[med-svn] [Git][med-team/melting][master] Update manpage
Pranav Ballaney
gitlab at salsa.debian.org
Fri Jun 12 05:31:56 BST 2020
Pranav Ballaney pushed to branch master at Debian Med / melting
Commits:
3a29a6d6 by Pranav Ballaney at 2020-06-12T10:01:48+05:30
Update manpage
- - - - -
3 changed files:
- + debian/createmanpages
- + debian/melting.1
- debian/melting.manpages
Changes:
=====================================
debian/createmanpages
=====================================
@@ -0,0 +1,28 @@
+#!/bin/sh
+MANDIR=debian
+mkdir -p $MANDIR
+
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
+NAME=`grep "^Description:" debian/control | sed 's/^Description: *//' | head -n1`
+PROGNAME=`grep "^Package:" debian/control | sed 's/^Package: *//' | head -n1`
+
+AUTHOR=".SH AUTHOR\n \
+This manpage was written by $DEBFULLNAME for the Debian distribution and\n \
+can be used for any other usage of the program.\
+"
+
+# If program name is different from package name or title should be
+# different from package short description change this here
+progname=${PROGNAME}
+help2man --no-info --no-discard-stderr --help-option="-h" \
+ --name="$NAME" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+echo "$MANDIR/*.1" > debian/manpages
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+ http://liw.fi/manpages/
+EOT
=====================================
debian/melting.1
=====================================
@@ -0,0 +1,376 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.13.
+.TH MELTING "1" "June 2020" "melting 5.2.0" "User Commands"
+.SH NAME
+melting \- compute the melting temperature of nucleic acid duplex
+.SH DESCRIPTION
+More information is available in the user\-guide. Type `man melting' to access it or consult one of the
+melting.xxx files, where xxx states for ps (postscript), pdf or html.
+.SH OPTIONS
+\fB\Information about MELTING 5:\fR
+.PP
+\fB\-h\fR Displays this help and quit.
+.PP
+\fB\-L\fR Displays legal information and quit.
+.PP
+\fB\-V\fR Print the version number.
+.PP
+\fB\-p\fR Return path where to find the calorimetric tables.
+.PP
+\fBMandatory options:\fR
+.PP
+\fB\-S\fR [sequence]
+.IP
+Nucleic acid sequence, mandatory. The sens of this sequence must be 5'\-3'.
+.PP
+\fB\-C\fR [complementary sequence]
+.IP
+Nucleic acid complementary sequence, mandatory only if there is inosine bases or azobenznes in the sequence entered with the opton \fB\-S\fR. The sens of this sequence must be 3'\-5''.
+.PP
+\fB\-E\fR [agent1=concentration1:agent2=concentration2]
+.IP
+Different agent concentrations in the solution. The agents can be cations (Na, K, Tris, Mg for Na+, K+, Tris+ and Mg2+), dNTP or other agents (DMSO, formamide). The concentrations must be in Mol/L but there are some exceptions : DMSO is a percentage, formamide is a percentage if the method lincorr is chosen and in Mol/L if the method bla96 is chosen. At least one cation concentration is mandatory, the other agents are optional. See the documentation for the concentration limits. It depends on the used correction.
+.PP
+\fB\-P\fR [nucleotide concentration]
+.IP
+Concentration in mol/L of the nucleic acid strand in excess, mandatory.
+.PP
+\fB\-H\fR [hybridization]
+.IP
+Type of hybridization, mandatory. Four types of hybridization are allowed : dnadna (DNA duplex), rnarna (RNA duplex), dnarna or rnadna (hybrid DNA/RNA) and mrnarna or rnamrna (2\-o\-methyl RNA/ RNA). The type of hybridization defines the kind of the sequence and its complementary.
+.IP
+Ex : dnarna = the sequence (entered with the option \fB\-S\fR) is a DNA sequence and its complementary (entered with the option \fB\-C\fR) is a RNA sequence.
