-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathblast92gff3_rnc.pl
1175 lines (1007 loc) · 42.1 KB
/
blast92gff3_rnc.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
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
#!/usr/bin/perl
use strict;
use warnings;
=head1 Modified Script Name
The following name is used to differentiate this script from the original:
blast92gff3_rnc.pl
=head1 DISCLAIMER
This script is derived from blast92gff3.pl version 2008 by Don Gilbert
(http://iubio.bio.indiana.edu/gmod/tandy/perls/blast92gff3.pl)
(http://eugenes.org/gmod/genogrid/scripts/blast92gff3.pl)
This disclaimer applies to this modified version (blast92gff3_rnc.pl) of blast92gff3.pl
THIS MODIFICATION (blast92gff3_rnc.pl) OF Don Gilbert's blast92gff3.pl
SOFTWARE IS PROVIDED "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING,
BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE AUTHORS, COPYRIGHT HOLDER, OR CONTRIBUTORS BE LIABLE
FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
=head1 CHANGES IN blast92gff3_rnc.pl FROM Don Gilbert's ORIGINAL CODE
My modifications were solely to simplify subsequent running of GeneWise.
=head2 Modifications
- Changed use of GetOpts to simple @ARGV iteration for moment
- Changed input from piping tabular BLAST output to loading named results file
- Loads in the protein fasta to compute sizes for each protein to enable
restriction to ranges of coverage
$protCov= sprintf("%0.2f", ($sum_align / $protLength) * 100 );
- Added coverage and query length gff3 attributes
- Added value for %coverage of protein in matchs
- Still prints gff3 to STDOUT by default unless output file parsed on command
line
- Compiles and writes commands to run genewise to a file called run_genewise.sh
* shell command script name is currently hard coded
* genewise command is as follows:
my $geneWiseCmd = "genewise -u $startPositionInDNA -v $stopPositionInDNA \
$strands -pseudo -genes -para -sum -cdna -trans -gff -kbyte 40000 \
$proteinFastaDir/${qid1}.fa $refFastaDir/$sid.fa \
1>$outDir/$genewiseStdoutCapture 2>$outDir/$genewiseStderrCapture\n";
* One command output per qualitying protein match
* Genewsie commands can subsequently be split by number of lines and
submitted to job schedular
* Running Genewise subsequen requires individual reference and query
sequences in named subdirectories for use with genewise command and these
must be provided on command line
- Original indenting changed
Otherwise Don Gilbert's code is unchanged.
=head1 SYNOPSIS
This applies to blast92gff3_rnc.pl.
=head2 Example BASH Shell Workflow
# Setup Blast Database and run blast comparison
PROJECTNAME=CompWithRosidProts
CPUS=16
WORKING_DIR=/workspace
REFERENCE_DIR=/reference
QUERY_DIR=/TBLASTNRosidProteins
REFERENCE_NAME=reference
QUERY_NAME=Rosid_Predicted_Proteins_unique
QUERY_FASTA=${QUERY_DIR}/${QUERY_NAME}.faa
REFERENCE_FASTA=${REFERENCE_DIR}/${REFERENCE_NAME}.fa
BLAST_DB_DIR=${WORKING_DIR}/Reference/BLAST_IDX
mkdir -p ${BLAST_DB_DIR}
cd ${BLAST_DB_DIR}
ln -s ${REFERENCE_FASTA} ${REFERENCE_NAME}
formatdb -i ${REFERENCE_NAME} -p F -o T
echo "blastall -p tblastn -m 8 -a $CPUS -i ${QUERY_FASTA} -d ${BLAST_DB_DIR}/${REFERENCE_NAME} -o ${QUERY_NAME}_${REFERENCE_NAME}_genes.tblastn" > run_tblastn.sh
bsub -n $CPUS -m "${PROJECTNAME}" -o `pwd`/ol.tblastn.stdout -e `pwd`/ol.tblastn.stderr < run_tblastn.sh
# Explode reference and query fasta file to get individual files (needed for genewise commands later)
REF_INDIVID_FILES_DIR=${REFERENCE_DIR}/Genome/Fasta/IndividualScaffolds
mkdir -p ${REF_INDIVID_FILES_DIR}
cp ${REFERENCE_FASTA} ${REF_INDIVID_FILES_DIR}
cd ${REF_INDIVID_FILES_DIR}
fastaexplode ${REFERENCE_FASTA}
rm ${REFERENCE_FASTA}
QUERY_INDIVID_FILES_DIR=QUERY_DIR/Protein/Fasta/IndividuaProteins
mkdir -p ${QUERY_INDIVID_FILES_DIR}
cp ${QUERY_FASTA} ${QUERY_INDIVID_FILES_DIR}
cd ${QUERY_INDIVID_FILES_DIR}
fastaexplode ${QUERY_FASTA}
rm ${QUERY_FASTA}
# Run tabular blast parser on tblastn results
GENEWISE_DIR=${WORKING_DIR}/GeneWise
blast92gff3_rnc.pl -gff3Outfile=modelproteins-mygenome.gff3 \
-proteinFastaFile=${QUERY_FASTA} \
-tblastnFile=${QUERY_NAME}_${REFERENCE_NAME}_genes.tblastn \
-refFastaDir=${REF_INDIVID_FILES_DIR} \
-proteinFastaDir=${QUERY_INDIVID_FILES_DIR} \
-genewiseResultsOutDir=${GENEWISE_DIR}
# Split genewise commands from above parsing - produces files named like myfile_1
cd ${GENEWISE_DIR}
file_splitter_by_line.pl run_genewise.sh 40
# Run genewise commands directly or submit to job schedular (not shown)
for n in `seq 0 39`; do (sh myfile_$n 1>myfile_$n.out 2>myfile_$n.err &); done
# Get list of individual results files from genewise runs
ls | grep ".stdout" > genewise.out.list
for file in `cat genewise.out.list`; do cat $file >> GeneWise.predictions; done
# Parse the genewise predictions
parse_genewise_prediction_results.pl -g=GeneWise.predictions
# Run evigene
tr2aacds.pl -NCPU 16 -MAXMEM 100000 -logfile `pwd`/evigene.log -cdnaseq `pwd`/GeneWise.predictions.fna -MINCDS 90 1>evigene.stderr 2>evigene.stdout &
=cut
=head1 ORIGINAL POD FOLLOWS
=head1 NAME
blast92gff3.pl
unpacked that is " BLAST tabular output (-m 9 or 8) conversion to GFF version 3 format "
=head1 SYNOPSIS
ncbi/blastall -m 9 -p tblastn -i daphnia_genes.aa -d aphid-genome -o aphid-daphnia_genes.tblastn
cat aphid-daphnia_genes.tblastn | sort -k1,1 | blast92gff2.pl > aphid-daphnia_genes.gff
Note: input must be sorted by query ID. Default .tblastn result is sorted by query.
