[med-svn] [seer] 04/13: Manpages and other enhancements
Andreas Tille
tille at debian.org
Thu Apr 14 09:49:55 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository seer.
commit 02518818599c7009abe6406a631f3c8ccc19d21b
Author: Andreas Tille <tille at debian.org>
Date: Thu Mar 31 12:39:20 2016 +0000
Manpages and other enhancements
---
debian/control | 8 +++--
debian/manpages | 1 +
debian/mans/blast_top_hits.1 | 28 +++++++++++++++++
debian/mans/combineKmers.1 | 26 +++++++++++++++
debian/mans/filter_seer.1 | 41 ++++++++++++++++++++++++
debian/mans/kmds.1 | 74 +++++++++++++++++++++++++++++++++++++++++++
debian/mans/map_back.1 | 26 +++++++++++++++
debian/mans/seer.1 | 75 ++++++++++++++++++++++++++++++++++++++++++++
debian/patches/series | 1 +
debian/rules | 2 ++
10 files changed, 279 insertions(+), 3 deletions(-)
diff --git a/debian/control b/debian/control
index c4f5daf..9060f5a 100644
--- a/debian/control
+++ b/debian/control
@@ -9,16 +9,18 @@ Build-Depends: debhelper (>= 9),
libhdf5-dev,
# libhdf5-mpi-dev,
libgzstream-dev,
- libboost-dev
+ libboost-dev,
+ libboost-program-options-dev
Standards-Version: 3.9.7
-Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/seer/trunk/
+Vcs-Browser: https://anonscm.debian.org/viewvc/debian-med/trunk/packages/seer/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/seer/trunk/
Homepage: https://github.com/johnlees/seer
Package: seer
Architecture: any
Depends: ${shlibs:Depends},
- ${misc:Depends}
+ ${misc:Depends},
+ libtext-csv-perl
Description: genomic sequence element (kmer) enrichment analysis
Bacterial genomes vary extensively in terms of both gene content and
gene sequence - this plasticity hampers the use of traditional SNP-based
diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..4f4649b
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/mans/*.1
diff --git a/debian/mans/blast_top_hits.1 b/debian/mans/blast_top_hits.1
new file mode 100644
index 0000000..15ce157
--- /dev/null
+++ b/debian/mans/blast_top_hits.1
@@ -0,0 +1,28 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.3.
+.TH BLAST_TOP_HITS "1" "March 2016" "blast_top_hits 1.1.0" "User Commands"
+.SH NAME
+blast_top_hits \- reduces a blast or blat output file to the top hit for each query sequence only
+.SH SYNOPSIS
+.B blast_top_hits.pl
+\fI\,--input blast_out --mode blast <options>\/\fR
+.SH DESCRIPTION
+Reduces a blast or blat output file to the top hit for each query sequence only.
+.P
+This program belongs to seer(1) (Sequence Element (kmer) Enrichment Analysis).
+.SH OPTIONS
+.SS Required
+.TP
+\fB\-\-input\fR
+BLAST output file in \fB\-m\fR 6/\-outfmt 6 or BLAT .psl file
+.TP
+\fB\-\-mode\fR
+Either blast or blat
+.SS Optional
+.TP
+\fB\-\-full_query\fR
+The entire query must be reported as a match to appear in the output
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+Shows this help.
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/combineKmers.1 b/debian/mans/combineKmers.1
new file mode 100644
index 0000000..51aaa5a
--- /dev/null
+++ b/debian/mans/combineKmers.1
@@ -0,0 +1,26 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.3.
+.TH COMBINEKMERS "1" "March 2016" "combineKmers 1.1.0" "User Commands"
+.SH NAME
+combineKmers \- basic algorithm to combine kmer counts across samples
+.P
+This program belongs to seer(1) (Sequence Element (kmer) Enrichment Analysis).
+.SH DESCRIPTION
+Basic algorithm to combine kmer counts across samples
+.SH OPTIONS
+.SS "Required options:"
+.TP
+\fB\-r\fR [ \fB\-\-samples\fR ] arg
+file with tab separated sample name and kmer file
+.TP
+\fB\-o\fR [ \fB\-\-output\fR ] arg
+output file prefix
+.SS "Other options:"
+.TP
+\fB\-\-min_samples\fR arg (=1)
+minimum number of samples kmer must occur in to be
+printed
+.TP
+\fB\-h\fR [ \fB\-\-help\fR ]
+full help message
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/filter_seer.1 b/debian/mans/filter_seer.1
new file mode 100644
index 0000000..f0c272b
--- /dev/null
+++ b/debian/mans/filter_seer.1
@@ -0,0 +1,41 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.3.
