[med-svn] [augustus] 01/01: add some more man pages

Wed Mar 23 22:33:41 UTC 2016

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sascha-guest pushed a commit to branch master
in repository augustus.

commit 2dea41b60918f7dfe2d7951c321c3e4067e33071
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date:   Wed Mar 23 22:33:27 2016 +0000

    add some more man pages
---
 debian/mansrc/bam2hints.1.adoc | 75 ++++++++++++++++++++++++++++++++++++++
 debian/mansrc/etraining.1.adoc | 28 ++++++++++++++
 debian/mansrc/joingenes.1.adoc | 83 ++++++++++++++++++++++++++++++++++++++++++
 3 files changed, 186 insertions(+)

diff --git a/debian/mansrc/bam2hints.1.adoc b/debian/mansrc/bam2hints.1.adoc
new file mode 100644
index 0000000..787fdc0
--- /dev/null
+++ b/debian/mansrc/bam2hints.1.adoc
@@ -0,0 +1,75 @@
+# bam2hints(1)
+
+## NAME
+
+bam2hints - convert mRNA-to-genome alignments in BAM format into a hint file for AUGUSTUS
+
+## SYNOPSIS
+
+*bam2hints* [parameters] --in=example.bam --out=hints.gff
+
+## OPTIONS
+
+The input BAM file must be sorted by target (=genome) sequence names and within the sequences by begin coordinates.
+
+###  Parameters:
+
+*--priority=n*/*-p*::
+  priority of hint group (set to 4)
+
+*--maxgaplen=n*/*-g*::
+   gaps at most this length are simply closed (set to 14)
+
+*--minintronlen=n*/*-m*::
+   alignments with gaps shorter than this and longer than maxgaplen are discarded (set to 32)
+
+*--maxintronlen=n*/*-M*::
+   alignments with longer gaps are discarded (set to 350000)
+
+*--MinEndBlockLen=n*/*-b*::
+   minimum length of a 'dangling' exon (set to 8)
+
+*--maxQgaplen=n*/*-q*::
+   maximum length of gap in query (cDNA) sequence (set to 5)
+
+*--exonhints*/*-x*::
+   compute exonpart, exon and splice site hints in addition to intron hints (set to 0=Off). You should generate exonpart hints from RNA-Seq using wiggle (.wig) input to wig2hints.
+
+*--ep_cutoff=n*/*-e*::
+   this many bp are cut off of each exonpart hint at end of alignment (set to 10)
+
+*--source=s*/*-s*::
+   source identifier (set to 'E')
+
+*--intronsonly*/*-I*::
+   only retrieve intron hints (e.g. because the exon(part) hints are retrieved by converting to a wig track, set to 1=On). Deprecated as this is the default now.
+
+*--nomult*/*-n*::
+   do not summarize multiple identical intron hints to a single one (set to 0=Off)
+
+*--remove_redundant*/*-r*::
+   only keep the strongest hint for a region (set to 0=Off)
+
+*--maxcoverage=n*/*-C*::
+   maximal number of hints at a given position (0: filtering deactivated). A high value causes long running time of AUGUSTUS in regions with thousands of cDNA alignments. (set to 0)
+
+*--ssOn*/*-S*::
+   include splice site (dss, ass) hints in output (set to 0=Off)
+
+*--trunkSS*/*-T*::
+   include splice sites hints from the ends of a truncated alignment (contig too short, set to 0=Off)
+
+*--score=f*/*-s*::
+   fill this number in in the score column (set to 0)
+
+*--maxgenelen=n*/*-G*::
+   alignments of the same clone are considered to be of the same gene if not separeted by more than this (set to 400000). Alignments that span more than this are ignored, but better filter long introns through an alignment program.
+
+## AUTHORS
+
+AUGUSTUS was written by M. Stanke, O. Keller, S. König, L. Gerischer and L. Romoth.
+
+## ADDITIONAL DOCUMENTATION
+
+An exhaustive documentation can be found in the file /usr/share/augustus/README.TXT.
+
diff --git a/debian/mansrc/etraining.1.adoc b/debian/mansrc/etraining.1.adoc
new file mode 100644
index 0000000..63d3c53
--- /dev/null
+++ b/debian/mansrc/etraining.1.adoc
@@ -0,0 +1,28 @@
+# etraining(1)
+
+## NAME
+
+etraining - train AUGUSTUS models
+
+## SYNOPSIS
+
+*etraining* [parameters] --species=SPECIES trainfilename
+
+## OPTIONS
+
+'trainfilename' is the filename (including relative path) to the file in genbank format containing the training sequences. These can be multi-gene sequences.
+SPECIES is a name for your species.
+
+### Further parameters:
+
+*--/genbank/verbosity=n*::
+  Choose one of 0,1,2 or 3. The larger the verbosity, the more (error) messages you get.
+
+## AUTHORS
+
+AUGUSTUS was written by M. Stanke, O. Keller, S. König, L. Gerischer and L. Romoth.
+
+## ADDITIONAL DOCUMENTATION
+
