[med-svn] [kmer-tools] 02/12: Add manpages for sim4db
Afif Elghraoui
afif-guest at moszumanska.debian.org
Sun Jan 3 00:54:25 UTC 2016
This is an automated email from the git hooks/post-receive script.
afif-guest pushed a commit to branch master
in repository kmer-tools.
commit d4766ff4ec587ecd1825e9fb6a43f62105c8fa10
Author: Afif Elghraoui <afif at ghraoui.name>
Date: Sat Jan 2 15:22:57 2016 -0800
Add manpages for sim4db
---
debian/man/sim4db/comparePolishes.1 | 1 +
debian/man/sim4db/convertPolishes.1 | 1 +
debian/man/sim4db/convertToAtac.1 | 1 +
debian/man/sim4db/convertToExtent.1 | 1 +
debian/man/sim4db/depthOfPolishes.1 | 1 +
debian/man/sim4db/detectChimera.1 | 1 +
debian/man/sim4db/filterPolishes.1 | 1 +
debian/man/sim4db/fixPolishesIID.1 | 1 +
debian/man/sim4db/headPolishes.1 | 1 +
debian/man/sim4db/mappedCoverage.1 | 1 +
debian/man/sim4db/mergePolishes.1 | 1 +
debian/man/sim4db/parseSNP.1 | 1 +
debian/man/sim4db/pickBestPolish.1 | 1 +
debian/man/sim4db/pickUniquePolish.1 | 1 +
debian/man/sim4db/plotCoverageVsIdentity.1 | 1 +
debian/man/sim4db/realignPolishes.1 | 1 +
debian/man/sim4db/removeDuplicate.1 | 1 +
debian/man/sim4db/reportAlignmentDifferences.1 | 1 +
debian/man/sim4db/sim4db.1 | 123 +++++++++++++++++++++++++
debian/man/sim4db/sim4dbutils.1 | 56 +++++++++++
debian/man/sim4db/sortPolishes.1 | 1 +
debian/man/sim4db/uniqPolishes.1 | 1 +
debian/man/sim4db/vennPolishes.1 | 1 +
debian/sim4db.manpages | 1 +
24 files changed, 201 insertions(+)
diff --git a/debian/man/sim4db/comparePolishes.1 b/debian/man/sim4db/comparePolishes.1
new file mode 120000
index 0000000..7a07503
--- /dev/null
+++ b/debian/man/sim4db/comparePolishes.1
@@ -0,0 +1 @@
+sim4dbutils.1
\ No newline at end of file
diff --git a/debian/man/sim4db/convertPolishes.1 b/debian/man/sim4db/convertPolishes.1
new file mode 120000
index 0000000..7a07503
--- /dev/null
+++ b/debian/man/sim4db/convertPolishes.1
@@ -0,0 +1 @@
+sim4dbutils.1
\ No newline at end of file
diff --git a/debian/man/sim4db/convertToAtac.1 b/debian/man/sim4db/convertToAtac.1
new file mode 120000
index 0000000..7a07503
--- /dev/null
+++ b/debian/man/sim4db/convertToAtac.1
@@ -0,0 +1 @@
+sim4dbutils.1
\ No newline at end of file
diff --git a/debian/man/sim4db/convertToExtent.1 b/debian/man/sim4db/convertToExtent.1
new file mode 120000
index 0000000..7a07503
--- /dev/null
+++ b/debian/man/sim4db/convertToExtent.1
@@ -0,0 +1 @@
+sim4dbutils.1
\ No newline at end of file
diff --git a/debian/man/sim4db/depthOfPolishes.1 b/debian/man/sim4db/depthOfPolishes.1
new file mode 120000
index 0000000..7a07503
--- /dev/null
+++ b/debian/man/sim4db/depthOfPolishes.1
@@ -0,0 +1 @@
+sim4dbutils.1
\ No newline at end of file
diff --git a/debian/man/sim4db/detectChimera.1 b/debian/man/sim4db/detectChimera.1
new file mode 120000
index 0000000..7a07503
--- /dev/null
+++ b/debian/man/sim4db/detectChimera.1
@@ -0,0 +1 @@
+sim4dbutils.1
\ No newline at end of file
diff --git a/debian/man/sim4db/filterPolishes.1 b/debian/man/sim4db/filterPolishes.1
new file mode 120000
index 0000000..7a07503
--- /dev/null
+++ b/debian/man/sim4db/filterPolishes.1
@@ -0,0 +1 @@
+sim4dbutils.1
\ No newline at end of file
diff --git a/debian/man/sim4db/fixPolishesIID.1 b/debian/man/sim4db/fixPolishesIID.1
new file mode 120000
index 0000000..7a07503
--- /dev/null
+++ b/debian/man/sim4db/fixPolishesIID.1
@@ -0,0 +1 @@
+sim4dbutils.1
\ No newline at end of file
diff --git a/debian/man/sim4db/headPolishes.1 b/debian/man/sim4db/headPolishes.1
new file mode 120000