+Ex : rnadna = the sequence (entered with the option \fB\-S\fR) is a RNA sequence and its complementary (entered with the option \fB\-C\fR) is a DNA sequence
+.PP
+\fBGeneral options:\fR
+.PP
+\fB\-v\fR
+.IP
+Switch ON the verbose mode, issuing lot more info. Default is OFF.
+.PP
+\fB\-T\fR [threshold value]
+.IP
+Threshold for approximative computation. Default is 60.
+.PP
+\fB\-nnpath\fR [folder pathway]
+.IP
+Change the default pathway (Data) where to find the default calorimetric tables (thermodynamic parameters).
+.PP
+\fB\-O\fR [filename]
+.IP
+To write the results in an output file. filename is the name or the pathway of the file.
+.PP
+\fB\-self\fR
+.IP
+To precise that the sequence entered with the option \fB\-S\fR is self complementary. No complementary sequence is mandatory. The program automatically can detect a self complementary sequence for perfect matching sequences or sequences with dangling ends. In these cases, the option \fB\-self\fR is not necessary, otherwise we need to precise that the sequences are self complementary.
+.PP
+\fB\-F\fR [factor value]
+.IP
+Correction for the concentration of nucleic acid. F is automatically 1 if the sequences are self complementary. Otherwise F is 4 if the both strands are present in equivalent amount and 1 if one strand is in excess. The default factor value is 4.
+.IP
+Set of thermodynamic parameters and methods :
+.PP
+By default, the approximative mode is used for oligonucleotides longer than 60 bases (the default threshold value), otherwise the nearest
+neighbor model is used.
+.PP
+\fB\-am\fR [optional name]
+.IP
+Forces to use a specific approximative formula. You can use one of the following :
+.TP
+(DNA)
+ahs01 (from von Ahsen et al. 2001)
+che93 (from Marmur 1962, Chester et al. 1993)
+che93corr (from von Ahsen et al. 2001, Marmur 1962, Chester et al. 1993)
+schdot (Marmur\-Schildkraut\-Doty formula)
+owe69 (from Owen et al. 1969)
+san98 (from Santalucia et al. 1998)
+wetdna91 (from Wetmur 1991) (by default)
+.TP
+(RNA)
+wetrna91 (from Wetmur 1991) (by default)
+.TP
+(DNA/RNA)
+wetdnarna91 (from Wetmur 1991) (by default)
+.IP
+If there is no formula name after the option \fB\-am\fR, we will compute the melting temperature with the default approximative formula.
+.PP
+\fB\-nn\fR [optional name]
+.IP
+Forces to use a specific nearest neighbor model. You can use one of the following :
+.TP
+(DNA)
+all97 (from Allawi and Santalucia 1997) (by default)
+bre86 (from Breslauer et al. 1986)
+san04 (from Hicks and Santalucia 2004)
+san96 (from Santalucia et al. 1996)
+sug96 (from Sugimoto et al 1996)
+tan04 (from Tanaka et al. 2004)
+.TP
+(RNA)
+fre86 (from Freier al. 1986)
+xia98 (from Xia et al. 1998) (by default)
+.TP
+(DNA/RNA)
+sug95 (from Sugimoto et al. 1995) (by default)
+.TP
+(mRNA/RNA)
+tur06 (from Kierzek et al. 2006) (by default)
+.IP
+If there is no formula name after the option \fB\-nn\fR, we will compute the melting temperature with the default nearest neighbor model.
+Each nearest neighbor model uses a specific xml file containing the thermodynamic values. If you want to use another file, write the file name or the file pathway preceded by ':' (\fB\-nn\fR [optionalname:optionalfile]).
+.IP
+Ex : \fB\-nn\fR tan04:fileName if you want to use the nearest neighbor model from Tanaka et al. 2004 with the thermodynamic parameters in the file fileName.
+Ex : \fB\-nn\fR :fileName if you want to use the default nearest neighbor model with the thermodynamic parameters in the file fileName.
