[med-svn] [blat] 01/03: Add gf Client and Server manpages

[Andreas Tille]

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tille pushed a commit to branch master
in repository blat.

commit 8d6dccbbdd720f74dfe0328d963d2690c9514ed4
Author: Andreas Tille <tille at debian.org>
Date:   Tue Feb 25 11:43:09 2014 +0100

    Add gf Client and Server manpages
---
 debian/mans/gfClient.1 | 106 ++++++++++++++++++++++++++++++++++++++++++++++
 debian/mans/gfServer.1 | 113 +++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 219 insertions(+)

diff --git a/debian/mans/gfClient.1 b/debian/mans/gfClient.1
new file mode 100644
index 0000000..63e7651
--- /dev/null
+++ b/debian/mans/gfClient.1
@@ -0,0 +1,106 @@
+.TH GFCLIENT "1" "February 2014" "gfClient 35" "User Commands"
+.SH NAME
+gfClient \- client for the genomic finding program that produces a .psl file
+.SH SYNOPSIS
+.B gfClient
+\fIhost port seqDir in.fa out.psl\fR
+.SH DESCRIPTION
+.P
+Blat is an alignment tool like BLAST, but it is structured differently.
+The target database of BLAT is not  a  set  of  GenBank  sequences,  but
+instead an index derived from the assembly of the entire genome.
+.P
+This is the client for the genomic finding program that produces a .psl file
+.SH OPTIONS
+.HP
+\fIhost\fR
+.IP
+the name of the machine running the gfServer
+.HP
+\fIport\fR
+.IP
+the same as you started the gfServer with
+.HP
+\fIseqDir\fR
+.IP
+the path of the .nib or .2bit files relative to the current dir
+(note these are needed by the client as well as the server)
+.HP
+\fIin.fa\fR
+.IP
+fasta format file.
+May contain multiple records
+.HP
+\fIout.psl\fR
+.IP
+where to put the output
+.TP
+\fB\-t\fR=\fItype\fR
+Database type.  \fIType\fR 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.  \fIType\fR 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
+.TP
+\fB\-prot\fR
+Synonymous with \fB\-d\fR=\fIprot\fR \fB\-q\fR=\fIprot\fR
+.TP
+\fB\-dots\fR=\fIN\fR
+Output a dot every N query sequences
+.TP
+\fB\-nohead\fR
+Suppresses psl five line header
+.TP
+\fB\-minScore\fR=\fIN\fR
+.IP
+sets minimum score. This is twice 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\-out\fR=\fItype\fR
+Controls output file format.  \fIType\fR is one of:
+.IP
+psl \- Default.
+Tab separated format without actual 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\-maxIntron\fR=\fIN\fR
+Sets maximum intron size. Default is 750000
diff --git a/debian/mans/gfServer.1 b/debian/mans/gfServer.1
new file mode 100644
index 0000000..a478a21
--- /dev/null
+++ b/debian/mans/gfServer.1
@@ -0,0 +1,113 @@
+.TH GFSERVER "1" "February 2014" "gfServer 35" "User Commands"
+.SH NAME
+gfServer \- make a server to quickly find where DNA occurs in genome
+.SH SYNOPSIS
+.SS Set up a server
+.IP
+.B gfServer
+\fBstart\fR \fIhost port file(s)\fR
+.IP
+The \fIfile(s)\fR are in .nib or .2bit format
+.SS Remove a server
+.IP
+.B gfServer
+\fBstop\fR \fIhost port\fR
+.SS Query a server with DNA sequence
+.IP
+.B gfServer
+\fBquery\fR \fIhost port probe.fa\fR
+.SS Query a server with protein sequence
+.IP
+.B gfServer
+\fBprotQuery\fR \fIhost port probe.fa\fR
+.SS Query a server with translated dna sequence
+.IP
+.B gfServer transQuery
+\fIhost port probe.fa\fR
+.SS Query server with PCR primers
+.IP
+.B gfServer pcr
+\fIhost port fPrimer rPrimer maxDistance\fR
+.SS Process one probe fa file against a .nib format genome
+.IP
+.B gfServer direct
+\fIprobe.fa file(s).nib\fR
+.IP
+The server is not started
+.SS Test pcr without starting server
+.IP
+.B gfServer pcrDirect
+\fIfPrimer rPrimer file(s).nib\fR
+.SS Figure out usage level
+.IP
+.B gfServer status
+\fIhost port\fR
+.SS Get input file list
+.IP
+.B gfServer files
+\fIhost port\fR
+.SH DESCRIPTION
+.P
+Blat is an alignment tool like BLAST, but it is structured differently.
+The target database of BLAT is not  a  set  of  GenBank  sequences,  but
+instead an index derived from the assembly of the entire genome.
+.P
+This is the server to quickly find where DNA occurs in genome.
+.SH OPTIONS
+.TP
+\fB\-tileSize\fR=\fIN\fR size of n\-mers to index.
+Default is 11 for nucleotides, 4 for
+proteins (or translated nucleotides).
+.TP
+\fB\-stepSize\fR=\fIN\fR spacing between tiles. Default is tileSize.
+.TP
+\fB\-minMatch\fR=\fIN\fR Number of n\-mer matches that trigger detailed alignment
+.IP
+Default is 2 for nucleotides, 3 for protiens.
+.TP
+\fB\-maxGap\fR=\fIN\fR
+Number of insertions or deletions allowed between n\-mers.
+Default is 2 for nucleotides, 0 for protiens.
+.TP
+\fB\-trans\fR
+Translate database to protein in 6 frames.  Note: it is best
+to run this on RepeatMasked data in this case.
+.TP
+\fB\-log\fR=\fIlogFile\fR keep a log file that records server requests.
+.TP
+\fB\-seqLog\fR
+Include sequences in log file (not logged with \fB\-syslog\fR)
+.TP
+\fB\-ipLog\fR
+Include user's IP in log file (not logged with \fB\-syslog\fR)
+.TP
+\fB\-syslog\fR
+Log to syslog
+.TP
+\fB\-logFacility\fR=\fIfacility\fR log to the specified syslog facility \- default local0.
+.TP
+\fB\-mask\fR
+Use masking from nib file.
+.TP
+\fB\-repMatch\fR=\fIN\fR Number of occurrences of a tile (nmer) that trigger repeat masking the tile.
+.IP
+Default is 1024.
+.TP
+\fB\-maxDnaHits\fR=\fIN\fR Maximum number of hits for a dna query that are sent from the server.
+.IP
+Default is 100.
+.TP
+\fB\-maxTransHits\fR=\fIN\fR Maximum number of hits for a translated query that are sent from the server.
+.IP
+Default is 200.
+.TP
+\fB\-maxNtSize\fR=\fIN\fR Maximum size of untranslated DNA query sequence
+.IP
+Default is 40000
+.TP
+\fB\-maxAaSize\fR=\fIN\fR Maximum size of protein or translated DNA queries
+.IP
+Default is 8000
+.TP
+\fB\-canStop\fR If set then a quit message will actually take down the
+server

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