split(";", "QUIDDAM;$TMP[7]",-1);}
}
#STORE
if($NOW[1] =~ /\w/){ $MIDS{$NOW[1]}=1; } #track mid names for later
if($NOW[2] =~ /\w/){ $MIDS{$NOW[2]}=2; } #track mid names for later
if($NOW[3] =~ /\w/){ $MIDS{$NOW[3]}=3; } #track mid names for later
if($NOW[4] =~ /\w/){ $MIDS{$NOW[4]}=4; } #track mid names for later
if($NOW[5] =~ /\w/){ $MIDS{$NOW[5]}=5; } #track mid names for later
$LINEAGES{$oid}=[@NOW];
}
#######################################
#######################################
#######################################
### INPUT THE NAME OF EACH RANK ###
#######################################
print "INPUT FULL LINEAGE\n";
$on=0;
while(<INDAT>){
if($_ !~/\w/){next;}
$_ = uc($_);
$_ =~ s/[\r\n]+//;
$line=$_;
@stuff = split("\t", $_,-1);
$tid = $stuff[0];
#FIX NAME
$name = $stuff[2];
if($tid==2787854){$name="MONA";} #make other sequences > mona
if($tid==2787823){$name="QUIDDAM";} #make unclassified > quiddam
if($tid==408169 ){$name="MICROBIOME";} #makes metagenome > microbiome
$name = fix_names($name);
$NAMES{$tid}=$name;
if($tid == 882018){print "882018 name1 $name\n";}
#GET THE MONA AND MICROBIOMES
if($line=~/CELLULAR.ORGANISMS/){next;}
elsif($line=~/OTHER.SEQUENCES/ && $line =~ /ARTIFICIAL|SYNTHETIC|VECTOR|COSMID|CONSTRUCT/){ $ODD{$tid}="MONA;CONSTRUCTS";}
elsif($line=~/OTHER.SEQUENCES/ && $line=~/PLASMID|MINICHROMOSOME/){ $ODD{$tid}="MONA;PLASMIDS";}
elsif($line=~/INSERTION.SEQUENCE|TRANSPOSON|INTEGRON/){ $ODD{$tid}="MONA;TRANSPOSONS";}
elsif($line=~/(ECOLOGICAL|ENVIRONMENTAL)/ && $line =~ /(METAGENOME|MICROBIOME)/){ $ODD{$tid}="MICROBIOME;ENVIRONMENTAL";}
elsif($line=~/(ORGANISMAL|HOST)/ && $line =~ /(METAGENOME|MICROBIOME)/){ $ODD{$tid}="MICROBIOME;HOST-ASSOCIATED";}
elsif($line=~/(ENGINEERED|SYNTHETIC|ARTIFICIAL)/ && $line =~ /(METAGENOME|MICROBIOME)/){ $ODD{$tid}="MICROBIOME;ENGINEERED";}
elsif($line=~/(METAGENOME|MICROBIOME)/){ $ODD{$tid}="MICROBIOME;UNCLASSIFIED_MICROBIOME";}
elsif($line=~/(UNCLASSIFIED.ENTRIES|OTHER.SEQUENCES)/){ $ODD{$tid}="QUIDDAM;$name";}
elsif($line=~/(SATELLITE|VIRUS.*SATELLIT)/){ $ODD{$tid}="MONA;VIRUSES;SATELLITES";}
elsif($line=~/(ALBETOVIRUS|AUMAIVIRUS|PAPANIVIRUS|VIRTOVIRUS|SARTHROVIRIDAE|MACRONOVIRUS)/){ $ODD{$tid}="MONA;VIRUSES;SATELLITES";}
elsif($line=~/PHAGE/ && $line=~/VIRUS/){ $ODD{$tid}="MONA;VIRUSES;PHAGE";}
elsif($line=~/(CAUDOVIRALES|ACKERMANNVIRIDAE|AUTOLYKIVIRIDAE|CORTICOVIRIDAE|CYSTOVIRIDAE|INOVIRIDAE)/){ $ODD{$tid}="MONA;VIRUSES;PHAGE";}
elsif($line=~/(LEVIVIRIDAE|MICROVIRIDAE|SPHAEROLIPOVIRIDAE|MYOVIRIDAE|PODOVIRIDAE|SIPHOVIRIDAE|TECTIVIRIDAE)/){ $ODD{$tid}="MONA;VIRUSES;PHAGE";}
elsif($line=~/VIRUSES|VIRUS[\_\b]/){
$stuff[4]=~s/\;\s+/\;/g;
@NOW=split(";",$stuff[4]);
push(@NOW,$name);
foreach my $lev (@NOW){ if(exists($VIRTYPE{$lev})){ $ODD{$tid}=$VIRTYPE{$lev}; }}
if($NOW[0] !~ /MONA/){ $ODD{$tid}="MONA;VIRUSES"; }
}
else{ $ODD{$tid}="QUIDDAM;$name";}
}
########################################
########################################
print "882018 name2 $NAMES{882018}\n";
