Author: sascha-guest Date: 2016-01-09 13:34:35 +0000 (Sat, 09 Jan 2016) New Revision: 21052
Added: trunk/packages/aegean/trunk/debian/man/tidygff3.1 Modified: trunk/packages/aegean/trunk/debian/man/canon-gff3.1 trunk/packages/aegean/trunk/debian/man/gaeval.1 trunk/packages/aegean/trunk/debian/man/locuspocus.1 trunk/packages/aegean/trunk/debian/man/parseval.1 trunk/packages/aegean/trunk/debian/man/pmrna.1 trunk/packages/aegean/trunk/debian/man/xtractore.1 Log: update man pages Modified: trunk/packages/aegean/trunk/debian/man/canon-gff3.1 =================================================================== --- trunk/packages/aegean/trunk/debian/man/canon-gff3.1 2016-01-09 12:30:37 UTC (rev 21051) +++ trunk/packages/aegean/trunk/debian/man/canon-gff3.1 2016-01-09 13:34:35 UTC (rev 21052) @@ -1,5 +1,5 @@ .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4. -.TH CANON-GFF3 "1" "July 2015" "canon-gff3 0.13" "User Commands" +.TH CANON-GFF3 "1" "January 2016" "canon-gff3 0.15.1" "User Commands" .SH NAME canon-gff3 \- create canonical GFF3 .SH SYNOPSIS Modified: trunk/packages/aegean/trunk/debian/man/gaeval.1 =================================================================== --- trunk/packages/aegean/trunk/debian/man/gaeval.1 2016-01-09 12:30:37 UTC (rev 21051) +++ trunk/packages/aegean/trunk/debian/man/gaeval.1 2016-01-09 13:34:35 UTC (rev 21052) @@ -1,12 +1,11 @@ .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4. -.TH GAEVAL "1" "July 2015" "gaeval 0.13" "User Commands" +.TH GAEVAL "1" "January 2016" "gaeval 0.15.1" "User Commands" .SH NAME gaeval \- calculate coverage and intergrity scores for gene models based on transcript alignments .SH SYNOPSIS .B gaeval [\fI\,options\/\fR] \fI\,alignments.gff3 genes.gff3 \/\fR[\fI\,moregenes.gff3 \/\fR...] .SH DESCRIPTION -.IP Basic options: .TP \fB\-h\fR|\-\-help Modified: trunk/packages/aegean/trunk/debian/man/locuspocus.1 =================================================================== --- trunk/packages/aegean/trunk/debian/man/locuspocus.1 2016-01-09 12:30:37 UTC (rev 21051) +++ trunk/packages/aegean/trunk/debian/man/locuspocus.1 2016-01-09 13:34:35 UTC (rev 21052) @@ -1,12 +1,11 @@ .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4. -.TH LOCUSPOCUS "1" "July 2015" "locuspocus 0.13" "User Commands" +.TH LOCUSPOCUS "1" "January 2016" "locuspocus 0.15.1" "User Commands" .SH NAME locuspocus \- calculate locus coordinates for the given gene annotation .SH SYNOPSIS .B locuspocus [\fI\,options\/\fR] \fI\,gff3file1 \/\fR[\fI\,gff3file2 gff3file3 \/\fR...] .SH DESCRIPTION -.IP Basic options: .TP \fB\-d\fR|\-\-debug @@ -27,19 +26,37 @@ regulatory regions; default is 500 .TP \fB\-s\fR|\-\-skipends -when enumerating interval loci, exclude gene\-less -iLoci at either end of the sequence +when enumerating interval loci, exclude +unannotated (and presumably incomplete) iLoci at +either end of the sequence .TP \fB\-e\fR|\-\-endsonly -report only empty iLoci at the ends of sequences -(complement of \fB\-\-skipends\fR) +report only incomplete iLocus fragments at the +unannotated ends of sequences (complement of +\fB\-\-skipends\fR) .TP -\fB\-y\fR|\-\-skipempty -do not report empty iLoci +\fB\-y\fR|\-\-skipiiloci +do not report intergenic iLoci .IP +Refinement options: +.TP +\fB\-r\fR|\-\-refine +by default genes are grouped in the same iLocus +if they have any overlap; 'refine' mode allows +for a more nuanced handling of overlapping genes +.TP +\fB\-c\fR|\-\-cds +use CDS rather than UTRs for determining gene +overlap; implies 'refine' mode +.TP +\fB\-m\fR|\-\-minoverlap: INT +the minimum number of nucleotides two genes must +overlap to be grouped in the same iLocus; default +is 1 +.IP Output options: .TP -\fB\-I\fR|\-\-idformat: STR +\fB\-n\fR|\-\-namefmt: STR provide a printf\-style format string to override the default ID format for newly created loci; default is 'locus%lu' (locus1, locus2, etc) for @@ -48,6 +65,10 @@ include a single %lu specifier