[med-svn] [blat] 04/04: Polishing main blat.1 manpage
Andreas Tille
tille at debian.org
Mon Feb 24 19:15:34 UTC 2014
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository blat.
commit f85b8c617902e95269d451feb4a62e31b43f0d35
Author: Andreas Tille <tille at debian.org>
Date: Mon Feb 24 20:15:04 2014 +0100
Polishing main blat.1 manpage
---
debian/createmanpages | 22 +++---
debian/mans/blat.1 | 201 ++++++++++++++++++++++++++++++++++++++++++++++++++
2 files changed, 212 insertions(+), 11 deletions(-)
diff --git a/debian/createmanpages b/debian/createmanpages
index 265fa78..f4c24be 100755
--- a/debian/createmanpages
+++ b/debian/createmanpages
@@ -6,35 +6,35 @@ VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*:
help2man --no-info --no-discard-stderr --help-option=" " \
--name='Standalone BLAT fast sequence search command line tool' \
- --version-string='$VERSION' blat > $MANDIR/blat.1
+ --version-string="$VERSION" blat > $MANDIR/blat.1
help2man --no-info --no-discard-stderr --help-option=" " \
--name='Convert from .fa to .nib format' \
- --version-string='$VERSION' faToNib > $MANDIR/faToNib.1
+ --version-string="$VERSION" faToNib > $MANDIR/faToNib.1
help2man --no-info --no-discard-stderr --help-option=" " \
--name='Convert DNA from fasta to 2bit format' \
- --version-string='$VERSION' faToTwoBit > $MANDIR/faToTwoBit.1
+ --version-string="$VERSION" faToTwoBit > $MANDIR/faToTwoBit.1
help2man --no-info --no-discard-stderr --help-option=" " \
--name='client for the genomic finding program that produces a .psl file' \
- --version-string='$VERSION' gfClient > $MANDIR/gfClient.1
+ --version-string="$VERSION" gfClient > $MANDIR/gfClient.1
help2man --no-info --no-discard-stderr --help-option=" " \
--name='make a server to quickly find where DNA occurs in genome' \
- --version-string='$VERSION' gfServer > $MANDIR/gfServer.1
+ --version-string="$VERSION" gfServer > $MANDIR/gfServer.1
help2man --no-info --no-discard-stderr --help-option=" " \
--name='Extract part of a nib file as .fa' \
- --version-string='$VERSION' nibFrag > $MANDIR/nibFrag.1
+ --version-string="$VERSION" nibFrag > $MANDIR/nibFrag.1
help2man --no-info --no-discard-stderr --help-option=" " \
--name='Convert PSL to human readable output' \
- --version-string='$VERSION' pslPretty > $MANDIR/pslPretty.1
+ --version-string="$VERSION" pslPretty > $MANDIR/pslPretty.1
help2man --no-info --no-discard-stderr --help-option=" " \
--name='analyse repeats and generate genome wide best' \
- --version-string='$VERSION' pslReps > $MANDIR/pslReps.1
+ --version-string="$VERSION" pslReps > $MANDIR/pslReps.1
help2man --no-info --no-discard-stderr --help-option=" " \
--name='merge and sort psCluster .psl output files' \
- --version-string='$VERSION' pslSort > $MANDIR/pslSort.1
+ --version-string="$VERSION" pslSort > $MANDIR/pslSort.1
help2man --no-info --no-discard-stderr --help-option=" " \
--name='get information about sequences in a .2bit file' \
- --version-string='$VERSION' twoBitInfo > $MANDIR/twoBitInfo.1
+ --version-string="$VERSION" twoBitInfo > $MANDIR/twoBitInfo.1
help2man --no-info --no-discard-stderr --help-option=" " \
--name='convert all or part of .2bit file to fasta' \
- --version-string='$VERSION' twoBitToFa > $MANDIR/twoBitToFa.1
+ --version-string="$VERSION" twoBitToFa > $MANDIR/twoBitToFa.1
diff --git a/debian/mans/blat.1 b/debian/mans/blat.1
new file mode 100644
index 0000000..3c3550c
--- /dev/null
+++ b/debian/mans/blat.1
@@ -0,0 +1,201 @@
+.TH BLAT "1" "February 2014" "blat 35" "User Commands"
+.SH NAME
+blat \- Standalone BLAT fast sequence search command line tool
+.SH SYNOPSIS
+.B blat
+\fBdatabase\fR \fBquery\fR [\fI\-ooc=11.ooc\fR] \fBoutput.psl\fR
+.SH DESCRIPTION
+Blat is an alignment tool like BLAST, but it is structured differently.
+he target database of BLAT is not a set of GenBank sequences, but
+instead an index derived from the assembly of the entire genome.
+.SH OPTIONS
+.PP
+The options \fBdatabase\fR and \fBquery\fR are each either a .fa , .nib or .2bit file,
+or a list these files one file name per line.
+\fI\-ooc=11.ooc\fR tells the program to load over\-occurring 11\-mers from
+an external file.
+.PP
+This will increase the speed
+by a factor of 40 in many cases, but is not required.
+.PP
+The file \fBoutput.psl\fR is where to put the output.
+Subranges of nib and .2bit files may specified using the syntax:
+.IP
+\fI/path/file.nib:seqid:start\-end\fP
+or
+.IP
+\fI/path/file.2bit:seqid:start\-end\fP
+or
+.IP
+\fI/path/file.nib:start\-end\fP
+.PP
+With the second form, a sequence id of file:start\-end will be used.