###############################################
### GET THE TYPE OF EACH TAXONOMIC RANK ###
### (EG. SPECIES, CLASS, SUPERKINGDOM...) ###
###############################################
print "INPUT LEVELS\n";
while(<INLEV>){
if($_ !~/^\d/){next;}
$_ = uc($_);
$_ =~ s/[\r\n]+//;
@stuff = split("\t", $_,-1);
$tid = $stuff[0];
$LEVS{$tid} = $stuff[4];
if($tid == 32561){ $LEVS{$tid} = "CLASS";} #fixes reptiles class
if($tid==2787854){ $LEVS{$tid} = "SUPERKINGDOM";} #makes "other sequences" = "MONA"
if($tid==2787823){ $LEVS{$tid} = "SUPERKINGDOM";} #makes "unclassified entries" = "quiddam"
if($tid==408169){ $LEVS{$tid} = "SUPERKINGDOM";} #makes metagenome a superkingdom
if($LEVS{$tid} eq "SUPERKINGDOM"){ $MIDS{$NAMES{$tid}}=0; } #track mid names for later
if($LEVS{$tid} eq "PHYLUM"){ $MIDS{$NAMES{$tid}}=1; } #track mid names for later
if($LEVS{$tid} eq "CLASS"){ $MIDS{$NAMES{$tid}}=2; } #track mid names for later
if($LEVS{$tid} eq "ORDER"){ $MIDS{$NAMES{$tid}}=3; } #track mid names for later
if($LEVS{$tid} eq "FAMILY"){ $MIDS{$NAMES{$tid}}=4; } #track mid names for later
if($LEVS{$tid} eq "GENUS"){ $MIDS{$NAMES{$tid}}=5; } #track mid names for later
}
###############################################
###############################################
print "882018 name3 $NAMES{882018}\n";
############################################
### USE RANKS AND CORRECTED NAMES TO ###
### GENERATE AN ORGANIZED LINEAGE ###
############################################
print "INPUT TAXIDLINEAGES\n";
$on=0;
while(<INLIN>){
if($_ !~/^\d/){next;}
$_ = uc($_);
$_ =~ s/[\r\n]+//;
@stuff = split('\t', $_,-1);
$tid = shift(@stuff);
@LIN = split('\s', $stuff[1],-1);
@NLIN = ();
foreach my $x (@LIN){ if($x =~ /\d/){ push(@NLIN,$x); }}
@LIN=@NLIN;
push(@LIN, $tid);
#FIRST GET MAIN 8 RANKS: K/P/C/O/F/G/S/T
%HoA=(); @NOW=();
for my $i (0..$#LIN){
$id = $LIN[$i];
@NOW=@{$HoA{$tid}};
if($id !~ /\d/){next;}
if($LEVS{$id} eq "SUPERKINGDOM"){ $HoA{$tid}[0]=$NAMES{$id}; $ch=1;}
elsif($LEVS{$id} eq "PHYLUM"){ $HoA{$tid}[1]=$NAMES{$id}; $ch=2;}
elsif($LEVS{$id} eq "CLASS"){ $HoA{$tid}[2]=$NAMES{$id}; $ch=3;}
elsif($LEVS{$id} eq "ORDER"){ $HoA{$tid}[3]=$NAMES{$id}; $ch=4;}
elsif($LEVS{$id} eq "FAMILY"){ $HoA{$tid}[4]=$NAMES{$id}; $ch=5;}
elsif($LEVS{$id} eq "GENUS"){ $HoA{$tid}[5]=$NAMES{$id}; $ch=6;}
elsif($LEVS{$id} eq "SPECIES"){ $HoA{$tid}[6]=$NAMES{$id}; $ch=7; }
elsif($LEVS{$id} eq "STRAIN"){ $HoA{$tid}[7]=$NAMES{$id}; $ch=8; }
elsif($HoA{$tid}[6] =~ /\w/ || $HoA{$tid}[7] =~ /\w/){#SPECIES IS FILLED - ALL HIGHER LEVS TREAT AS STRAIN SO LCA WILL BE SPECIES LATER
@NOW = @{$HoA{$tid}}; $ch=9;
$HoA{$id} = [@NOW];
$HoA{$id}[7]=$NAMES{$id};
}
else{ @NOW=@{$HoA{$tid}}; $HoA{$id} = [@NOW]; $ch=10;} #else is a lower junk level, give curent position id since going in order
}
#NOW EXTRA RANKS ARE ACCOUNTED FOR IN PRIMARY RANK CONTEXT
#LOOP THROUGH TID AND OTHER MID-LEVELS
foreach my $xid (keys %HoA){
@TMP=();
@NOW=@{$HoA{$xid}};
#GET MICROBIOME AND MONA LEVELS