=head2 BlastX and tBlastN
This should work the same for BlastX, if you sort on column 2 and use -swap:
blastall -p blastx -d genes.aa -i genome | sort -k2,2 | blast92gff2.pl -swap
It should work for DNA queries like EST/cDNA mapped to a genome also.
=head1 ABOUT
Separate BLAST tabular output (-m 9 or 8) into gene models (match,HSP) by parsing distinct,
duplicate gene matches using the query locations as well as source locations.
This works on one query gene at a time. The result likely will have many overlapped
different genes of declining quality. You can filter those in a 2nd step:
$td/overbestgene2.perl -in aphid-daphnia_genes.gff > aphid-daphnia_genes-best.gff
Learn more on the subject of accurately locating duplicate genes at
http://eugenes.org/gmod/tandy/
See this note on how BioPerl combines distinct gene matches from blat, blast in its
searchio module
http://www.bioperl.org/wiki/Talk:GFF_code_audit
=head2 TEST data
lots of "insect" cuticle tandem duplicate genes in
daphnia_pulex/scaffold_14:1294000..1322000
http://insects.eugenes.org/cgi-bin/gbrowsenew/gbrowse/daphnia_pulex/?name=scaffold_14:1294000..1322000
Pick the protein of one cuticle gene, daphnia:NCBI_GNO_546144
Run tblastn at wfleabase.org of NCBI_GNO_546144 protein x genome, saving tabular blast result
blast92gff2.pl < result.tblastn
=head1 AUTHOR
Don Gilbert, [email protected] June 2008
=head1 NOTES
=cut
my $MAX_EXON_SEPARATION = 10000;
my $QBASEOVER = 5; # query hsp overlap slop in bases
# use constant GFF_LOC => 1;
my $tblastnFile = "";
my $proteinFastaFile = "";
my @geneWiseCommands = (); # Array to store genewise commands
my $refFastaDir = ""; # Directory in which reference (subject) sequence is stored
my $proteinFastaDir = ""; # Directory in which protein sequence is stored
my $genewiseResultsOutDir = `pwd`; # Using backticks not ideal - change later.
my $minCoverage = 80; # Minimum default coverage value
my $OVERLAP_SLOP_QUERY = 0.15; # was 0.15; for protein query HSPs
my $OVERLAP_SLOP_GENOME = 0.05; # was 0.50; for genome source HSPs
my $BIN10000= 10000; # binsize
my $GAPSIZE = 400; # what ?? for nearover1() test
my $LOWSCORE_SKIP = 0.20; # i.e. skip matchs < 50% of max match score
use vars qw(
$swap_querytarget
$faprefix $debug
$querySource $exonType
$geneType $dotarget
$max_bit_score
$bitcutoff $stringent2ndary
%besthash %sumhash @qparthsps @sourcehsps
@mainexons @secondexons @allsaved %moregenes $species $queryid $npart
%shredhash %tandhash $tophsp $lqid $lsid $nwarn $outfile
$gffout %didid
);
my $addgene = 1;
$geneType="match"; # or "protein_match" ...;
$exonType="HSP"; # or "match_part";
$querySource="blast";
$faprefix= 'gnl\|'; # drop NCBI extra id prefix
$stringent2ndary=1;
$dotarget= 1;
# do own sorting for score, loc : still need queryID sort ...
# ** WARNING : input blast must be sorted by queryID, and best score (sort -k1,1 -k12,12nr) **
# cat modelproteins-mygenome.tblastn| sort -k1,1 -k12,12nr |\
# Changed the use of GetOptions::Long to simple @ARGV iteration for the moment
(@ARGV) or usage();
foreach my $arg (@ARGV)
{
($arg =~ m/\-(h|help)$/) and usage();
($arg =~ m/\-gff3Outfile=(.+)$/) and $outfile = $1;
($arg =~ m/\-proteinFastaFile=(.+)$/) and $proteinFastaFile = $1;
($arg =~ m/\-tblastnFile=(.+)$/) and $tblastnFile = $1;
($arg =~ m/\-refFastaDir=(.+)$/) and $refFastaDir = $1;
($arg =~ m/\-proteinFastaDir=(.+)$/) and $proteinFastaDir = $1;
($arg =~ m/\-genewiseResultsOutDir=(.+)$/) and $genewiseResultsOutDir = $1;
($arg =~ m/\-minCoverage=(\d+)$/) and $minCoverage = $1;
($arg =~ m/\-qoverlap=(.+)$/) and $OVERLAP_SLOP_QUERY = $1;
($arg =~ m/\-overlap=(.+)$/) and $OVERLAP_SLOP_GENOME = $1;
($arg =~ m/\-LOWSCORE_SKIP=(.+)$/) and $LOWSCORE_SKIP = $1;
($arg =~ m/\-source=(.+)$/) and $querySource = $1;
($arg =~ m/\-geneType=(.+)$/) and $geneType = $1;
($arg =~ m/\-exonType=(.+)$/) and $exonType = $1;
($arg =~ m/\-(swap|swap_querytarget)$/) and $swap_querytarget = 2;
($arg =~ m/\-nostringent2ndary$/) and $stringent2ndary = 0;
($arg =~ m/\-notarget$/) and $dotarget = 0;
($arg =~ m/\-nomatch$/) and $addgene = 0;
($arg =~ m/\-debug$/) and $debug = 1;
($arg =~ m/\-max_exon_separation=(\d+)$/) and $MAX_EXON_SEPARATION = $1;
($arg =~ m/\-qbaseover=(\d+)$/) and $QBASEOVER = $1;
}
mkdir $genewiseResultsOutDir;