+.PP
+\fB\-sinMM\fR [name]
+.IP
+Forces to use a specific nearest neighbor model for single mismatch(es) in the sequences. You can use one of the following :
+.TP
+(DNA)
+allsanpey (from Allawi, Santalucia and Peyret 1997, 1998 and 1999) (by default)
+.IP
+(DNA/RNA)
+.IP
+wat10 (from Watkins et al. 2011) (by default)
+(RNA)
+.TP
+tur06 (from Lu et al. 2006)
+zno07 (from Davis et al. 2007) (by default)
+zno08 (from Davis et al. 2008)
+.IP
+To change the file containing the thermodynamic parameters for single mismatch computation, the same syntax as the one for the \fB\-nn\fR option is used.
+.PP
+\fB\-GU\fR [name]
+.IP
+Forces to use a specific nearest neighbor model for GU base pairs in RNA sequences. You can use one of the following :
+.IP
+tur99 (from Turner et al. 1999).
+ser12 (from Serra et al. 2012) (by default)
+.IP
+To change the file containing the thermodynamic parameters for GU base pairs computation, the same syntax as the one for the \fB\-nn\fR option is used.
+.PP
+\fB\-tanMM\fR [name]
+.IP
+Forces to use a specific nearest neighbor model for tandem mismatches in the sequences. You can use one of the following :
+.TP
+(DNA)
+allsanpey (from Allawi, Santalucia and Peyret 1997, 1998 and 1999) (by default)
+.TP
+(RNA)
+tur99 (from Mathews et al. 1999) (by default)
+.IP
+To change the file containing the thermodynamic parameters for tandem mismatches computation, the same syntax as the one for the \fB\-nn\fR option is used.
+.PP
+\fB\-intLP\fR [name]
+.IP
+Forces to use a specific nearest neighbor model for internal loop in the sequences. You can use one of the following :
+.TP
+(DNA)
+san04 (from Hicks and Santalucia 2004) (by default)
+.TP
+(RNA)
+tur06 (from Lu et al. 2006) (by default)
+zno07 (from Badhwarr et al. 2007, only for 1x2 loop)
+.IP
+To change the file containing the thermodynamic parameters for internal loop computation, the same syntax as the one for the \fB\-nn\fR option is used.
+.PP
+\fB\-sinDE\fR [name]
+.IP
+Forces to use a specific nearest neighbor model for single dangling end(s) in the sequences. You can use one of the following :
+.TP
+(DNA)
+bom00 (from Bommarito et al. 2000) (by default)
+sugdna02 (from Ohmichi et al. 2002, only for polyA dangling ends)
+.TP
+(RNA)
+sugrna02 (from Ohmichi et al. 2002, only for polyA dangling ends)
+ser08 (from Miller et al. 2008) (by default)
+.IP
+To change the file containing the thermodynamic parameters for single dangling end computation, the same syntax as the one for the \fB\-nn\fR option is used.
+.PP
+\fB\-secDE\fR [name]
+.IP
+Forces to use a specific nearest neighbor model for second dangling end(s) in the sequences. You can use one of the following :
+.TP
+(DNA)
+sugdna02 (from Ohmichi et al. 2002, only for polyA dangling ends) (by default)
+.TP
+(RNA)
+sugrna02 (from Ohmichi et al. 2002, only for polyA dangling ends)
+ser05 (from O'toole et al. 2005)
+ser06 (from O'toole et al. 2006) (by default)
+.IP
+To change the file containing the thermodynamic parameters for second dangling end computation, the same syntax as the one for the \fB\-nn\fR option is used.
+.PP
+\fB\-lonDE\fR [name]
+.IP
+Forces to use a specific nearest neighbor model for long dangling end(s) in the sequences (self complementary sequences). You can use one of the following :
+.TP
+(DNA)
+sugdna02 (from Ohmichi et al. 2002, only for polyA dangling ends) (by default)
+.TP
+(RNA)
+sugrna02 (from Ohmichi et al. 2002, only for polyA dangling ends) (by default)
+.IP
+To change the file containing the thermodynamic parameters for long dangling end computation, the same syntax as the one for the \fB\-nn\fR option is used.
