[med-svn] [seer] 02/02: Just keep the plain autogeneration here
Andreas Tille
tille at debian.org
Thu Mar 23 13:17:05 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch manpages
in repository seer.
commit 451163e95dc3acecaa6fc6e86ea9aa4a4c724d8b
Author: Andreas Tille <tille at debian.org>
Date: Thu Mar 23 14:16:12 2017 +0100
Just keep the plain autogeneration here
---
debian/mans/blast_top_hits.1 | 29 ++++++++++++++---------------
debian/mans/combineKmers.1 | 6 ++----
debian/mans/filter_seer.1 | 9 +++++----
debian/mans/kmds.1 | 22 +++++++---------------
debian/mans/map_back.1 | 6 ++----
debian/mans/seer.1 | 20 +++++---------------
6 files changed, 35 insertions(+), 57 deletions(-)
diff --git a/debian/mans/blast_top_hits.1 b/debian/mans/blast_top_hits.1
index 4ecb915..1eec8db 100644
--- a/debian/mans/blast_top_hits.1
+++ b/debian/mans/blast_top_hits.1
@@ -1,3 +1,4 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
.TH BLAST_TOP_HITS "1" "March 2017" "blast_top_hits 1.1.2" "User Commands"
.SH NAME
blast_top_hits \- reduces a blast or blat output file to the top hit for each query sequence only
@@ -5,21 +6,19 @@ blast_top_hits \- reduces a blast or blat output file to the top hit for each qu
.B blast_top_hits
\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
+Reduces a blast or blat output file to the top hit for each query sequence
+only
+.IP
+Options
+.IP
+Required
+\fB\-\-input\fR BLAST output file in \fB\-m\fR 6/\-outfmt 6 or BLAT .psl file
+\fB\-\-mode\fR Either blast or blat
+.IP
+Optional
+\fB\-\-full_query\fR The entire query must be reported as a match to appear
+.IP
+in the output
.TP
\fB\-h\fR, \fB\-\-help\fR
Shows this help.
diff --git a/debian/mans/combineKmers.1 b/debian/mans/combineKmers.1
index 8dee120..0e5111b 100644
--- a/debian/mans/combineKmers.1
+++ b/debian/mans/combineKmers.1
@@ -1,11 +1,9 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
.TH COMBINEKMERS "1" "March 2017" "combineKmers 1.1.2" "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
+combineKmers: basic algorithm to combine kmer counts across samples
.SS "Required options:"
.TP
\fB\-r\fR [ \fB\-\-samples\fR ] arg
diff --git a/debian/mans/filter_seer.1 b/debian/mans/filter_seer.1
index 77f075e..702994b 100644
--- a/debian/mans/filter_seer.1
+++ b/debian/mans/filter_seer.1
@@ -1,11 +1,9 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
.TH FILTER_SEER "1" "March 2017" "filter_seer 1.1.2" "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
+filter_seer: post filtering of significant kmers
.SS "Required options:"
.TP
\fB\-k\fR [ \fB\-\-kmers\fR ] arg
@@ -34,6 +32,9 @@ output positive effect sizes only
\fB\-s\fR [ \fB\-\-sort\fR ] arg
field to sort on: chisq, pval, maf or beta
.TP
+\fB\-\-version\fR
+prints version and exits
+.TP
\fB\-h\fR [ \fB\-\-help\fR ]
full help message
.SH AUTHOR
diff --git a/debian/mans/kmds.1 b/debian/mans/kmds.1
index 60eaa38..247fd19 100644
--- a/debian/mans/kmds.1
+++ b/debian/mans/kmds.1
@@ -1,18 +1,18 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
.TH KMDS "1" "March 2017" "kmds 1.1.2" "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
+kmds: control for population structure
+kmds
+.IP
1) filter and subsample with \fB\-\-no_mds\fR and \fB\-\-size\fR
-.P
2) combine, and do metric multidimensional scaling with \fB\-\-mds_concat\fR
.SS "Required options:"
.TP
\fB\-k\fR [ \fB\-\-kmers\fR ] arg
-dsm kmer output file
+dsm kmer output file (not needed if using
+\fB\-\-mds_concat\fR)
.TP
\fB\-p\fR [ \fB\-\-pheno\fR ] arg
\&.pheno metadata
@@ -52,7 +52,7 @@ maximum kmer length
minimum kmer frequency
.TP
\fB\-\-min_words\fR arg
-minimum kmer occurrences. Overrides \fB\-\-maf\fR
+minimum kmer occurences. Overrides \fB\-\-maf\fR
.SS "Other options:"
.TP
\fB\-\-version\fR
@@ -60,13 +60,5 @@ prints version and exits
.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
index e18a4b6..6c56bca 100644
--- a/debian/mans/map_back.1
+++ b/debian/mans/map_back.1
@@ -1,11 +1,9 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
.TH MAP_BACK "1" "March 2017" "map_back 1.1.2" "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
+map_back: context of significant kmers
.SS "Required options:"
.TP
\fB\-k\fR [ \fB\-\-kmers\fR ] arg
diff --git a/debian/mans/seer.1 b/debian/mans/seer.1
index 4454604..02a5177 100644
--- a/debian/mans/seer.1
+++ b/debian/mans/seer.1
@@ -1,11 +1,9 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
.TH SEER "1" "March 2017" "seer 1.1.2" "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
+seer: sequence element enrichment analysis
.SS "Required options:"
.TP
\fB\-k\fR [ \fB\-\-kmers\fR ] arg
@@ -31,8 +29,8 @@ number of threads. Suggested: 4
.SS "Filtering options:"
.TP
\fB\-\-no_filtering\fR
-turn off all filtering and peform tests on all kmers
-input
+turn off all filtering and perform tests on all
+kmers input
.TP
\fB\-\-max_length\fR arg (=100)
maximum kmer length
@@ -41,7 +39,7 @@ maximum kmer length
minimum kmer frequency
.TP
\fB\-\-min_words\fR arg
-minimum kmer occurrences. Overrides \fB\-\-maf\fR
+minimum kmer occurences. Overrides \fB\-\-maf\fR
.TP
\fB\-\-chisq\fR arg (=10e\-5)
p\-value threshold for initial chi squared test. Set
@@ -61,13 +59,5 @@ prints version and exits
.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.
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