# Get protein sequences for length calc.
open(FA,"<$proteinFastaFile") or die "Can not open fasta file $proteinFastaFile, $!\n";
my $oldSep = $/;
$/=">";
my %proteinLengths = ();
foreach my $record (<FA>)
{
chomp $record;
#$recordCounter++;
next if $record eq "";
next if $record eq ">";
my ($nameLine, @sequence) = split/\n/, $record;
my $name = $nameLine;
if ($nameLine =~ m/\s/)
{
my @nameData = split/\s+/, $nameLine;
$name = $nameData[0];
}
my $sequence = join("", @sequence);
($sequence) or die "no sequence for $record\n";
$sequence =~ s/>//gs;
$proteinLengths{$name} = length($sequence);
}
$/ = $oldSep;
my $hascomm=0;
$gffout = *STDOUT;
if( $outfile && open(OUTH,">$outfile")) { $gffout= *OUTH; }
print $gffout "##gff-version 3\n"; ## if($dolocs);
# Load in tblastn tabular format results
open(IN, "<$tblastnFile") or die "Can not open tblastnFile $tblastnFile $!\n";
while(<IN>)
{
chomp;
if(/^\w/) { # dont assume blast input has comments .. -m8
my @v= split "\t";
my ($qid, $sid, $pctident, $alignment_length, $mismatches, $gap_openings, $q_start, $q_end, $s_start, $s_end, $prob, $bit_score ) = @v;
next unless($bit_score); # some error logs mixed in.. ## warn, die ??
cleanid($qid);
cleanid($sid);
if($swap_querytarget)
{
($qid,$sid,$q_start,$q_end,$s_start,$s_end) = ($sid,$qid,$s_start,$s_end,$q_start,$q_end);
}
if(1) { # query/gene batching, not target/scaffold, with sort -k1,1 input
reset_target_vars($lqid) if($qid ne $lqid);
} else {
reset_target_vars($lsid) if($sid ne $lsid);
}
my($s_strand,$q_strand)= ('+','+');
if ($s_start > $s_end) { $s_strand='-'; ($s_start,$s_end)= ($s_end,$s_start); }
if ($q_start > $q_end) { $q_strand='-'; ($q_start,$q_end)= ($q_end,$q_start); }
# my($sh_id,$sh_start,$sh_end)= deshredloc($sid);
# $s_start= $sh_start + $s_start;
# $s_end = $sh_start + $s_end;
# $sid = $sh_id;
# my $skey="$sid.$q_start.$s_start.$s_end.$bit_score";
# next if($shredhash{$skey});
# $shredhash{$skey}++;
# if ( $bitcutoff == 0 ) { $bitcutoff= $bit_score * 0.75; } #? 1st == best; also $npart == 0
# elsif ( $stringent2ndary && $bit_score < $bitcutoff && ($sid ne $lsid) ) { next; }
## binned top hits for filterBesthits ; can we do this inline ?
# NOT USED NOW# storeBesthits($qid,$sid,$s_start,$s_end,$bit_score);
# count hsps same query loc, diff db loc
$tophsp= $sid if ($npart==0);
my $tkey= "$qid-HSP:$q_start,$q_end";
my $saved= 0;
my $qoverlapped=0;
my $soverlapped=0; ## need only for genelocs.other ?
# if(0) { # need this anymore ?
# foreach my $ex (@qparthsps) {
# my($bs,$be)= ($$ex[3],$$ex[4]);
# $qoverlapped= overlap1($q_start, $q_end, $bs, $be, $OVERLAP_SLOP_QUERY);
# if ($qoverlapped) { $tkey="$qid-HSP:$bs,$be"; last; }
# }
#
# foreach my $ex (@sourcehsps) {
# unless($$ex[1] ne $sid || $$ex[0] ne $qid) {
# my($bs,$be)= ($$ex[5],$$ex[6]);
# $soverlapped= overlap1($s_start, $s_end, $bs, $be, $OVERLAP_SLOP_GENOME);
# last if $soverlapped;
# }
# }
# }
# this is where we assume input is sorted by query-id and top bitscore :
# we drop overlapped hsps silently here ... should reinstitute stringent2ndary test
next if( $qoverlapped && $soverlapped ); # this happens only for same query, same scaffold
##next if($stringent2ndary && $bit_score < $bitcutoff && ($sid ne $lsid));
my $hspval= [$qid,$sid,$alignment_length, $q_start,$q_end,$s_start,$s_end, $bit_score, $prob, $tkey, $s_strand, $soverlapped, $qoverlapped];
push(@qparthsps, $hspval) unless($qoverlapped);
push(@sourcehsps, $hspval); # unless($qoverlapped && $soverlapped); # use this as recycled hits/scaffold
$npart++; $lqid= $qid; $lsid= $sid;
} # blast line
} # while(<>)
reset_target_vars($lqid); ## printGeneLocations();
close($gffout) if($gffout);
if(1) { # debug/verbose / stats of parts saved ...
