[med-svn] r14282 - trunk/packages/mothur/trunk/debian

Andreas Tille tille at alioth.debian.org
Tue Jul 30 19:43:27 UTC 2013 

Author: tille
Date: 2013-07-30 19:43:27 +0000 (Tue, 30 Jul 2013)
New Revision: 14282

Added:
   trunk/packages/mothur/trunk/debian/uchime.1
Modified:
   trunk/packages/mothur/trunk/debian/changelog
   trunk/packages/mothur/trunk/debian/manpages
Log:
Add manpage for uchime


Modified: trunk/packages/mothur/trunk/debian/changelog
===================================================================
--- trunk/packages/mothur/trunk/debian/changelog	2013-07-30 19:32:08 UTC (rev 14281)
+++ trunk/packages/mothur/trunk/debian/changelog	2013-07-30 19:43:27 UTC (rev 14282)
@@ -11,6 +11,7 @@
      - debhelper 9
      - use anonscm for Vcs fields
   * debian/patches/uchime_hardening.patch: Hardening for uchime
+  * debian/uchime.1
 
  -- Andreas Tille <tille at debian.org>  Tue, 30 Jul 2013 14:32:44 +0200
 

Modified: trunk/packages/mothur/trunk/debian/manpages
===================================================================
--- trunk/packages/mothur/trunk/debian/manpages	2013-07-30 19:32:08 UTC (rev 14281)
+++ trunk/packages/mothur/trunk/debian/manpages	2013-07-30 19:43:27 UTC (rev 14282)
@@ -1 +1 @@
-debian/mothur.1
+debian/*.1

Added: trunk/packages/mothur/trunk/debian/uchime.1
===================================================================
--- trunk/packages/mothur/trunk/debian/uchime.1	                        (rev 0)
+++ trunk/packages/mothur/trunk/debian/uchime.1	2013-07-30 19:43:27 UTC (rev 14282)
@@ -0,0 +1,719 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.43.3.
+.TH UCHIME "1" "July 2013" "uchime v4.2.40" "User Commands"
+.SH NAME
+uchime \- reads a fasta file and reference file and outputs potentially chimeric sequences
+.SH DESCRIPTION
+The chimera.uchime command reads a fasta file and reference file and outputs potentially
+chimeric sequences. The original uchime program was written by Robert C. Edgar.
+.SH SYNOPSIS
+.B uchime
+\fB\-\-input\fR query.fasta [\-\-db db.fasta] [\-\-uchimeout results.uchime]
+.IP
+[\-\-uchimealns results.alns]
+.SH OPTIONS
+.PP
+\fB\-\-input\fR filename
+.IP
+Query sequences in FASTA format.
+If the \fB\-\-db\fR option is not specificed, uchime uses de novo
+detection. In de novo mode, relative abundance must be given
+by a string /ab=xxx/ somewhere in the label, where xxx is a
+floating\-point number, e.g. >F00QGH67HG/ab=1.2/.
+.PP
+\fB\-\-db\fR filename
+.IP
+Reference database in FASTA format.
+Optional, if not specified uchime uses de novo mode.
+.IP
+***WARNING*** The database is searched ONLY on the plus strand.
+You MUST include reverse\-complemented sequences in the database
+if you want both strands to be searched.
+.PP
+\fB\-\-abskew\fR x
+.IP
+Minimum abundance skew. Default 1.9. De novo mode only.
+Abundance skew is:
+.IP
+min [ abund(parent1), abund(parent2) ] / abund(query).
+.PP
+\fB\-\-uchimeout\fR filename
+.IP
+Output in tabbed format with one record per query sequence.
+First field is score (h), second field is query label.
+For details, see manual.
+.PP
+\fB\-\-uchimealns\fR filename
+.IP
+Multiple alignments of query sequences to parents in humanreadable format. Alignments show columns with differences
+that support or contradict a chimeric model.
+.PP
+\fB\-\-minh\fR h
+.IP
+Mininum score to report chimera. Default 0.3. Values from 0.1
+to 5 might be reasonable. Lower values increase sensitivity
+but may report more false positives. If you decrease \fB\-\-xn\fR,
+you may need to increase \fB\-\-minh\fR, and vice versa.
