| 9 |
|
|
| 10 |
|
#define USAGE "Usage:\n\ |
| 11 |
|
gffread <input_gff> [-g <genomic_seqs_fasta> | <dir>][-s <seq_info.fsize>] \n\ |
| 12 |
< |
[-o <outfile.gff>] [-t <tname>] [-r [[<strand>]<chr>:]<start>..<end>] \n\ |
| 13 |
< |
[-CTVNJMKQAFGRUVBHZWTOLE] [-w <spl_exons.fa>] [-x <spl_cds.fa>] [-y <tr_cds.fa>]\n\ |
| 12 |
> |
[-o <outfile.gff>] [-t <tname>] [-r [[<strand>]<chr>:]<start>..<end> [-R]]\n\ |
| 13 |
> |
[-CTVNJMKQAFGUBHZWTOLE] [-w <exons.fa>] [-x <cds.fa>] [-y <tr_cds.fa>]\n\ |
| 14 |
|
[-i <maxintron>] \n\ |
| 15 |
|
Filters and/or converts GFF3/GTF2 records.\n\ |
| 16 |
|
<input_gff> is a GFF file, use '-' if the GFF records will be given at stdin\n\ |
| 24 |
|
<seq-name> <seq-length> <seq-description>\n\ |
| 25 |
|
(useful for -A option with mRNA/EST/protein mappings)\n\ |
| 26 |
|
-i discard transcripts having an intron larger than <maxintron>\n\ |
| 27 |
< |
-r only show transcripts crossing coordinate range <start>..<end>\n\ |
| 27 |
> |
-r only show transcripts overlapping coordinate range <start>..<end>\n\ |
| 28 |
|
(on chromosome/contig <chr>, strand <strand> if provided)\n\ |
| 29 |
|
-R for -r option, discard all transcripts that are not fully \n\ |
| 30 |
< |
contained within given range\n\ |
| 30 |
> |
contained within the given range\n\ |
| 31 |
|
-U discard single-exon transcripts\n\ |
| 32 |
|
-C coding only: discard mRNAs that have no CDS feature\n\ |
| 33 |
|
-F full GFF attribute preservation (all attributes are shown)\n\ |
| 52 |
|
\n\ |
| 53 |
|
-M/--merge : cluster the input transcripts into loci, collapsing matching\n\ |
| 54 |
|
transcripts (those with the same exact introns and fully contained)\n\ |
| 55 |
+ |
-d <dupinfo> : for -M option, write collapsing info to file <dupinfo>\n\ |
| 56 |
|
--cluster-only: same as --merge but without collapsing matching transcripts\n\ |
| 57 |
|
-K for -M option: also collapse shorter, fully contained transcripts\n\ |
| 58 |
|
with fewer introns than the container\n\ |
| 602 |
|
if (reftbl.Count()>0) { |
| 603 |
|
GStr refname(gffrec->getRefName()); |
| 604 |
|
RefTran* rt=reftbl.Find(refname.chars()); |
| 605 |
< |
if (rt==NULL && refname[-2]=='.' && isdigit(refname[-1])) { |
| 606 |
< |
//try removing the version |
| 605 |
> |
if (rt==NULL && refname.length()>2 && refname[-2]=='.' && isdigit(refname[-1])) { |
| 606 |
> |
//try removing the version suffix |
| 607 |
|
refname.cut(-2); |
| 608 |
|
//GMessage("[DEBUG] Trying ref name '%s'...\n", refname.chars()); |
| 609 |
|
rt=reftbl.Find(refname.chars()); |
| 639 |
|
if (rfltStart!=0 || rfltEnd!=MAX_UINT) { |
| 640 |
|
if (rfltWithin) { |
| 641 |
|
if (gffrec->start<rfltStart || gffrec->end>rfltEnd) { |
| 642 |
< |
return false; |
| 642 |
> |
return false; //not within query range |
| 643 |
|
} |
| 644 |
|
} |
| 645 |
|
else { |
| 713 |
|
exit(1); |
| 714 |
|
} |
| 715 |
|
} |
| 715 |
– |
//protmap=(args.getOpt('P')!=NULL); |
| 716 |
|
if (fullCDSonly) validCDSonly=true; |
| 717 |
|
if (verbose) { |
| 718 |
|
fprintf(stderr, "Command line was:\n"); |
| 785 |
|
rfltEnd=(uint)gsend.asInt(); |
| 786 |
|
if (rfltEnd==0) rfltEnd=MAX_UINT; |
| 787 |
|
} |
| 788 |
– |
|
| 788 |
|
} //gseq/range filtering |
| 789 |
|
else { |
| 790 |
|
if (rfltWithin) |
| 791 |
< |
GError("Error: option -R doesn't make sense without -r!\n"); |
| 791 |
> |
GError("Error: option -R requires -r!\n"); |
| 792 |
> |
//if (rfltWholeTranscript) |
| 793 |
> |
// GError("Error: option -P requires -r!\n"); |
| 794 |
|
} |
| 795 |
|
s=args.getOpt('m'); |
| 796 |
|
if (!s.is_empty()) { |
