[med-svn] [ecopcr] 01/01: Manpage for ecoisundertaxon; manually formatted ecoPCR.1
Andreas Tille
tille at debian.org
Wed Jun 24 19:35:36 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository ecopcr.
commit d56943e00520de07b4230b04b824710fde51e046
Author: Andreas Tille <tille at debian.org>
Date: Wed Jun 24 21:35:05 2015 +0200
Manpage for ecoisundertaxon; manually formatted ecoPCR.1
---
debian/createmanpages | 3 ++
debian/man/ecoPCR.1 | 86 ++++++++++++++++++++++++--------------------
debian/man/ecoisundertaxon.1 | 38 ++++++++++++++++++++
3 files changed, 89 insertions(+), 38 deletions(-)
diff --git a/debian/createmanpages b/debian/createmanpages
index d0ab362..ecd3101 100755
--- a/debian/createmanpages
+++ b/debian/createmanpages
@@ -14,6 +14,9 @@ help2man --no-info --no-discard-stderr --help-option="-h" \
--name='filtering ecoPCR result based on taxonomic id filter and regular expression pattern' \
--version-string="$VERSION" ecogrep > $MANDIR/ecogrep.1
help2man --no-info --no-discard-stderr --help-option="-h" \
+ --name='searching relationship in taxonomy' \
+ --version-string="$VERSION" ecoisundertaxon > $MANDIR/ecoisundertaxon.1
+help2man --no-info --no-discard-stderr --help-option="-h" \
--name='tool belonging to ecoPCR package' \
--version-string="$VERSION" ecoPCRFormat > $MANDIR/ecoPCRFormat.1
sed -i 's/ecoPCRFormat\.py/ecoPCRFormat/g' $MANDIR/ecoPCRFormat.1
diff --git a/debian/man/ecoPCR.1 b/debian/man/ecoPCR.1
index 26ddaef..4e613b9 100644
--- a/debian/man/ecoPCR.1
+++ b/debian/man/ecoPCR.1
@@ -2,95 +2,105 @@
.TH ECOPCR "1" "June 2015" "ecoPCR 0.5.0" "User Commands"
.SH NAME
ecoPCR \- searching for sequence and taxonomy hybriding with given primers
+.SH SYNOPSIS
+.B ecoPCR
+\fB[options]\fR \fI<nucleotidic patterns>\fR
.SH DESCRIPTION
-\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
-.IP
-ecoPCR Version 0.2
-.PP
-\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
-synopsis : searching for sequence and taxonomy hybriding with given primers
-usage: ecoPCR [options] <nucleotidic patterns>
-\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
-options:
+ecoPCR is an electronic PCR software developed by LECA and
+Helix-Project. It helps to estimate Barcode primers quality.
+.SH OPTIONS
+.TP
\fB\-a\fR : Salt concentration in M for Tm computation (default 0.05 M)
-.PP
+.TP
\fB\-c\fR : Consider that the database sequences are [c]ircular
-.PP
+.TP
\fB\-d\fR : [D]atabase : to match the expected format, the database
-.IP
-has to be formated first by the ecoPCRFormat.py program located.
-in the tools directory.
-ecoPCRFormat.py creates three file types :
+has to be formated first by the ecoPCRFormat(1) program.
+ecoPCRFormat(1) creates three file types:
.IP
\&.sdx : contains the sequences
+.IP
\&.tdx : contains information concerning the taxonomy
+.IP
\&.rdx : contains the taxonomy rank
.IP
ecoPCR needs all the file type. As a result, you have to write the
database radical without any extension. For example \fI\,/ecoPCRDB/gbmam\/\fP
-.PP
+.TP
\fB\-D\fR : Keeps the specified number of nucleotides on each side of the in silico
-.IP
amplified sequences (including the amplified DNA fragment plus the two target
sequences of the primers).
-.PP
+.TP
\fB\-e\fR : [E]rror : max errors allowed by oligonucleotide (0 by default)
-.PP
+.TP
\fB\-h\fR : [H]elp \- print <this> help
-.PP
+.TP
\fB\-i\fR : [I]gnore the given taxonomy id.
-.IP
Taxonomy id are available using the ecofind program.
see its help typing ecofind \fB\-h\fR for more information.
-.PP
+.TP
\fB\-k\fR : [K]ingdom mode : set the kingdom mode
-.IP
super kingdom mode by default.
-.PP
+.TP
\fB\-l\fR : minimum [L]ength : define the minimum amplication length.
-.PP
+.TP
\fB\-L\fR : maximum [L]ength : define the maximum amplicationlength.
-.PP
+.TP
\fB\-m\fR : Salt correction method for Tm computation (SANTALUCIA : 1
-.IP
or OWCZARZY:2, default=1)
-.PP
+.TP
\fB\-r\fR : [R]estricts the search to the given taxonomic id.
-.IP
Taxonomy id are available using the ecofind program.
see its help typing ecofind \fB\-h\fR for more information.
-.PP
-\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
+.TP
first argument : oligonucleotide for direct strand
-.PP
+.TP
second argument : oligonucleotide for reverse strand
-.PP
-\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
+.TP
Table result description :
+.TP
column 1 : accession number
+.TP
column 2 : sequence length
+.TP
column 3 : taxonomic id
+.TP
column 4 : rank
+.TP
column 5 : species taxonomic id
+.TP
column 6 : scientific name
+.TP
column 7 : genus taxonomic id
+.TP
column 8 : genus name
+.TP
column 9 : family taxonomic id
+.TP
column 10 : family name
+.TP
column 11 : super kingdom taxonomic id
+.TP
column 12 : super kingdom name
+.TP
column 13 : strand (direct or reverse)
+.TP
column 14 : first oligonucleotide
+.TP
column 15 : number of errors for the first strand
+.TP
column 16 : Tm for hybridization of primer 1 at this site
+.TP
column 17 : second oligonucleotide
+.TP
column 18 : number of errors for the second strand
+.TP
column 19 : Tm for hybridization of primer 1 at this site
+.TP
column 20 : amplification length
+.TP
column 21 : sequence
+.TP
column 22 : definition
-\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
-.IP
+.SH SEE ALSO
http://www.grenoble.prabi.fr/trac/ecoPCR/
-.PP
-\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
diff --git a/debian/man/ecoisundertaxon.1 b/debian/man/ecoisundertaxon.1
new file mode 100644
index 0000000..bae4d51
--- /dev/null
+++ b/debian/man/ecoisundertaxon.1
@@ -0,0 +1,38 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.1.
+.TH ECOISUNDERTAXON "1" "June 2015" "ecoisundertaxon 0.5.0" "User Commands"
+.SH NAME
+ecoisundertaxon \- searching relationship in taxonomy
+.SH DESCRIPTION
+\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
+.IP
+ecoisundertaxon Version 0.1
+.PP
+\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
+.IP
+synopsis : searching relationship in taxonomy
+usage: ecoisundertaxon [options] database
+.PP
+\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
+.IP
+options:
+\fB\-1\fR : [FIRST] taxomic id of the hypothetical son
+.TP
+\fB\-2\fR
+: [SECOND] taxonomic id of the hypothetical parent
+.TP
+\fB\-h\fR
+: [H]elp \- print <this> help
+.TP
+\fB\-v\fR
+: [V]erbose mode. Display taxonomic information for both
+: taxonomic id.
+.PP
+\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
+.IP
+database : to match the expected format, the database
+has to be formated first by the ecoPCRFormat.py program located.
+in the tools directory. Type the radical only, leaving out the extension
+.PP
+\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
+.IP
+https://www.grenoble.prabi.fr/trac/ecoPCR/wiki\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-
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