+.PP
+\fB\-\-mindiv\fR div
+.IP
+Minimum divergence ratio, default 0.5. Div ratio is 100% \-
+%identity between query sequence and the closest candidate for
+being a parent. If you don't care about very close chimeras,
+then you could increase \fB\-\-mindiv\fR to, say, 1.0 or 2.0, and
+also decrease \fB\-\-min\fR h, say to 0.1, to increase sensitivity.
+How well this works will depend on your data. Best is to
+tune parameters on a good benchmark.
+.PP
+\fB\-\-xn\fR beta
+.IP
+Weight of a no vote, also called the beta parameter. Default 8.0.
+Decreasing this weight to around 3 or 4 may give better
+performance on denoised data.
+.PP
+\fB\-\-dn\fR n
+.IP
+Pseudo\-count prior on number of no votes. Default 1.4. Probably
+no good reason to change this unless you can retune to a good
+benchmark for your data. Reasonable values are probably in the
+range from 0.2 to 2.
+.PP
+\fB\-\-xa\fR w
+.IP
+Weight of an abstain vote. Default 1. So far, results do not
+seem to be very sensitive to this parameter, but if you have
+a good training set might be worth trying. Reasonable values
+might range from 0.1 to 2.
+.PP
+\fB\-\-chunks\fR n
+.IP
+Number of chunks to extract from the query sequence when searching
+for parents. Default 4.
+.PP
+\fB\-\-[no]ovchunks\fR
+.IP
+[Do not] use overlapping chunks. Default do not.
+.PP
+\fB\-\-minchunk\fR n
+.IP
+Minimum length of a chunk. Default 64.
+.PP
+\fB\-\-idsmoothwindow\fR w
+.IP
+Length of id smoothing window. Default 32.
+.PP
+\fB\-\-minsmoothid\fR f
+.IP
+Minimum factional identity over smoothed window of candidate parent.
+Default 0.95.
+.PP
+\fB\-\-maxp\fR n
+.IP
+Maximum number of candidate parents to consider. Default 2. In tests so
+far, increasing \fB\-\-maxp\fR gives only a very small improvement in sensivity
+but tends to increase the error rate quite a bit.
+.PP
+\fB\-\-[no]skipgaps\fR
+\fB\-\-[no]skipgaps2\fR
+.IP
+These options control how gapped columns affect counting of diffs.
+If \fB\-\-skipgaps\fR is specified, columns containing gaps do not found as diffs.
+If \fB\-\-skipgaps2\fR is specified, if column is immediately adjacent to
+a column containing a gap, it is not counted as a diff.
+Default is \fB\-\-skipgaps\fR \fB\-\-skipgaps2\fR.
+.PP
+\fB\-\-minlen\fR L
+\fB\-\-maxlen\fR L
+.IP
+Minimum and maximum sequence length. Defaults 10, 10000.
+Applies to both query and reference sequences.
+.PP
+\fB\-\-ucl\fR
+.IP
+Use local\-X alignments. Default is global\-X. On tests so far, global\-X
+is always better; this option is retained because it just might work
+well on some future type of data.
+.PP
+\fB\-\-queryfract\fR f
+.IP
+Minimum fraction of the query sequence that must be covered by a local\-X
+alignment. Default 0.5. Applies only when \fB\-\-ucl\fR is specified.
+.PP
+\fB\-\-quiet\fR
+.IP
+Do not display progress messages on stderr.
+.PP
+\fB\-\-log\fR filename
+.IP
+Write miscellaneous information to the log file. Mostly of interest
+to me (the algorithm developer). Use \fB\-\-verbose\fR to get more info.
+.PP
+\fB\-\-self\fR
+.IP
+In reference database mode, exclude a reference sequence if it has
+the same label as the query. This is useful for benchmarking by using
+the ref db as a query to test for false positives.