my ($tpart,@tkeys,$v);
my @sumkeys= sort keys %sumhash;
warn "# Summary of HSPs saved\n";
foreach $tpart (@sumkeys) {
@tkeys= sort keys %{$sumhash{$tpart}};
foreach (@tkeys) { $v= $sumhash{$tpart}{$_}; warn "# $tpart $_ = $v\n"; }
}
}
close(IN);
# Print out genewise commands to run on job scheduler later
open(GW, ">run_genewise.sh") or die "Can not open run_genewise.sh $!\n";
select GW;
foreach my $cmd (@geneWiseCommands)
{
print GW $cmd;
}
close(GW);
# end ...................................................
=head2 yet another BLAST assignBestgene algorithm
algo1 isnt good enough: sort by qgene, source-loc; join hsp by next-nooverlap
new algo3:
1. input sort by query-gene, top bitscore
2. save list of top hsp (score), resort hsp by source-location
3. for top-hsp down, join any next-door left & right same-strand hsp
mark these as G1..n, save
4. continue w/ next-top hsp, eliminating source-overlapped w/ saved G hsp
=head2 original algorithm from blast9protstats (messy)
# step1: -p loc
gtar -Ozxf $soc/${dp}?prot9.blout*.tgz | \
perl -n $bg/blast/blast9protstats.pl -p loc > ! ${dp}prot9.blexons &
# step2: sort hsps with location bins ; should add this to perl
# ** need this binning to separate, keep best hits/region
# makeblexonsort.sh
foreach ble ($dp*.blexons)
set blo=`echo $ble | sed -e's/blexons/blexonsort/'`
echo ====== $ble : $blo
cat $ble | perl -ne\
'($id)=m/tkey=(\S+)\-HSP:/; ($r)=m/^\w+:(\S+)/; ($tb,$te)=m/tloc=(\d+),(\d+)/;\
@v=split; $db=$v[1]; $sbin=10000*int($v[3]/10000); \
print join("\t",$db,$r,$sbin,$v[5],$v[3],$v[4],$id,$tb,$te),"\n";' \
| sort -k1,2 -k3,3n -k4,4nr \
> $blo
echo
end
# step3: -p table (default)
gtar -Ozxf $soc/${dp}?prot9.blout*.tgz | \
perl -n $bg/blast/blast9protstats.pl -over 0.5 -besthits ${dp}prot9.blexonsort -out ${dp}prot9.bltab7 &
=cut
sub reset_target_vars {
printGeneLocations(@_);
$npart= 0;
$max_bit_score= 0;
$bitcutoff=0;
%shredhash=();
%tandhash=(); #? keep? this ids query regardless of target
$tophsp='';
@qparthsps= @sourcehsps= @allsaved= @mainexons= @secondexons= ();
%moregenes=();
}
sub _sortHsp_Score {
my($ap)= $a->[7];
my($bp)= $b->[7];
return ($bp <=> $ap); # top score 1st
}
sub _sortHsp_SrcLocation {
my($ar,$ab,$ae,$ao)= @{$a}[1,5,6,10];
my($br,$bb,$be,$bo)= @{$b}[1,5,6,10];
my $ocmp= ($ao eq $bo)? 0 : ($ao eq "-") ? 1 : -1;
return ($ar cmp $br || $ocmp || $ab <=> $bb || $be <=> $ae); # sort all -strand last
}
sub bestlocHspset {
my($hsploc, $tsid, $ts_start, $ts_end, $ts_strand)= @_;
my @before=(); my @after=();
my $skiphsp= 0;
my($trange0, $trange1)= ($ts_start - $MAX_EXON_SEPARATION, $ts_end + $MAX_EXON_SEPARATION);
foreach my $hspval (@$hsploc)
{ # instead of foreach can we hash-find nearby hsps?
my($qid,$sid,$alignment_length, $q_start,$q_end,$s_start,$s_end, $bit_score, $prob, $tkey, $s_strand, $soverlapped, $qoverlapped) = @$hspval;
next unless($sid eq $tsid && $s_strand eq $ts_strand && $s_start > $trange0 && $s_end < $trange1);
if($s_end <= $ts_start + $QBASEOVER) { unshift(@before, $hspval); }
elsif($s_start >= $ts_end - $QBASEOVER) { push(@after, $hspval); }
}
return (\@before, \@after); # sorted around hspbest
}
sub assignBestgene { # version 3
#? my($theqid) = @_; # not used
my($topsid);
$npart=0;
my $saved=0;
my $genenum = 0; my $lastgenenum= 0;
my $lastexon= undef;
@allsaved=(); # dont need global
my @hspbest = sort _sortHsp_Score @sourcehsps;
my @hsploc = sort _sortHsp_SrcLocation @sourcehsps;
# input sourcehsp should all be for same query-gene, sorted by location (NOT/was bitscore)
# need location-sort to match up exon parts of genes
my %donehsp=();
my($qid,$sid,$alignment_length, $q_start,$q_end,$s_start,$s_end,
$bit_score, $prob, $tkey, $s_strand,
$soverlapped, $qoverlapped);
foreach my $hspbest (@hspbest)
{
($qid,$sid,$alignment_length, $q_start,$q_end,$s_start,$s_end, $bit_score, $prob, $tkey, $s_strand, $soverlapped, $qoverlapped) = @$hspbest;
my $topkey="$qid.$sid.$q_start.$s_start.$s_end.$bit_score";
# warn "#top $topkey\n"; #DEBUG
next if $donehsp{$topkey}++;
next if overlapsome($s_start, $s_end, \@allsaved, $OVERLAP_SLOP_GENOME);
$genenum++;
$topsid= $sid; ## if ($npart==0);
my $keynum= $genenum;
unless(ref $moregenes{$keynum}) { $moregenes{$keynum}= []; }
push( @{$moregenes{$keynum}}, $hspbest); $saved=1;
$sumhash{'other'}{($saved?'saved':'notsaved')}++;
if ($saved)
{
push(@allsaved, $hspbest);
$sumhash{'ALL'}{($saved?'saved':'notsaved')}++;
}
my($tsid, $tq_start, $tq_end, $ts_start, $ts_end, $ts_strand)= ($sid, $q_start, $q_end, $s_start, $s_end, $s_strand);
my($trange0, $trange1)= ($ts_start - $MAX_EXON_SEPARATION, $ts_end + $MAX_EXON_SEPARATION);
my($srange0, $srange1)= ($ts_start, $ts_end);
my($qrange0, $qrange1)= ($tq_start, $tq_end);