+An exhaustive documentation can be found in the file /usr/share/augustus/README.TXT.
+
diff --git a/debian/mansrc/joingenes.1.adoc b/debian/mansrc/joingenes.1.adoc
new file mode 100644
index 0000000..055a89a
--- /dev/null
+++ b/debian/mansrc/joingenes.1.adoc
@@ -0,0 +1,83 @@
+# joingenes(1)
+
+## NAME
+
+joingenes - merge several gene sets into one
+
+## SYNOPSIS
+
+*joingenes* [parameters] --genesets=file1,file2,...	 --output=ofile
+
+## DESCRIPTION
+
+This program works in several steps:
+
+  1. divide the set of all transcripts into smaller sets, in which all transcripts are on the same sequence and are overlapping at least with one other transcript in this set (set is called "overlap")
+
+  2. delete all duplications of transcripts and save the variant with the highest "score"
+
+  3. if sequence ranges are set for some transcripts, the program detects, whether the distance to that range is dangerously close
+
+  4. join:
+    - if there is a transcript dangerously close to one/both end(s) of a sequence range, the program creates a copy without the corresponding terminal exon
+    - if there is a transcript with start or stop codon in a set and a second one without this codon and they are "joinable", than this step joins the corresponding terminal exons
+
+  	5. selection: selects the "best" gene structure out of all possible "maximum" gene structures
+    - "maximum" gene structure is a set of transcripts from an overlap so that there is no other transcript in the overlap, which can be added to the set without producing a "contradiction"
+    - a gene structure is "better" than another one, if it has the transcript with the highest "score", which is not present in the other gene structure.
+
+## OPTIONS
+
+### Mandatory parameters:
+
+*--genesets=file1,file2,...*/*-g file1,file2,...*::
+	where "file1,file2,...,filen" have to be data files with genesets in GTF format
+
+*--output=ofile*/*-o ofile*::
+	where "ofile" is the name for an output file (GTF)
+
+### Optional parameters:
+
+*--priorities=pr1,pr2,...*/*-p pr1,pr2,...*::
+		where "pr1,pr2,...,prn" have to be positiv integers (different from 0).
+		Have to be as many as filenames are added. Bigger numbers means a higher priority.
+		If no priorities are added, the program will set all priorties to 1.
+		This option is only useful if there is more than one geneset.
+		If there is a conflict between two transcripts, so that they can not be picked in the same genestructure, joingenes decides for the one with the highest priority.
+
+*--errordistance=x*/*-e x*::
+			where "x" is a non-negative integer. If a prediction is <=x bases next to a prediction range border, the program supposes, that there could be a mistake. Default is 1000.
+			To disable the function, set errordistance to a negative number (e.g. -1).
+
+*--genemodel=x*/*-m x*::
+			where "x" is a genemodel from the set {eukaryote, bacterium}. Default is eukaryotic.
+
+*--alternatives*/*-a*::
+			If this flag is set, the program joins different genes if the transcripts of the genes are alternative variants.
+
+*--suppress=pr1,pr2,..*/*-s pr1,pr2,...*::
+		where "pr1,pr2,...,prm" have to be positive integers (different from 0). Default is none.
+		If the core of a joined/non-joined transcript has one of these priorities it will not occur in the output file.
+
+*--stopincoding*/*-i*::
+		If this flag is set, the program joins the stop_codons to the CDS.
+
+*--nojoin*/*-j*::
+		If this flag is set, the program will not join/merge/shuffle; it will only decide between the unchanged input transcripts and output them.
+
+*--noselection*/*-l*::
+		If this flag is set, the program will NOT select at the end between "contradictory" transcripts. "contradictory" is self defined with respect to known biological terms.
+		The selection works with a self defined scoring function.
+
+*--onlycompare*/*-c*::
+		If this flag is set, it disables the normal function of the program and
+		activates a compare and separate mode to separate equal transcripts from non equal ones.
+
+## AUTHORS
+
+AUGUSTUS was written by M. Stanke, O. Keller, S. König, L. Gerischer and L. Romoth.
+
+## ADDITIONAL DOCUMENTATION
+
+An exhaustive documentation can be found in the file /usr/share/augustus/README.TXT.
+

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