+.TP
+\fB\-\-abskew\fR <float>
+help
+.TP
+\fB\-\-absort\fR <str>
+help
+.TP
+\fB\-\-abx\fR <float>
+help
+.TP
+\fB\-\-allpairs\fR <str>
+help
+.TP
+\fB\-\-alpha\fR <str>
+help
+.TP
+\fB\-\-band\fR <uint>
+help
+.TP
+\fB\-\-blast6out\fR <str>
+help
+.TP
+\fB\-\-[no]blast_termgaps\fR
+help
+.TP
+\fB\-\-blastout\fR <str>
+help
+.TP
+\fB\-\-bump\fR <uint>
+help
+.TP
+\fB\-\-[no]cartoon_orfs\fR
+help
+.TP
+\fB\-\-cc\fR <str>
+help
+.TP
+\fB\-\-chain_evalue\fR <float>
+help
+.TP
+\fB\-\-chain_targetfract\fR <float>
+help
+.TP
+\fB\-\-chainhits\fR <str>
+help
+.TP
+\fB\-\-chainout\fR <str>
+help
+.TP
+\fB\-\-chunks\fR <uint>
+help
+.TP
+\fB\-\-clstr2uc\fR <str>
+help
+.TP
+\fB\-\-clump\fR <str>
+help
+.TP
+\fB\-\-clump2fasta\fR <str>
+help
+.TP
+\fB\-\-clumpfasta\fR <str>
+help
+.TP
+\fB\-\-clumpout\fR <str>
+help
+.TP
+\fB\-\-cluster\fR <str>
+help
+.TP
+\fB\-\-compilerinfo\fR
+Write info about compiler types and #defines to stdout.
+.TP
+\fB\-\-computekl\fR <str>
+help
+.TP
+\fB\-\-db\fR <str>
+help
+.TP
+\fB\-\-dbstep\fR <uint>
+help
+.TP
+\fB\-\-[no]denovo\fR
+help
+.TP
+\fB\-\-derep\fR
+help
+.TP
+\fB\-\-diffchar\fR <str>
+help
+.TP
+\fB\-\-dn\fR <float>
+help
+.TP
+\fB\-\-doug\fR <str>
+help
+.TP
+\fB\-\-droppct\fR <uint>
+help
+.TP
+\fB\-\-evalue\fR <float>
+help
+.TP
+\fB\-\-evalue_g\fR <float>
+help
+.TP
+\fB\-\-exact\fR
+help
+.TP
+\fB\-\-[no]fastalign\fR
+help
+.TP
+\fB\-\-fastapairs\fR <str>
+help
+.TP
+\fB\-\-fastq2fasta\fR <str>
+help
+.TP
+\fB\-\-findorfs\fR <str>
+help
+.TP
+\fB\-\-[no]flushuc\fR
+help
+.TP
+\fB\-\-frame\fR <int>
+help
+.TP
+\fB\-\-fspenalty\fR <float>
+help
+.TP
+\fB\-\-gapext\fR <str>
+help
+.TP
+\fB\-\-gapopen\fR <str>
+help
+.TP
+\fB\-\-getseqs\fR <str>
+help
+.TP
+\fB\-\-global\fR
+help
+.TP
+\fB\-\-hash\fR
+help
+.TP
+\fB\-\-hashsize\fR <uint>
+help
+.TP
+\fB\-\-help\fR
+Display command\-line options.
+.TP
+\fB\-\-hireout\fR <str>
+help
+.TP
+\fB\-\-hspalpha\fR <str>
+help
+.TP
+\fB\-\-id\fR <float>
+help
+.TP
+\fB\-\-idchar\fR <str>
+help
+.TP
+\fB\-\-iddef\fR <uint>
+help
+.TP
+\fB\-\-idprefix\fR <uint>
+help
+.TP
+\fB\-\-ids\fR <str>
+help
+.TP
+\fB\-\-idsmoothwindow\fR <uint>
+help
+.TP
+\fB\-\-idsuffix\fR <uint>
+help
+.TP
+\fB\-\-indexstats\fR <str>
+help
+.TP
+\fB\-\-input\fR <str>
+help
+.TP
+\fB\-\-[no]isort\fR
+help
+.TP
+\fB\-\-k\fR <uint>
+help
+.TP
+\fB\-\-ka_dbsize\fR <float>
+help
+.TP
+\fB\-\-ka_gapped_k\fR <float>
+help
+.TP
+\fB\-\-ka_gapped_lambda\fR <float>
+help
+.TP
+\fB\-\-ka_ungapped_k\fR <float>
+help
+.TP
+\fB\-\-ka_ungapped_lambda\fR <float>
+help
+.TP
+\fB\-\-[no]label_ab\fR
+help
+.TP
+\fB\-\-labels\fR <str>
+help
+.TP
+\fB\-\-[no]leftjust\fR
+help
+.TP
+\fB\-\-lext\fR <float>
+help
+.TP
+\fB\-\-local\fR
+help
+.TP
+\fB\-\-log\fR <str>
+Log file name.