+.PP
+\fB\-sinBU\fR [name]
+.IP
+Forces to use a specific nearest neighbor model for single bulge loop(s) in the sequences. You can use one of the following :
+.TP
+(DNA)
+san04 (from Hicks and Santalucia 2004)
+tan04 (from Tanaka et al. 2004) (by default)
+.TP
+(RNA)
+ser07 (from Blose et al. 2007)
+tur06 (from Lu et al. 1999 and 2006) (by default)
+.IP
+To change the file containing the thermodynamic parameters for single bulge loop computation, the same syntax as the one for the \fB\-nn\fR option is used.
+.PP
+\fB\-lonBU\fR [name]
+.IP
+Forces to use a specific nearest neighbor model for long bulge loop(s) in the sequences. You can use one of the following :
+.TP
+(DNA)
+san04 (from Hicks and Santalucia 2004) (by default)
+.TP
+(RNA)
+tur06 (from Mathews et al. 1999 and Lu et al 2006) (by default)
+.PP
+
+.IP
+To change the file containing the thermodynamic parameters for long bulge loop computation, the same syntax as the one for the \fB\-nn\fR option is used.
+.PP
+\fB\-CNG\fR [name]
+.IP
+Forces to use a specific nearest neighbor model for RNA sequences composed of CNG repeats (G(CNG)xC where N is a single N/N mismatch). You can only use bro05 (from Magdalena et al. 2005).
+To change the file containing the thermodynamic parameters for RNA sequences composed of CNG repeats computation, the same syntax as the one for the \fB\-nn\fR option is used.
+.PP
+\fB\-ino\fR [name]
+.IP
+Forces to use a specific nearest neighbor model for inosine base (I) in the sequences. You can use one of the following :
+.TP
+(DNA)
+san05 (from Watkins and Santalucia 2005) (by default)
+.TP
+(RNA)
+zno07 (from Wright et al. 2007) (by default)
+.PP
+
+.IP
+To change the file containing the thermodynamic parameters for inosine base computation, the same syntax as the one for the \fB\-nn\fR option is used.
+.PP
+\fB\-ha\fR [name]
+.IP
+Forces to use a specific nearest neighbor model for hydroxyadenine base (A*) in DNA sequences. You can only use sug01 (from Kawakami et al. 2001).
+To change the file containing the thermodynamic parameters for hydroxyadenine base computation, the same syntax as the one for the \fB\-nn\fR option is used.
+.PP
+\fB\-azo\fR [name]
+.IP
+Forces to use a specific nearest neighbor model for DNA sequences containing azobenzene (cis : X_C or trans : X_T). You can only use asa05 (from Asanuma et al. 2005).
+To change the file containing the thermodynamic parameters for azobenzene computation, the same syntax as the one for the \fB\-nn\fR option is used.
+.PP
+\fB\-lck\fR [name]
+.IP
+Forces to use a specific nearest neighbor model for DNA sequences containing locked nucleic acid (Al, Tl, Cl or Gl). You can use mct04 (from McTigue et al. 2004) or
+owc11 (from Owczarzy et al. 2011, by default).
+To change the file containing the thermodynamic parameters for locked acid nucleic computation, the same syntax as the one for the \fB\-nn\fR option is used.
+.PP
+\fB\-tanLck\fR [name]
+.IP
+Forces to use a specific nearest neighbor model for DNA sequences containing consecutive locked nucleic acid (Al, Tl, Cl or Gl). You can only use owc11 (from Owczarzy et al. 2011, by default).
+To change the file containing the thermodynamic parameters for locked acid nucleic computation, the same syntax as the one for the \fB\-nn\fR option is used.
+.PP
+\fB\-sinMMLck\fR [name]
+.IP
+Forces to use a specific nearest neighbor model for DNA sequences containing consecutive locked nucleic acid with one single mismatch (Al, Tl, Cl or Gl).
+You can use only owc11 (from Owczarzy et al. 2011, by default).
+To change the file containing the thermodynamic parameters for locked acid nucleic computation, the same syntax as the one for the \fB\-nn\fR option is used.
