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commit d4766ff4ec587ecd1825e9fb6a43f62105c8fa10 Author: Afif Elghraoui <[email protected]> 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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/kmer-tools.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