+.TP
+\fB\-\-[no]log_hothits\fR
+help
+.TP
+\fB\-\-[no]log_query\fR
+help
+.TP
+\fB\-\-[no]logmemgrows\fR
+help
+.TP
+\fB\-\-logopts\fR
+Log options.
+.TP
+\fB\-\-[no]logwordstats\fR
+help
+.TP
+\fB\-\-lopen\fR <float>
+help
+.TP
+\fB\-\-makeindex\fR <str>
+help
+.TP
+\fB\-\-match\fR <float>
+help
+.TP
+\fB\-\-matrix\fR <str>
+help
+.TP
+\fB\-\-max2\fR <uint>
+help
+.TP
+\fB\-\-maxaccepts\fR <uint>
+help
+.TP
+\fB\-\-maxclump\fR <uint>
+help
+.TP
+\fB\-\-maxlen\fR <uint>
+help
+.TP
+\fB\-\-maxovd\fR <uint>
+help
+.TP
+\fB\-\-maxp\fR <uint>
+help
+.TP
+\fB\-\-maxpoly\fR <uint>
+help
+.TP
+\fB\-\-maxqgap\fR <uint>
+help
+.TP
+\fB\-\-maxrejects\fR <uint>
+help
+.TP
+\fB\-\-maxspan1\fR <uint>
+help
+.TP
+\fB\-\-maxspan2\fR <uint>
+help
+.TP
+\fB\-\-maxtargets\fR <uint>
+help
+.TP
+\fB\-\-maxtgap\fR <uint>
+help
+.TP
+\fB\-\-mcc\fR <str>
+help
+.TP
+\fB\-\-mergeclumps\fR <str>
+help
+.TP
+\fB\-\-mergesort\fR <str>
+help
+.TP
+\fB\-\-minchunk\fR <uint>
+help
+.TP
+\fB\-\-mincodons\fR <uint>
+help
+.TP
+\fB\-\-mindiffs\fR <uint>
+help
+.TP
+\fB\-\-mindiv\fR <float>
+help
+.TP
+\fB\-\-minh\fR <float>
+help
+.TP
+\fB\-\-minhsp\fR <uint>
+help
+.TP
+\fB\-\-minlen\fR <uint>
+help
+.TP
+\fB\-\-minorfcov\fR <uint>
+help
+.TP
+\fB\-\-minspanratio1\fR <float>
+help
+.TP
+\fB\-\-minspanratio2\fR <float>
+help
+.TP
+\fB\-\-[no]minus_frames\fR
+help
+.TP
+\fB\-\-mismatch\fR <float>
+help
+.TP
+\fB\-\-mkctest\fR <str>
+help
+.TP
+\fB\-\-[no]nb\fR
+help
+.TP
+\fB\-\-optimal\fR
+help
+.TP
+\fB\-\-orfstyle\fR <uint>
+help
+.TP
+\fB\-\-otusort\fR <str>
+help
+.TP
+\fB\-\-output\fR <str>
+help
+.TP
+\fB\-\-[no]output_rejects\fR
+help
+.TP
+\fB\-\-probmx\fR <str>
+help
+.TP
+\fB\-\-query\fR <str>
+help
+.TP
+\fB\-\-queryfract\fR <float>
+help
+.TP
+\fB\-\-querylen\fR <uint>
+help
+.TP
+\fB\-\-quiet\fR
+Turn off progress messages.