+.TP
+\fB\-t\fR=\fItype\fR
+Database type. Type is one of:
+.IP
+dna \- DNA sequence
+.IP
+prot \- protein sequence
+.IP
+dnax \- DNA sequence translated in six frames to protein
+.IP
+The default is dna
+.TP
+\fB\-q\fR=\fItype\fR
+Query type. Type is one of:
+.IP
+dna \- DNA sequence
+.IP
+rna \- RNA sequence
+.IP
+prot \- protein sequence
+.IP
+dnax \- DNA sequence translated in six frames to protein
+.IP
+rnax \- DNA sequence translated in three frames to protein
+.IP
+The default is dna
+.TP
+\fB\-prot\fR
+Synonymous with \fB\-t\fR=\fIprot\fR \fB\-q\fR=\fIprot\fR
+.TP
+\fB\-ooc\fR=\fIN\fR.ooc
+Use overused tile file \fIN\fR.ooc. \fIN\fR should correspond to
+the tileSize
+.HP
+\fB\-tileSize\fR=\fIN\fR
+.IP
+sets the size of match that triggers an alignment.
+Usually between 8 and 12
+Default is 11 for DNA and 5 for protein.
+.HP
+\fB\-stepSize\fR=\fIN\fR
+.IP
+spacing between tiles. Default is tileSize.
+.TP
+\fB\-oneOff\fR=\fIN\fR
+If set to 1 this allows one mismatch in tile and still
+triggers an alignments. Default is 0.
+.TP
+\fB\-minMatch\fR=\fIN\fR
+.IP
+sets the number of tile matches. Usually set from 2 to 4
+Default is 2 for nucleotide, 1 for protein.
+.TP
+\fB\-minScore\fR=\fIN\fR
+.IP
+sets minimum score. This is the matches minus the
+mismatches minus some sort of gap penalty.
+Default is 30
+.TP
+\fB\-minIdentity\fR=\fIN\fR
+.IP
+Sets minimum sequence identity (in percent). Default is
+90 for nucleotide searches, 25 for protein or translated
+protein searches.
+.TP
+\fB\-maxGap\fR=\fIN\fR
+.IP
+sets the size of maximum gap between tiles in a clump. Usually
+set from 0 to 3. Default is 2. Only relevent for minMatch > 1.
+.TP
+\fB\-noHead\fR
+.IP
+suppress .psl header (so it's just a tab\-separated file)
+.HP
+\fB\-makeOoc\fR=\fIN\fR.ooc
+.IP
+Make overused tile file. Target needs to be complete genome.
+.HP
+\fB\-repMatch\fR=\fIN\fR
+.IP
+sets the number of repetitions of a tile allowed before it is marked as overused.
+Typically this is 256 for tileSize
+.IP
+12, 1024 for tile size 11, 4096 for tile size 10.
+Default is 1024. Typically only comes into play with makeOoc.
+Also affected by stepSize. When stepSize is halved repMatch is
+doubled to compensate.
+.TP
+\fB\-mask\fR=\fItype\fR
+Mask out repeats. Alignments won't be started in masked region
+but may extend through it in nucleotide searches. Masked areas
+are ignored entirely in protein or translated searches. Types are
+.IP
+lower \- mask out lower cased sequence
+.IP
+upper \- mask out upper cased sequence
+.IP
+out \- mask according to database.out RepeatMasker .out file
+.IP
+file.out \- mask database according to RepeatMasker file.out
+.TP
+\fB\-qMask\fR=\fItype\fR
+.IP
+Mask out repeats in query sequence. Similar to \fB\-mask\fR above but
+for query rather than target sequence.
+.TP
+\fB\-repeats\fR=\fItype\fR
+.IP
+Type is same as mask types above. Repeat bases will not be
+masked in any way, but matches in repeat areas will be reported
+separately from matches in other areas in the psl output.
+.HP
+\fB\-minRepDivergence\fR=\fINN\fR
+.IP
+minimum percent divergence of repeats to allow
+them to be unmasked.
+Default is 15. Only relevant for
+masking using RepeatMasker .out files.
+.TP
+\fB\-dots\fR=\fIN\fR
+Output dot every N sequences to show program's progress
+.TP
+\fB\-trimT\fR
+Trim leading poly\-T
+.TP
+\fB\-noTrimA\fR
+Don't trim trailing poly\-A
+.TP
+\fB\-trimHardA\fR
+Remove poly\-A tail from qSize as well as alignments in
+psl output
+.TP
+\fB\-fastMap\fR
+Run for fast DNA/DNA remapping \- not allowing introns,
+requiring high %ID. Query sizes must not exceed 5000.
+.TP
+\fB\-out\fR=\fItype\fR
+Controls output file format. Type is one of:
+.IP
+psl \- (Default) Tab separated format, no sequence
+.IP
+pslx \- Tab separated format with sequence
+.IP
+axt \- blastz\-associated axt format
+.IP
+maf \- multiz\-associated maf format
+.IP
+sim4 \- similar to sim4 format
+.IP
+wublast \- similar to wublast format
+.IP
+blast \- similar to NCBI blast format
+.IP
+blast8\- NCBI blast tabular format
+.IP
+blast9 \- NCBI blast tabular format with comments
+.TP
+\fB\-fine\fR
+.IP
+For high quality mRNAs look harder for small initial and
+terminal exons. Not recommended for ESTs
+.TP
+\fB\-maxIntron\fR=\fIN\fR
+.IP
+Sets maximum intron size. Default is 750000
+.HP
+\fB\-extendThrough\fR=\fIN\fR
+.IP
+Allows extension of alignment through large blocks of N's
--
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