index 0000000..7a07503
--- /dev/null
+++ b/debian/man/sim4db/headPolishes.1
@@ -0,0 +1 @@
+sim4dbutils.1
\ No newline at end of file
diff --git a/debian/man/sim4db/mappedCoverage.1 b/debian/man/sim4db/mappedCoverage.1
new file mode 120000
index 0000000..7a07503
--- /dev/null
+++ b/debian/man/sim4db/mappedCoverage.1
@@ -0,0 +1 @@
+sim4dbutils.1
\ No newline at end of file
diff --git a/debian/man/sim4db/mergePolishes.1 b/debian/man/sim4db/mergePolishes.1
new file mode 120000
index 0000000..7a07503
--- /dev/null
+++ b/debian/man/sim4db/mergePolishes.1
@@ -0,0 +1 @@
+sim4dbutils.1
\ No newline at end of file
diff --git a/debian/man/sim4db/parseSNP.1 b/debian/man/sim4db/parseSNP.1
new file mode 120000
index 0000000..7a07503
--- /dev/null
+++ b/debian/man/sim4db/parseSNP.1
@@ -0,0 +1 @@
+sim4dbutils.1
\ No newline at end of file
diff --git a/debian/man/sim4db/pickBestPolish.1 b/debian/man/sim4db/pickBestPolish.1
new file mode 120000
index 0000000..7a07503
--- /dev/null
+++ b/debian/man/sim4db/pickBestPolish.1
@@ -0,0 +1 @@
+sim4dbutils.1
\ No newline at end of file
diff --git a/debian/man/sim4db/pickUniquePolish.1 b/debian/man/sim4db/pickUniquePolish.1
new file mode 120000
index 0000000..7a07503
--- /dev/null
+++ b/debian/man/sim4db/pickUniquePolish.1
@@ -0,0 +1 @@
+sim4dbutils.1
\ No newline at end of file
diff --git a/debian/man/sim4db/plotCoverageVsIdentity.1 b/debian/man/sim4db/plotCoverageVsIdentity.1
new file mode 120000
index 0000000..7a07503
--- /dev/null
+++ b/debian/man/sim4db/plotCoverageVsIdentity.1
@@ -0,0 +1 @@
+sim4dbutils.1
\ No newline at end of file
diff --git a/debian/man/sim4db/realignPolishes.1 b/debian/man/sim4db/realignPolishes.1
new file mode 120000
index 0000000..7a07503
--- /dev/null
+++ b/debian/man/sim4db/realignPolishes.1
@@ -0,0 +1 @@
+sim4dbutils.1
\ No newline at end of file
diff --git a/debian/man/sim4db/removeDuplicate.1 b/debian/man/sim4db/removeDuplicate.1
new file mode 120000
index 0000000..7a07503
--- /dev/null
+++ b/debian/man/sim4db/removeDuplicate.1
@@ -0,0 +1 @@
+sim4dbutils.1
\ No newline at end of file
diff --git a/debian/man/sim4db/reportAlignmentDifferences.1 b/debian/man/sim4db/reportAlignmentDifferences.1
new file mode 120000
index 0000000..7a07503
--- /dev/null
+++ b/debian/man/sim4db/reportAlignmentDifferences.1
@@ -0,0 +1 @@
+sim4dbutils.1
\ No newline at end of file
diff --git a/debian/man/sim4db/sim4db.1 b/debian/man/sim4db/sim4db.1
new file mode 100644
index 0000000..6730647
--- /dev/null
+++ b/debian/man/sim4db/sim4db.1
@@ -0,0 +1,123 @@
+.TH SIM4DB 1 "January 2016"
+.SH NAME
+sim4db \- batch spliced alignment of cDNA sequences to a target genome
+.SH SYNOPSIS
+A simple command line invocation:
+
+sim4db -genomic g.fasta -cdna c.fasta -scr script -output o.sim4db
+
+where:
+ - 'c.fasta' and 'g.fasta' are the multi-fasta cDNA and genome sequence files
+ - 'script' is a script file indicating individual alignments to be computed
+ - output in sim4db format will be sent to the file 'o.sim4db' ('-' for standard output)
+
+
+A more complex invocation:
+
+sim4db -genomic g.fasta -cdna c.fasta -output o.sim4db [options]
+.SH DESCRIPTION
+.B sim4db
+performs fast batch alignment of large cDNA (EST, mRNA) sequence
+sets to a set of eukaryotic genomic regions. It uses the sim4 and sim4cc
+algorithms to determine the alignments, but incorporates a fast sequence
+indexing and retrieval mechanism, implemented in the sister package
+.BR leaff (1),
+to speedily process large volumes of sequences.