+.TP
+\fB\-\-randseed\fR <uint>
+help
+.TP
+\fB\-\-realign\fR
+help
+.TP
+\fB\-\-[no]rev\fR
+help
+.TP
+\fB\-\-[no]rightjust\fR
+help
+.TP
+\fB\-\-rowlen\fR <uint>
+help
+.TP
+\fB\-\-secs\fR <uint>
+help
+.TP
+\fB\-\-seeds\fR <str>
+help
+.TP
+\fB\-\-seedsout\fR <str>
+help
+.TP
+\fB\-\-seedt1\fR <float>
+help
+.TP
+\fB\-\-seedt2\fR <float>
+help
+.TP
+\fB\-\-self\fR
+help
+.TP
+\fB\-\-[no]selfid\fR
+help
+.TP
+\fB\-\-simcl\fR <str>
+help
+.TP
+\fB\-\-[no]skipgaps\fR
+help
+.TP
+\fB\-\-[no]skipgaps2\fR
+help
+.TP
+\fB\-\-sort\fR <str>
+help
+.TP
+\fB\-\-sortuc\fR <str>
+help
+.TP
+\fB\-\-sparsedist\fR <str>
+help
+.TP
+\fB\-\-sparsedistparams\fR <str>
+help
+.TP
+\fB\-\-split\fR <float>
+help
+.TP
+\fB\-\-[no]ssort\fR
+help
+.TP
+\fB\-\-sspenalty\fR <float>
+help
+.TP
+\fB\-\-[no]stable_sort\fR
+help
+.TP
+\fB\-\-staralign\fR <str>
+help
+.TP
+\fB\-\-stepwords\fR <uint>
+help
+.TP
+\fB\-\-strand\fR <str>
+help
+.TP
+\fB\-\-targetfract\fR <float>
+help
+.TP
+\fB\-\-targetlen\fR <uint>
+help
+.TP
+\fB\-\-tmpdir\fR <str>
+help
+.TP
+\fB\-\-[no]trace\fR
+help
+.TP
+\fB\-\-tracestate\fR <str>
+help
+.TP
+\fB\-\-[no]trunclabels\fR
+help
+.TP
+\fB\-\-[no]twohit\fR
+help
+.TP
+\fB\-\-uc\fR <str>
+help
+.TP
+\fB\-\-uc2clstr\fR <str>
+help
+.TP
+\fB\-\-uc2fasta\fR <str>
+help
+.TP
+\fB\-\-uc2fastax\fR <str>
+help
+.TP
+\fB\-\-uchime\fR <str>
+help
+.TP
+\fB\-\-uchimealns\fR <str>
+help
+.TP
+\fB\-\-uchimeout\fR <str>
+help
+.TP
+\fB\-\-[no]ucl\fR
+help
+.TP
+\fB\-\-uhire\fR <str>
+help
+.TP
+\fB\-\-ungapped\fR
+help
+.TP
+\fB\-\-userfields\fR <str>
+help
+.TP
+\fB\-\-userout\fR <str>
+help
+.TP
+\fB\-\-usersort\fR
+help
+.TP
+\fB\-\-uslink\fR <str>
+help
+.TP
+\fB\-\-[no]usort\fR
+help
+.TP
+\fB\-\-utax\fR <str>
+help
+.TP
+\fB\-\-[no]verbose\fR
+help
+.TP
+\fB\-\-version\fR
+Show version and exit.
+.TP
+\fB\-\-w\fR <uint>
+help
+.TP
+\fB\-\-weak_evalue\fR <float>
+help
+.TP
+\fB\-\-weak_id\fR <float>
+help
+.TP
+\fB\-\-[no]wordcountreject\fR
+help
+.TP
+\fB\-\-[no]wordweight\fR
+help
+.TP
+\fB\-\-xa\fR <float>
+help
+.TP
+\fB\-\-xdrop_g\fR <float>
+help
+.TP
+\fB\-\-xdrop_nw\fR <float>
+help
+.TP
+\fB\-\-xdrop_u\fR <float>
+help
+.TP
+\fB\-\-xdrop_ug\fR <float>
+help
+.TP
+\fB\-\-xframe\fR <str>
+help
+.TP
+\fB\-\-xlat\fR
+help
+.TP
+\fB\-\-xn\fR <float>
+help
+.SH AUTHOR
+Robert C. Edgar
+.SH SEE ALSO
+http://www.drive5.com/uchime

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