## FIXME.3 this really needs to step thru @hsploc starting at $hspbest loc and go down,up from there
## otherwise qrange, srange are bad. are getting two genes made from very good pieces of 1 gene match
## due to interior hsp's skipped in first pass nearest to hspbest.
my(@before,@after);
my($before, $after)= bestlocHspset(\@hsploc, $tsid, $ts_start, $ts_end, $ts_strand);
foreach my $hspval (@$after, @$before) { # instead of foreach can we hash-find nearby hsps?
# next unless (ref $hspval); #?
($qid,$sid,$alignment_length, $q_start,$q_end,$s_start,$s_end, $bit_score, $prob, $tkey, $s_strand, $soverlapped, $qoverlapped) = @$hspval;
## FIXME here; should not skip, but keep some of these to check;
## should not look far away if nearby exon fits; it it is done already or overlaps, count in qrange and skip on
## FIXME.2 new problem with this; far-hsp already done can eat away query-range; need to skip those
## already done# next unless($sid eq $tsid && $s_strand eq $ts_strand && $s_start > $trange0 && $s_end < $trange1);
my $skiphsp= 0;
my $atlockey="$qid.$sid.$q_start.$s_start.$s_end.$bit_score";
## warn "#at $atlockey\n"; #DEBUG
next if($atlockey eq $topkey);
$skiphsp=1 if $donehsp{$atlockey};
$skiphsp=1 if $skiphsp || overlapsome($s_start, $s_end, \@allsaved, $OVERLAP_SLOP_GENOME);
my $qover= overlap1($q_start, $q_end, $qrange0, $qrange1, $OVERLAP_SLOP_QUERY);
next if($qover); # last?
# $skiphsp=1 if ($qover);
## FIXME: need to look at qloc vs top-qloc; if -strand, @before must be higher qloc, @after lower
## and v.v.
# if($skiphsp) now check that s_start,s_end is *near* top hsp; skip if not
my $nearover= nearover1($s_start, $s_end, $srange0, $srange1, $OVERLAP_SLOP_GENOME, 5000); # GAPSIZE
if($nearover >= 0) { next if $skiphsp; }
if($s_end <= $ts_start + $QBASEOVER)
{ # before
# if($s_strand eq '-') { $qrange1 = $q_end if($q_end> $qrange1); }
# else { $qrange0 = $q_start if($q_start< $qrange0); } # not before
if($s_strand eq '-')
{
next if($q_start + $QBASEOVER < $qrange1);
$qrange1 = $q_end if($q_end> $qrange1);
}
else
{
next if($q_end - $QBASEOVER > $qrange0);
$qrange0 = $q_start if($q_start< $qrange0);
} # not before
unshift(@before, $hspval) unless $skiphsp;
$srange0 = $s_start unless $skiphsp;
}
elsif($s_start >= $ts_end - $QBASEOVER)
{
# after; bug in next here
# if($s_strand eq '-') { $qrange0 = $q_start if($q_start < $qrange0); }
# else { $qrange1 = $q_end if($q_end > $qrange1); } # not after
if($s_strand eq '-')
{
next if($q_end - $QBASEOVER > $qrange0);
$qrange0 = $q_start if($q_start< $qrange0);
}
else
{
next if($q_start + $QBASEOVER < $qrange1);
$qrange1 = $q_end if($q_end> $qrange1);
} # not after
push(@after, $hspval) unless $skiphsp;
$srange1 = $s_end unless $skiphsp;
}
##warn "#skip=$skiphsp $atlockey\n"; #DEBUG
}
#? limit before, after size? dont try to find what isn't there by too far a match
foreach my $hspval (@before, @after)
{ # .. and after
($qid,$sid,$alignment_length, $q_start,$q_end,$s_start,$s_end,$bit_score, $prob, $tkey, $s_strand, $soverlapped, $qoverlapped) = @$hspval;
my $atlockey="$qid.$sid.$q_start.$s_start.$s_end.$bit_score";
$saved= 0; ##no## $genenum= 0;
if(1) {
#my $keynum= "G" . $genenum;
my $keynum= $genenum;
unless(ref $moregenes{$keynum}) { $moregenes{$keynum}= []; }
push( @{$moregenes{$keynum}}, $hspval); $saved=1;
$sumhash{'other'}{($saved?'saved':'notsaved')}++;
}
if ($saved)