+.IP
+Set of melting temperature corrections
+.PP
+\fB\-ion\fR [name]
+.IP
+Forces to use a specific ion correction. You can use one of the following corrections :
+Sodium corrections :
+.TP
+(DNA)
+ahs01 (from von Ahsen et al. 2001)
+kam71 (from Frank\-Kamenetskii et al 2001)
+owc1904 (equation 19 from Owczarzy et al. 2004)
+owc2004 (equation 20 from Owczarzy et al. 2004)
+owc2104 (equation 21 from Owczarzy et al. 2004)
+owc2204 (equation 21 from Owczarzy et al. 2004) (by default)
+san96 (from Santalucia et al. 1996)
+san04 (from Santalucia et al. 1998, 2004)
+schlif (from Schildkraut and Lifson 1965)
+tanna06 (from Tan et al. 2006)
+wetdna91 (from Wetmur 1991)
+.TP
+(RNA or 2\-o methyl RNA)
+tanna07 (from Tan et al. 2007) (by default)
+wetrna91 (from Wetmur 1991)
+.TP
+(RNA/DNA)
+wetdnarna91 (from Wetmur 1991) (by default)
+.IP
+Magnesium corrections :
+.TP
+(DNA)
+owcmg08 (from Owczarzy et al. 2008) (by default)
+tanmg06 (from Tan et al. 2006)
+.TP
+(RNA or 2\-o methyl RNA)
+tanmg07 (from Tan et al. 2007) (by default)
+.IP
+Mixed Na Mg corrections
+.TP
+(DNA)
+owcmix08 (from Owczarzy et al. 2008) (by default)
+tanmix07 (from Tan et al. 2007)
+.TP
+(RNA or 2\-o methyl RNA)
+tanmix07 (from Tan et al. 2007) (by default)
+.IP
+By default, the program use the algorithm from Owczarzy et al 2008 : ratio = Mg^0.5 and monovalent = Na + Tris + K
+.IP
+if monovalent = 0, a magnesium correction is used.
+if ratio < 0.22, a sodium correction is used.
+if 0.22 <= ratio < 6, a mixed Na Mg correction is used.
+if ratio >= 6, a magnesium correction is used.
+.PP
+\fB\-naeq\fR [name]
+.IP
+Forces to use a specific ion correction which gives a sodium equivalent concentration if other cations are present. You can use one of the following :
+.TP
+(DNA)
+ahs01 (from von Ahsen et al 2001) (by default)
+mit96 (from Mitsuhashi et al. 1996)
+pey00 (from Peyret 2000)
+.IP
+For the other types of hybridization, the DNA default correction is used but there is no guaranty of accuracy.
+.PP
+\fB\-DMSO\fR [name]
+.IP
+Forces to use a specific DMSO correction (DMSO is always in percent). You can use one of the following :
+.TP
+(DNA)
+ahs01 (from von Ahsen et al 2001) (by default)
+mus81 (from Musielski et al. 1981)
+cul76 (from Cullen et al. 1976)
+esc80 (from Escara et al. 1980).
+.IP
+For the other types of hybridization, the DNA default correction is used but there is no guaranty of accuracy.
+.PP
+\fB\-for\fR [name]
+.IP
+Forces to use a specific formamide correction. You can use one of the following :
+.TP
+(DNA)
+bla96 (from Blake et al 1996) with formamide concentration in mol/L (by default)
+lincorr (linear correction) with a percent of formamide volume
+.IP
+For the other types of hybridization, the DNA default correction is used but there is no guaranty of accuracy.
+.SH AUTHOR
+ This manpage was written by Pranav Ballaney for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/melting.manpages
=====================================
@@ -1 +1 @@
-doc/*.1
+debian/*.1
View it on GitLab: https://salsa.debian.org/med-team/melting/-/commit/3a29a6d6725d825d106fcce59aa96dabce415bfd
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View it on GitLab: https://salsa.debian.org/med-team/melting/-/commit/3a29a6d6725d825d106fcce59aa96dabce415bfd
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