if(exists($ODD{$xid})){
@TMP = split(";", $ODD{$xid},-1);
if($TMP[0] =~ /QUIDDAM|MICROBIOME/){
#FIND THE MOST DESCRIPTIVE NAME FOR THE MICROBIOME THAT MIGHT BE SHARED
if($TMP[0] eq "MICROBIOME"){ for my $x (2..5){ if($NOW[$x] ne "UNCLASSIFIED" && $NOW[$x] ne ""){ $TMP[2]=$NOW[$x]; }}}
@NOW=@TMP;
}
else{ for my $i (0..$#TMP){ $NOW[$i]=$TMP[$i]; }} #MONAs
}
if($NOW[0]=~/VIRUS/){ $NOW[0]="MONA"; $NOW[1]="VIRUSES"; }
if($NOW[0]!~/\w/){ $NOW[0]="QUIDDAM"; }
#MOVE CLEANED SPECIES BECOME MID-NAMES FROM SPECIES
#(unclassified salmonella -> salmonella, move to genus, empty species)
if(exists($MIDS{$NOW[6]})){ #species is bad
if($NOW[7]=~/\w/){ #strain might be good
if(exists($MIDS{$NOW[7]})){ $NOW[$MIDS{$NOW[6]}]=$NOW[6]; $NOW[6]=''; $NOW[7]=''; } #both bad
else{$NOW[6]=$NOW[7];} #strain was good
}
else{ $NOW[$MIDS{$NOW[6]}]=$NOW[6]; $NOW[6]=''; }
}
while($NOW[$#NOW] !~ /\w/){pop(@NOW);}
$LINEAGES{$xid}=[@NOW];
}
$on++;
}
################################################
################################################
##########################################
### OUTPUT FIRST DRAFT OF LINEAGES ###
##########################################
foreach my $tid (keys %LINEAGES){
@NOW = @{$LINEAGES{$tid}};
#HANDLE BAD MID-LEVELS (HAVE MIXED/SPLIT/NONSENSE NAMES
if( $NOW[0] =~ /QUIDDAM|MICROBIOME/ || $NOW[2] =~ /[DR]NA\_/ ){ $lin=join("\t",@{$LINEAGES{$tid}}); print OUTPUT "$tid\t$lin\n"; next;}
$test = join(";", @NOW[0..5]);
if($test =~ /\_/){
if($NOW[4] !~ /\w/ && $NOW[5]=~/([A-Z]+I[ND]AE)\_/){ $NOW[4]=$1; }
for my $i (0..4){ if($NOW[$i] =~ /\_/){ $NOW[$i]='';}}
$NOW[5] =~ s/.*\_(GEN|GENUS)\_.*//;
if($NOW[5]=~/\w/){$NOW[5] =~ s/\_.*//;}
}
$LINEAGES{$tid}=[@NOW];
$lin=join("\t",@{$LINEAGES{$tid}});
print OUTPUT "$tid\t$lin\n";
}
#######################
### SUBROUTINES ###
#######################
sub fix_names{
my $name = $_[0];
#fix the species/strain name
$name =~ s/([A-Z]+)\s(PROTEOBACTER)(IA|IUM)/$1$2$3/;
$name =~ s/\bPROPIONIBACTERIUM/CUTIBACTERIUM/g;
$name =~ s/\bLEPIDOSAURIA/SAURIA/g;
$name =~ s/ENDOSYMBIONT.OF\s+/ENDOSYMBIONT-/;
$name =~ s/COMPOSITE.GENOME.*//;
$name =~ s/MARINE.GROUP.(\w+)/MARINE-GROUP-$1/;
$name =~ s/\s+METAGENOME//;
$name =~ s/OOMYCETES/OOMYCOTA/;
$name =~ s/LILIOPSIDA/MAGNOLIOPSIDA/;
$name =~ s/^NR[^A-Z]//;
$name =~ s/.*INCERTAE.SEDIS.*//;
$name =~ s/\_(PHYLUM|CLASS|ORDER|FAMILY|GENUS)[\b\_].*/\_/;
$name =~ s/ENRICHMENT.CULTURE.CLONES*|ENRICHMENT.CULTURES*//;
$name =~ s/\_(SENSU\_LATO|AFF|GEN|CF)\_/\_/g;
$name =~ s/^(SENSU\_LATO|AFF|GEN|CF)\_//g;
$name =~ s/\b(SENSU\_LATO|AFF|GEN|CF)\_//g;
#remove ambiguous junk
$name =~ s/(CANDIDATUS|CANDIDATUAS|CANDIDATE.\S+|VOUCHERED|UNDESCRIBED|UNSCREENED|UNKNOWN|UNCULTIVATED|UNCULTURED)\s*/\_/g;
$name =~ s/(UNIDENTIFIED|UNCLASSIFIED|CONTAMINATION|SCREENED|UNASSIGNED|PUTATIVE|\-*LIKE)\s*/\_/g;
#remove junk punctuation/standardize
$name =~ s/\s+/_/g;
$name =~ s/[^\w]+/_/g;
$name =~ s/\_+/\_/g;
$name =~ s/(^\_+|\_+$)//g;
$name =~ s/^(X|CF)\_//;
return($name);
}