{
$lastexon= $hspval;
$lastgenenum= $genenum;
$donehsp{$atlockey}++;
push(@allsaved, $hspval);
$sumhash{'ALL'}{($saved?'saved':'notsaved')}++;
}
$npart++;
}
}
}
sub printGeneLocations {
my($qid) = @_; # not used
if(@sourcehsps && $qid && 0 < $didid{$qid}++) { select STDERR; print STDERR "ERROR: $qid already seen\n"; usage(); }
assignBestgene(); # NEW
my $ng= printOneLocation(\@mainexons, 'G1'); # not used now
$ng += printOneLocation(\@secondexons, 'G2'); # not used now
foreach my $keynum (sort{$a<=>$b} keys %moregenes)
{ ## NOW NUMERIC KEY
(my $gnum= $keynum) =~ s/^(.)[a-z]+/$1/; ## S2..S9; o2..o9
$gnum = 'G'.$gnum;
$ng += printOneLocation($moregenes{$keynum}, $gnum);
}
return $ng;
}
sub printOneLocation {
my($exons, $igene) = @_;
return 0 unless(ref $exons && @$exons > 0);
my $qdb=".";
my @locs= ();
my($sum_bit_score,$sum_align,$iex)=(0)x10;
my($qid1,$qid,$sid,$alignment_length,$q_start,$q_end,$s_start,$s_end, $bit_score, $prob, $tkey,$s_strand, $soverlapped, $qoverlapped);
my @gffout= ();
my($g_start,$g_end, $g_strand)=(undef,0);
foreach my $ex ((sort{ $$a[5] <=> $$b[5] } @$exons))
{
($qid,$sid,$alignment_length, $q_start,$q_end,$s_start,$s_end, $bit_score, $prob, $tkey, $s_strand, $soverlapped, $qoverlapped)= @$ex;
$qdb= $querySource; # default
($qdb,$qid1)= ($qid =~m/:/) ? split(/[:]/, $qid,2) : ($qdb,$qid);
$g_start= $s_start unless(defined $g_start);
$g_end= $s_end;
$g_strand= $s_strand;
$iex++;
$sum_bit_score += $bit_score;
$sum_align += $alignment_length;
if(1)
{ # == GFF_LOC
$tkey =~ s/^\w+://; $tkey =~ s/,/-/g; # extra dbid and no commas in values
#was# $attr= "Parent=${qid1}_${igene};tkey=$tkey;tloc=$q_start-$q_end;align=$alignment_length";
my $attr= "Parent=${qid1}_${igene}";
$attr.= ";Target=$qid $q_start $q_end;align=$alignment_length" if($dotarget);
# print $gffout
push @gffout, join("\t",
($sid, $qdb, $exonType, $s_start, $s_end, $bit_score, $s_strand,".",$attr)). "\n";
}
# else { push(@locs,"$s_start..$s_end"); }
}
$max_bit_score = $sum_bit_score if($sum_bit_score > $max_bit_score ); # assumes output by best match 1st
return if ($sum_bit_score / $max_bit_score < $LOWSCORE_SKIP);
if($addgene)
{
my $attr= "ID=${qid1}_${igene};Name=${qid1}";
my $protLength = $proteinLengths{${qid1}};
my $protCov= sprintf("%0.2f", ($sum_align / $protLength) * 100 );
$attr.= ";Target=$qid;align=$sum_align;queryLen=$protLength;coverage=$protCov" if($dotarget);
unshift @gffout, join("\t", ($sid, $qdb, $geneType, $g_start, $g_end, $sum_bit_score, $g_strand,".",$attr)). "\n";
if ($protCov >= $minCoverage)
{
my $startPositionInDNA = $g_start - 1000; ($startPositionInDNA < 0) and $startPositionInDNA = 1;
my $stopPositionInDNA = $g_end + 1000; #($stopPositionInDNA < 0) and $stopPositionInDNA = 1; # No way to get this unless loading scaffold fasta
my $strands = "-tfor"; ($g_strand eq "-") and $strands = "-trev";
my $genewiseStdoutCapture = $sid . "_" . ${qid1} . ".stdout";
my $genewiseStderrCapture = $sid . "_" . ${qid1} . ".stderr";
my $geneWiseCmd = "genewise -u $startPositionInDNA -v $stopPositionInDNA $strands -pseudo -genes -para -sum -cdna -trans -gff -kbyte 40000 $proteinFastaDir/${qid1}.fa $refFastaDir/$sid.fa 1>$genewiseResultsOutDir/$genewiseStdoutCapture 2>$genewiseResultsOutDir/$genewiseStderrCapture\n";
push(@geneWiseCommands, $geneWiseCmd);
}
}
print $gffout @gffout;
return 1;
}
sub overlapsome { # need scaffold?