+.TH FILTER_SEER "1" "March 2016" "filter_seer 1.1.0" "User Commands"
+.SH NAME
+filter_seer \- post filtering of significant kmers
+.SH DESCRIPTION
+Post filtering of significant kmers.
+.P
+This program belongs to seer(1) (Sequence Element (kmer) Enrichment Analysis).
+.SH OPTIONS
+.SS "Required options:"
+.TP
+\fB\-k\fR [ \fB\-\-kmers\fR ] arg
+file of output from seer
+.SS "Filtering options:"
+.TP
+\fB\-\-chisq\fR arg
+minimum unadjusted p\-value to output
+.TP
+\fB\-\-pval\fR arg
+minimum adjusted p\-value to output
+.TP
+\fB\-\-maf\fR arg
+minimum maf/max 1\-maf to output
+.TP
+\fB\-\-beta\fR arg
+minimum |beta| to output
+.TP
+\fB\-\-substr\fR
+remove smaller kmers completely represented elsewhere
+.TP
+\fB\-\-pos_beta\fR
+output positive effect sizes only
+.SS "Other options:"
+.TP
+\fB\-s\fR [ \fB\-\-sort\fR ] arg
+field to sort on: chisq, pval, maf or beta
+.TP
+\fB\-h\fR [ \fB\-\-help\fR ]
+full help message
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/kmds.1 b/debian/mans/kmds.1
new file mode 100644
index 0000000..c02e1c9
--- /dev/null
+++ b/debian/mans/kmds.1
@@ -0,0 +1,74 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.3.
+.TH KMDS "1" "March 2016" "kmds 1.1.0" "User Commands"
+.SH NAME
+kmds \- control for population structure
+.SH DESCRIPTION
+Control for population structure. Filter kmers and create a matrix representing population structure.
+.P
+This program belongs to seer(1) (Sequence Element (kmer) Enrichment Analysis).
+.SH OPTIONS
+1) filter and subsample with \fB\-\-no_mds\fR and \fB\-\-size\fR
+.P
+2) combine, and do metric multidimensional scaling with \fB\-\-combine_mds\fR
+.SS "Required options:"
+.TP
+\fB\-k\fR [ \fB\-\-kmers\fR ] arg
+dsm kmer output file
+.TP
+\fB\-p\fR [ \fB\-\-pheno\fR ] arg
+\&.pheno metadata
+.SS "MDS options:"
+.TP
+\fB\-o\fR [ \fB\-\-output\fR ] arg
+output prefix for new dsm file
+.TP
+\fB\-\-no_mds\fR
+do not perform MDS; output subsampled matrix instead
+.TP
+\fB\-\-write_distances\fR
+write csv of distance matrix
+.TP
+\fB\-\-mds_concat\fR arg
+list of subsampled matrices to use in MDS. Performs
+only MDS; implies \fB\-\-no_filtering\fR
+.TP
+\fB\-\-pc\fR arg (=3)
+number of principal coordinates to output
+.TP
+\fB\-\-size\fR arg (=1000000)
+number of kmers to use in MDS
+.TP
+\fB\-\-threads\fR arg (=1)
+number of threads. Suggested: 4
+.SS "Filtering options:"
+.TP
+\fB\-\-no_filtering\fR
+turn off all filtering and do not output new kmer
+file
+.TP
+\fB\-\-max_length\fR arg (=100)
+maximum kmer length
+.TP
+\fB\-\-maf\fR arg (=0.01)
+minimum kmer frequency
+.TP
+\fB\-\-min_words\fR arg
+minimum kmer occurrences. Overrides \fB\-\-maf\fR
+.TP
+\fB\-\-chisq\fR arg (=10e\-5)
+p\-value threshold for initial chi squared test. Set
+to 1 to show all
+.SS "Other options:"
+.TP
+\fB\-h\fR [ \fB\-\-help\fR ]
+full help message
+.SH EXAMPLE
+Filter kmers and create a matrix representing population structure with kmds
+.IP
+kmds -k dsm_input.txt.gz --pheno metadata.pheno -o filtered
+.P
+To spread this process out, run the following command on each dsm file
+.IP
+kmds -k dsm_input.txt.gz --pheno metadata.pheno --no_mds --size 10000
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/map_back.1 b/debian/mans/map_back.1
new file mode 100644
index 0000000..ca1c85a
--- /dev/null
+++ b/debian/mans/map_back.1
@@ -0,0 +1,26 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.3.