+.PP
+While
+.B sim4db
+produces alignments in the same way as sim4 or sim4cc, it
+has additional features to make it more amenable for use with whole-genome
+annotation pipelines. A script file can be used to group pairings between
+cDNAs and their corresponding genomic regions, to be aligned as one run
+and using the same set of parameters. Sim4db also optionally reports more
+than one alignment for the same cDNA within a genomic region, as long
+as they meet user-defined criteria such as minimum length, percentage
+sequence identity or coverage. This feature is instrumental in finding
+all alignments of a gene family at one locus. Lastly, the output is
+presented either as custom sim4db alignments or as GFF3 gene features.
+
+.SH OPTIONS
+Salient options:
+ -cdna use these cDNA sequences (multi-fasta file)
+ -genomic use these genomic sequences (multi-fasta file)
+ -script use this script file
+ -pairwise sequentially align pairs of sequences
+
+ If none of the '-script' and '-pairwise' options
+ is specified, sim4db performs all-against-all
+ alignments between pairs of cDNA and genomic sequences.
+
+ -output write output to this file
+ -gff3 report output in GFF3 format
+ -interspecies use sim4cc for inter-species alignments (default sim4)
+
+Filter options:
+ -mincoverage iteratively find all exon models with the specified
+ minimum PERCENT COVERAGE
+ -minidentity iteratively find all exon models with the specified
+ minimum PERCENT EXON IDENTITY
+ -minlength iteratively find all exon models with the specified
+ minimum ABSOLUTE COVERAGE (number of bp matched)
+ (default 0)
+ -alwaysreport always report <number> exon models, even if they
+ are below the quality thresholds
+
+ If no mincoverage or minidentity or minlength is given, only
+ the best exon model is returned. This is the DEFAULT operation.
+
+ You will probably want to specify ALL THREE of mincoverage,
+ minidentity and minlength! Don't assume the default values
+ are what you want!
+
+ You will DEFINITELY want to specify at least one of mincoverage,
+ minidentity and minlength with alwaysreport! If you don't,
+ mincoverage will be set to 90 and minidentity to 95 -- to reduce
+ the number of spurious matches when a good match is found.
+
+Auxiliary options:
+ -nodeflines don't include the defline in the sim4db output
+ -alignments print alignments
+
+ -polytails DON'T mask poly-A and poly-T tails
+ -cut trim marginal exons if A/T % > x (poly-AT tails)
+
+ -noncanonical don't force canonical splice sites
+ -splicemodel use the following splice model: 0 - original sim4;
+ 1 - GeneSplicer; 2 - Glimmer; options 1 and 2 are
+ only available with '-interspecies'.
+ Default for sim4 is 0, and for sim4cc is 1.
+
+ -forcestrand Force the strand prediction to always be
+ one of 'forward' or 'reverse'
+
+Execution options:
+ -threads Use n threads.
+ -touch create this file when the program finishes execution
+
+Debugging options:
+ -v print status to stderr while running
+ -V print script lines (stderr) as they are being processed
+
+Developer options:
+ -Z set the spaced seed pattern
+ -H set the relink weight factor (H=1000 recommended for mRNAs)
+ -K set the first MSP threshold
+ -C set the second MSP threshold
+ -Ma set the limit of the number of MSPs allowed
+ -Mp same, as percentage of bases in cDNA
+ NOTE: If used, both -Ma and -Mp must be specified!