my($s_start, $s_end, $exons, $OVERLAP_SLOP)= @_;
foreach my $ex (@$exons)
{
return 1 if overlap1($s_start, $s_end, $$ex[5], $$ex[6], $OVERLAP_SLOP);
}
return 0;
}
sub overlap1 {
my($s_start, $s_end, $b_start, $b_end, $OVERLAP_SLOP)= @_;
return 0 unless ( $s_start < $b_end && $s_end > $b_start ); ## no overlap
return 1 if ( $s_start >= $b_start && $s_end <= $b_end ); # contained-in
if ( $s_end > $b_start && $s_start < $b_end )
{
## e.g. s= 20,50 ; b = 10,30 : o= 10* or 40
my $b_len= 1 + $b_end - $b_start;
my $s_len= 1 + $s_end - $s_start; # choose ? biggest
my $olp1 = $b_end - $s_start; # 30-20 = 10
my $olp2 = $s_end - $b_start; # 50-10 = 40
$olp1= $olp2 if ($olp2<$olp1);
$s_len= $b_len if ($s_len<$b_len);
return 1 if (($olp1 / $s_len) > $OVERLAP_SLOP);
}
return 0;
}
sub nearover1 { # near == -1; over == +1; other == 0
my($s_start, $s_end, $b_start, $b_end, $OVERLAP_SLOP, $gapsize)= @_;
# need some overlap slop here; note locs here are QUERY == protein; should not be large
unless ( $s_start < ($b_end - $QBASEOVER) && $s_end > ($b_start + $QBASEOVER) ) {
if($s_start >= $b_end) { return ($s_start - $b_end < $gapsize) ? -1 : 0; }
elsif($b_start >= $s_end) { return ($b_start - $s_end < $gapsize) ? -1 : 0; }
return 0;
}
return overlap1($s_start, $s_end, $b_start, $b_end, $OVERLAP_SLOP);
}
sub minabs {
my($a,$b)= @_;
$a= abs($a); $b= abs($b);
return ($a>$b)? $b : $a;
}
sub toofar1 {
my($q_start, $q_end, $b_start, $b_end)= @_;
return 1 if minabs($b_end - $q_start,$q_end - $b_start) > $MAX_EXON_SEPARATION;
return 0;
}
sub cleanid {
unless( $_[0] =~ s/$faprefix//) { $_[0] =~ s/^gi\|\d+\|(\S+)/$1/; } # drop gi nums for ids
$_[0] =~ s/\|$//; ## some ids have '|' at end of id; chomp
$_[0] =~ s/\|/:/; #?? change pipe to db:id format
}
sub usage {
print "\nUSAGE: $0 <option>\n\n";
print "This script is a modification of Don Gilbert's 2008 version of blast92gff3.pl\n";
print ")http://eugenes.org/gmod/genogrid/scripts/blast92gff3.pl)\n\n";
print "Mods were mainly to simplify running of Genewise subsequently,\notherwise original code is unchanged.\n\n";
print "\n\nCommand Line Options:\n\n";
print " -gff3Outfile=path\n";
print " Name and path for gff3 output file (if not given then output goes to STDOUT)\n";
print " -proteinFastaFile=path\n";
print " Name and path to fasta format protein sequences used as queried in TBLASTn comparison\n";
print " Used for getting lengths of query proteins\n";
print " -tblastnFile=path\n";
print " Name and path for tBLASTN results in tabular format\n";
print " -refFastaDir=path\n";
print " Name of directory in which reference sequence is stored,\n";
print " and used during construction of genewise run command. Each reference\n";
print " sequence is expected in the directory as an individual sequence file\n";
print " -proteinFastaDir=path\n";
print " Name of directory in which protein sequence is stored,\n";
print " and used during construction of genewise run command. Each protein\n";
print " sequence is expected in the directory as an individual sequence file\n";
print " -genewiseResultsOutDir=path\n";
print " Name of output directory that will be used to stored genewise run outputs\n";
print " -minCoverage=int\n";
print " Value of minimum coverage threshold (1-100; default $minCoverage)\n";
print " Protein coverage is sum of alignments / protein length\n";
print " -qoverlap=float\n";
print " Default value = $OVERLAP_SLOP_QUERY for protein query HSPs\n";
print " -overlap=float\n";
print " Default value = $OVERLAP_SLOP_GENOME for genome query HSPs\n";
print " -LOWSCORE_SKIP=float\n";
print " Default value = $LOWSCORE_SKIP, skip matchs < 50% of max match score\n";
print " -source=string\n";
print " String value to use for source field in gff3 records\n";
print " -geneType=string\n";
print " String value to use for type field in gff3 records (default: $geneType)\n";
print " -exonType=string\n";
print " String value to use for type field in gff3 records (default: $exonType)\n";
print " -max_exon_separation=int\n";
print " Max exon separation (default: $MAX_EXON_SEPARATION)\n";
print " -qbaseover=int\n";
print " Query hsp overlap slop in bases (default: $QBASEOVER)\n";
print " -swap|swap_querytarget\n";
print " Swap the query and target for use with BLASTx\nor when the comparison was done the other way round\n";
print " -nostringent2ndary\n";
print " Switch\n";
print " -notarget\n";
print " Switch\n";
print " -nomatch\n";
print " Switch\n";
print " -debug\n";
print " Turn on degubbing\n";
exit(0);
}
__END__
my $bestsort=0; # fixme
# NOT USED NOW
sub storeBesthits {
my($qid,$sid,$s_start,$s_end,$bit_score)= @_;