+.TH MAP_BACK "1" "March 2016" "map_back 1.1.0" "User Commands"
+.SH NAME
+map_back \- context of significant kmers
+.SH DESCRIPTION
+Context of significant kmers.
+.P
+This program belongs to seer(1) (Sequence Element (kmer) Enrichment Analysis).
+.SH OPTIONS
+.SS "Required options:"
+.TP
+\fB\-k\fR [ \fB\-\-kmers\fR ] arg
+seer kmer output file
+.TP
+\fB\-r\fR [ \fB\-\-references\fR ] arg
+file with tab separated reference name and fasta
+file
+.SS "Other options:"
+.TP
+\fB\-\-threads\fR arg (=1)
+number of threads. Suggested: 4
+.TP
+\fB\-h\fR [ \fB\-\-help\fR ]
+full help message
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/seer.1 b/debian/mans/seer.1
new file mode 100644
index 0000000..888a132
--- /dev/null
+++ b/debian/mans/seer.1
@@ -0,0 +1,75 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.3.
+.TH SEER "1" "March 2016" "seer 1.1.0" "User Commands"
+.SH NAME
+seer \- sequence element enrichment analysis
+.SH DESCRIPTION
+Sequence Element Enrichment Analysis
+.P
+The .pheno file format is tab separated, two columns with sample name, one with phenotype. Phenotypes of only 0 or 1 will be treated as binary, any other value and the phenotype will be treated as quantitative. Therefore for missing phenotype values the sample should simply be excluded from this file.
+.SH OPTIONS
+.SS "Required options:"
+.TP
+\fB\-k\fR [ \fB\-\-kmers\fR ] arg
+dsm kmer output file
+.TP
+\fB\-p\fR [ \fB\-\-pheno\fR ] arg
+\&.pheno metadata
+.SS "Covariate options:"
+.TP
+\fB\-\-struct\fR arg
+mds values from kmds
+.TP
+\fB\-\-covar_file\fR arg
+file containing covariates
+.TP
+\fB\-\-covar_list\fR arg
+list of columns covariates to use. Format is 1,2q,3
+(use q for quantitative)
+.SS "Performance options:"
+.TP
+\fB\-\-threads\fR arg (=1)
+number of threads. Suggested: 4
+.SS "Filtering options:"
+.TP
+\fB\-\-no_filtering\fR
+turn off all filtering and peform tests on all kmers
+input
+.TP
+\fB\-\-max_length\fR arg (=100)
+maximum kmer length
+.TP
+\fB\-\-maf\fR arg (=0.01)
+minimum kmer frequency
+.TP
+\fB\-\-min_words\fR arg
+minimum kmer occurrences. Overrides \fB\-\-maf\fR
+.TP
+\fB\-\-positive_only\fR
+only test words with a predicted positive effect
+direction
+.TP
+\fB\-\-chisq\fR arg (=10e\-5)
+p\-value threshold for initial chi squared test. Set
+to 1 to show all
+.TP
+\fB\-\-pval\fR arg (=10e\-8)
+p\-value threshold for final logistic test. Set to 1
+to show all
+.SS "Other options:"
+.TP
+\fB\-\-print_samples\fR
+print lists of samples significant kmers were found
+in
+.TP
+\fB\-h\fR [ \fB\-\-help\fR ]
+full help message
+.SH EXAMPLES
+Basic usage:
+.IP
+seer -k dsm_input.txt.gz --pheno metadata.pheno > significant_kmers.txt
+.P
+To use the kmds output, increase execution speed and give the most complete output
+.IP
+seer -k filtered.gz --pheno metadata.pheno --struct filtered.dsm --threads 4 --print_samples
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/patches/series b/debian/patches/series
index a6cca31..797e2d5 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +1,2 @@
fix_lib_location.patch
+hardening.patch
diff --git a/debian/rules b/debian/rules
index 0fff49c..030bfb2 100755
--- a/debian/rules
+++ b/debian/rules
@@ -9,6 +9,8 @@ export LIBRARY_PATH := /usr/lib/$(DEB_TARGET_MULTIARCH)/hdf5/serial
export LDFLAGS+=-pthread
+export DEB_BUILD_MAINT_OPTIONS = hardening=+all
+
override_dh_auto_install:
dh_auto_install -- PREFIX=$(CURDIR)/debian/$(DEBPKGNAME)/usr
cp -a scripts/blast_top_hits.pl $(CURDIR)/debian/$(DEBPKGNAME)/usr/bin/blast_top_hits
--
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