+.SH SEE ALSO
+README.sim4db
+.br
+http://kmer.sourceforge.net/wiki/index.php/Getting_Started_with_Sim4db
+.PP
+The
+.BR sim4dbutils(1)
+package contains a range of utilities to work with
+sim4db-generated alignment files, of particular note being
+.BR convertPolishes (1),
+.BR filterPolishes (1),
+.BR mergePolishes (1),
+and
+.BR sortPolishes (1)
diff --git a/debian/man/sim4db/sim4dbutils.1 b/debian/man/sim4db/sim4dbutils.1
new file mode 100644
index 0000000..12f0d00
--- /dev/null
+++ b/debian/man/sim4db/sim4dbutils.1
@@ -0,0 +1,56 @@
+.TH SIM4DBUTILS 1 "January 2016"
+.SH NAME
+sim4dbutils \- utilities to work with sim4db-generated alignment files
+.PP
+convertPolishes \- convert between sim4db and GFF3 formats
+.br
+filterPolishes \- filter alignments based on sequence identity, coverage and length.
+.br
+mergePolishes \- merge alignments from multiple files
+.br
+sortPolishes \- sort alignments by cDNA or genomic sequence index or sequence name
+.br
+convertToExtent \- Convert from sim4db format to a single-line tab-delimited format
+.br
+fixPolishesIID \- Updates a sim4db file to use the sequence index of a specific fasta file. Can also be used to extract a subset of the alignments from the sim4db file.
+.br
+depthOfPolishes \- Outputs a tab-delimited histogram of the depth of polishes at various window sizes.
+.br
+headPolishes \- print the first N alignments in a file, similar to
+.BR head (1)
+.br
+pickBestPolish \- report only the 'best' alignment for each cDNA
+.br
+pickUniquePolish \- reports alignments where there is a clear single best alignment for each cDNA.
+.br
+plotCoverageVsIdentity \- Generates (1) a histogram of the percent identity, (2) a histogram of the percent coverage, and (3) a list of percent identity and coverage (for use in a scatter plot).
+.br
+uniqPolishes \- Filters out all alignments for cDNA with multiple alignments (-uniq) or with a single alignment (-dupl). Similar to
+.BR uniq (1)
+.br
+realignPolishes \- recompute the alignments listed in a sim4db file.
+.br
+reportAlignmentDifferences \- generates a histogram of the types of errors in a set of alignments
+.B Unsupported and Deprecated
+.br
+comparePolishes \- Correlate alignments in two files.
+.br
+convertToAtac \- Converts from sim4db format to ATAC format.
+.br
+detectChimera \- Examines alignments for sequences that might be chimeric.
+.br
+mappedCoverage \- Reports the amount of the query sequence (EST, cDNA) that is covered by alignments.
+.br
+parseSNP \- Analyzes alignments for SNPs.
+.br
+removeDuplicate \- searches the input for duplicate alignments.
+.br
+vennPolishes \- Generates a Venn diagram for multiple sim4db files.
+.SH DESCRIPTION
+These programs are a range of utilities to work with
+.BR sim4db (1)-generated
+alignment files.
+.SH SEE ALSO
+.BR sim4db (1),
+.br
+http://kmer.sourceforge.net/wiki/index.php/Sim4db_Files
diff --git a/debian/man/sim4db/sortPolishes.1 b/debian/man/sim4db/sortPolishes.1
new file mode 120000
index 0000000..7a07503
--- /dev/null
+++ b/debian/man/sim4db/sortPolishes.1
@@ -0,0 +1 @@
+sim4dbutils.1
\ No newline at end of file
diff --git a/debian/man/sim4db/uniqPolishes.1 b/debian/man/sim4db/uniqPolishes.1
new file mode 120000
index 0000000..7a07503
--- /dev/null
+++ b/debian/man/sim4db/uniqPolishes.1
@@ -0,0 +1 @@
+sim4dbutils.1
\ No newline at end of file
diff --git a/debian/man/sim4db/vennPolishes.1 b/debian/man/sim4db/vennPolishes.1
new file mode 120000
index 0000000..7a07503
--- /dev/null
+++ b/debian/man/sim4db/vennPolishes.1
@@ -0,0 +1 @@
+sim4dbutils.1
\ No newline at end of file
diff --git a/debian/sim4db.manpages b/debian/sim4db.manpages
new file mode 100644
index 0000000..04935ad
--- /dev/null
+++ b/debian/sim4db.manpages
@@ -0,0 +1 @@
+debian/man/sim4db/*.1
--
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