## binned top hits for filterBesthits ; can we do this inline ?
my($qdb,$qid1)= ($qid =~m/:/) ? split(/[:]/, $qid,2) : ($querySource,$qid);
my ($sbin)= ($BIN10000 * int($s_start/$BIN10000)) ; # must match besthash bin size
my $bestkey="$qdb.$sid.$sbin";
my @bv= ($bit_score,$s_start,$s_end,$qid);
push( @{$besthash{$bestkey}}, \@bv); # arrayref of arrayref
$bestkey="$qdb"; # best over all genome == _G1
if( ! $besthash{$bestkey} ) {
$besthash{$bestkey}= [\@bv];
} elsif($bit_score > $besthash{$bestkey}->[0]->[0]) {
$besthash{$bestkey}->[0]= \@bv;
}
}
# NOT USED NOW
sub filterBesthits {
my($qid,$sid,$s_start,$s_end,$s_strand,$bit_score)= @_;
unless($bestsort>0) {
$bestsort++;
foreach my $akey (sort keys %besthash) {
my @blocs= sort{$b->[0] <=> $a->[0]} @ { $besthash{$akey} };
$besthash{$akey}= \@blocs;
}
}
my $snotbest= 0;
return 0 unless(scalar(%besthash));
my ($qdb,$qid1)= ($qid =~m/:/) ? split(/[:]/, $qid,2) : ($querySource,$qid);
my ($sbin)= ($BIN10000 * int($s_start/$BIN10000)) ; # must match besthash bin size
my($sdb,$sid1)= ($sid =~/:/) ? split(/[:]/, $sid,2) : ('',$sid);
my $bestkey="$qdb.$sid1.$sbin";
my $isbest = $besthash{$bestkey};
if($isbest) {
my @blocs= @ { $besthash{$bestkey} };
foreach my $bl (@blocs) {
my($bbits,$bb,$be,$bqid)= @$bl;
$snotbest= overlap1($s_start, $s_end, $bb, $be, $OVERLAP_SLOP_GENOME);
if($snotbest) {
$snotbest= 0 if($bit_score >= $bbits || $qid eq $bqid); # keep self match
last;
}
}
$sumhash{'besthits'}{($snotbest?'no':'yes')}++;
}
else {
$sumhash{'besthits'}{'missed'}++;
}
return $snotbest;
}
# NOT USED NOW
sub pushGeneExons {
my($exons, $hspval, $q_start,$q_end,$s_start,$s_end) = @_;
my $qoverlapped=0;
my $toofar= -1;
foreach my $ex (@$exons) {
my ($bs,$be)= ($$ex[3],$$ex[4]);
$qoverlapped= overlap1($q_start,$q_end, $bs, $be, $OVERLAP_SLOP_QUERY);
last if ($qoverlapped);
if($toofar != 0) { $toofar= toofar1($s_start,$s_end, $$ex[5],$$ex[6]); }
}
return 0 if($qoverlapped || $toofar>0);
push(@$exons, $hspval); # [$qid,$sid,$alignment_length, $q_start,$q_end,$s_start,$s_end, $bit_score, $prob]
return 1;
}
## this one is out; not good enough
#
# sub assignBestgene1 {
# my($tophsp);
# $npart=0;
# my $saved=0;
# my $genenum = 0; my $lastgenenum= 0;
# my $lastexon= undef;
#
# # input sourcehsp should all be for same query-gene, sorted by location (NOT/was bitscore)
# # need location-sort to match up exon parts of genes
#
# foreach my $hspval (@sourcehsps) {
# my($qid,$sid,$alignment_length, $q_start,$q_end,$s_start,$s_end,
# $bit_score, $prob, $tkey, $s_strand,
# $soverlapped, $qoverlapped)
# = @$hspval;
# $saved= 0; $genenum= 0;
#
# ## test this; not working right
# ## really need to test, for each hsp?, nearby hsp both directions and need to keep strand same
# my $overlast=0;
# foreach my $ex ($lastexon) {
# my ($bsid,$bs,$be)= ($$ex[1],$$ex[3],$$ex[4]);
# next unless($bsid eq $sid);
# # $overlast= overlap1($q_start, $q_end, $bs, $be, $OVERLAP_SLOP_QUERY);
# # last if ($overlast);
# my $nearlast= nearover1($q_start, $q_end, $bs, $be, $OVERLAP_SLOP_QUERY);
# if ($nearlast<0) { $genenum= $lastgenenum; last; }
# elsif($nearlast>0) { $overlast=1; last; }
# }
# # next if $overlast; #??
#
# $tophsp= $sid if ($npart==0);
# my $issame= ($sid eq $tophsp);
# my $scafpart;
# if($npart==0 || $issame) { $tandhash{'Samescaf'}{$tkey}++; $scafpart='Samescaf'; }
# if($npart==0 || !$issame) { $tandhash{'otherscaf'}{$tkey}++; $scafpart= 'otherscaf' if($npart>0); }
#
# $genenum = $tandhash{$scafpart}{$tkey} unless ($genenum);
# # ^^ this is easily bad : tkey and messes up joining exon-parts of gene : splits too much
#
# if( $soverlapped ) {
# $sumhash{'other_soverlap'}{($saved?'saved':'notsaved')}++;
#
# #} elsif( $overlast ) { # this is problem
# # $sumhash{'other_qoverlap'}{($saved?'saved':'notsaved')}++;
#
# } elsif($sid eq $tophsp && $genenum == 1) { # primary-match exons
# my $snotbest= 0; #?? filterBesthits($qid,$sid,$s_start,$s_end,$s_strand,$bit_score);
# if ($snotbest) { $saved=0; }
# else { $saved= pushGeneExons(\@mainexons, $hspval, $q_start,$q_end, $s_start,$s_end); }
# $sumhash{'G1'}{($saved?'saved':'notsaved')}++;
# }
#
# ## test off; need this?
# # elsif($sid eq $tophsp && $genenum == 2) { # 2nd-match exons
# # my $snotbest= filterBesthits($qid,$sid,$s_start,$s_end,$s_strand,$bit_score);
# # if ($snotbest) { $saved=0; }
# # else { $saved= pushGeneExons(\@secondexons, $hspval, $q_start,$q_end, $s_start,$s_end); }
# # $sumhash{'G2'}{($saved?'saved':'notsaved')}++;
# # }
#
# elsif( !$soverlapped ) { # other-match exons
# my $snotbest= filterBesthits($qid,$sid,$s_start,$s_end,$s_strand,$bit_score);
# $saved= 0;
# unless($snotbest) {
# my $keynum= $scafpart . $genenum;
# unless(ref $moregenes{$keynum}) { $moregenes{$keynum}= []; }
# $saved= pushGeneExons( $moregenes{$keynum}, $hspval, $q_start,$q_end, $s_start,$s_end);
# }
# $sumhash{'other'}{($saved?'saved':'notsaved')}++;
# }
#
# if ($saved) {
# $lastexon= $hspval;
# $lastgenenum= $genenum;
# push(@allsaved, $hspval);
# $sumhash{'ALL'}{($saved?'saved':'notsaved')}++;
# }
# $npart++;
# }
# }
## this one is out; not good enough
# sub assignBestgene_OLD {
# my($tophsp);
# $npart=0;