to be filled in with a long unsigned integer value .TP +\fB\-i\fR|\-\-ilens: FILE +create a file with the lengths of each intergenic +iLocus +.TP \fB\-g\fR|\-\-genemap: FILE print a mapping from each gene annotation to its corresponding locus to the given file @@ -56,6 +77,11 @@ name of file to which results will be written; default is terminal (standard output) .TP +\fB\-T\fR|\-\-retainids +retain original feature IDs from input files; +conflicts will arise if input contains duplicated +ID values +.TP \fB\-t\fR|\-\-transmap: FILE print a mapping from each transcript annotation to its corresponding locus to the given file Modified: trunk/packages/aegean/trunk/debian/man/parseval.1 =================================================================== --- trunk/packages/aegean/trunk/debian/man/parseval.1 2016-01-09 12:30:37 UTC (rev 21051) +++ trunk/packages/aegean/trunk/debian/man/parseval.1 2016-01-09 13:34:35 UTC (rev 21052) @@ -1,12 +1,11 @@ .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4. -.TH PARSEVAL "1" "July 2015" "parseval 0.13" "User Commands" +.TH PARSEVAL "1" "January 2016" "parseval 0.15.1" "User Commands" .SH NAME parseval \- comparative analysis of two alternative sources of annotation .SH SYNOPSIS .B parseval [\fI\,options\/\fR] \fI\,reference.gff3 prediction.gff3\/\fR .SH DESCRIPTION -.IP Basic options: .TP \fB\-d\fR|\-\-debug: @@ -47,9 +46,9 @@ File/directory to which output will be written; default is the terminal (STDOUT) .TP -\fB\-p\fR|\-\-png: -Generate individual PNG graphics for each -gene locus (HTML mode only) +\fB\-p\fR|\-\-nopng: +In HTML output mode, skip generation of PNG +graphics for each gene locus .TP \fB\-s\fR|\-\-summary: Only print summary statistics, do not print Modified: trunk/packages/aegean/trunk/debian/man/pmrna.1 =================================================================== --- trunk/packages/aegean/trunk/debian/man/pmrna.1 2016-01-09 12:30:37 UTC (rev 21051) +++ trunk/packages/aegean/trunk/debian/man/pmrna.1 2016-01-09 13:34:35 UTC (rev 21052) @@ -1,12 +1,11 @@ .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4. -.TH PMRNA "1" "July 2015" "pmrna 0.13" "User Commands" +.TH PMRNA "1" "January 2016" "pmrna 0.15.1" "User Commands" .SH NAME pmrna \- filter out all but the primary isoform from each gene of the input .SH SYNOPSIS .B pmrna [\fI\,options\/\fR] \fI\,< annot.gff3 > new.gff3\/\fR .SH DESCRIPTION -.IP Options: .TP \fB\-h\fR|\-\-help Added: trunk/packages/aegean/trunk/debian/man/tidygff3.1 =================================================================== --- trunk/packages/aegean/trunk/debian/man/tidygff3.1 (rev 0) +++ trunk/packages/aegean/trunk/debian/man/tidygff3.1 2016-01-09 13:34:35 UTC (rev 21052) @@ -0,0 +1,11 @@ +.TH TIDYGFF3 "1" "January 2016" "tidygff3 0.15.1" "User Commands" +.SH NAME +tidygff3 \- tidy GFF3 file +.SH SYNOPSIS +.B tidygff3 +< +.IR features.gff3 +.SH DESCRIPTION +.IP +Cleans up GFF3 format files read from stdin for further use in AEGeAn by +printing the clean version on stdout. \ No newline at end of file Modified: trunk/packages/aegean/trunk/debian/man/xtractore.1 =================================================================== --- trunk/packages/aegean/trunk/debian/man/xtractore.1 2016-01-09 12:30:37 UTC (rev 21051) +++ trunk/packages/aegean/trunk/debian/man/xtractore.1 2016-01-09 13:34:35 UTC (rev 21052) @@ -1,14 +1,16 @@ .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4. -.TH XTRACTORE "1" "July 2015" "xtractore 0.13" "User Commands" +.TH XTRACTORE "1" "January 2016" "xtractore 0.15.1" "User Commands" .SH NAME xtractore \- extract sequences corresponding to annotated features from the given sequence file .SH SYNOPSIS .B xtractore [\fI\,options\/\fR] \fI\,features.gff3 sequences.fasta\/\fR .SH DESCRIPTION -.IP Options: .TP +\fB\-d\fR|\-\-debug +print debugging output +.TP \fB\-h\fR|\-\-help print this help message and exit .TP _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
