[med-svn] [trnascan-se] 07/08: Add manpages for remaining executables based on upstream docs

[Afif Elghraoui]

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afif-guest pushed a commit to branch master
in repository trnascan-se.

commit 72eaaf06d89de18cef2abbf056e7c6f76f87e291
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Fri Oct 30 22:53:13 2015 -0700

    Add manpages for remaining executables based on upstream docs
---
 debian/man/covels-SE.1    |  1 +
 debian/man/covels.1       | 41 +++++++++++++++++++++++++++++++++++++++++
 debian/man/coves-SE.1     |  1 +
 debian/man/coves.1        | 21 +++++++++++++++++++++
 debian/man/eufindtRNA.1   | 13 +++++++++++++
 debian/man/trnascan-1.4.1 | 10 ++++++++++
 debian/manpages           |  1 +
 7 files changed, 88 insertions(+)

diff --git a/debian/man/covels-SE.1 b/debian/man/covels-SE.1
new file mode 120000
index 0000000..194899c
--- /dev/null
+++ b/debian/man/covels-SE.1
@@ -0,0 +1 @@
+covels.1
\ No newline at end of file
diff --git a/debian/man/covels.1 b/debian/man/covels.1
new file mode 100644
index 0000000..325461a
--- /dev/null
+++ b/debian/man/covels.1
@@ -0,0 +1,41 @@
+.TH COVELS 1 "October 2015"
+.SH NAME
+covels \- search DNA sequence databases for similar RNAs
+.SH DESCRIPTION
+
+Covariance models (CM's) are adaptive statistical models of the the
+secondary structure and primary sequence consensus of an RNA family.
+
+CM's are adaptive because a new model is learned from a set
+of example training sequences.  CM's are statistical because
+they embody a probabilistic description of the consensus; mismatches,
+insertions, and deletions are permitted, and the penalties paid are
+learned from the training sequences that the model was constructed
+from.
+
+.SH EXAMPLE
+
+.B    covels -w 50 mymodel.cm /genbank/gbrna.seq
+
+This command would search a database
+(here, a hypothetical GenBank structural RNA database) and print
+scores and locations of all hits with positive scores (i.e., good
+matches to the model). The difference between
+.BR coves (1)
+and
+.B covels
+is that
+.B covels
+is a local search program instead of global alignment; it will find
+optimal matches to subsequences in a long sequence.  The
+.BI -w \050
+parameter sets the maximum length of match you expect to find
+(here, 50 bases). (The 'w' comes from ``window''; it sets the size of
+the search scanning window.)  This parameter affects the running time and
+the memory consumption of
+.B covels
+significantly, so you want to set it as small as you can get
+away with.
+.SH SEE ALSO
+.BR tRNAscan-SE (1),
+/usr/share/doc/trnascan-se/MANUAL.gz
diff --git a/debian/man/coves-SE.1 b/debian/man/coves-SE.1
new file mode 120000
index 0000000..4334cbe
--- /dev/null
+++ b/debian/man/coves-SE.1
@@ -0,0 +1 @@
+coves.1
\ No newline at end of file
diff --git a/debian/man/coves.1 b/debian/man/coves.1
new file mode 100644
index 0000000..b692c09
--- /dev/null
+++ b/debian/man/coves.1
@@ -0,0 +1,21 @@
+.TH COVES 1 "October 2015"
+.SH NAME
+coves \- produce individual RNA structure predictions for sequences
+.SH DESCRIPTION
+
+This command computes the score of each whole sequence individually,
+and prints the scores.  You might use it to detect sequences which,
+according to the model, don't belong to the same structural consensus;
+sequences which don't fit the model get negative scores.
+
+.SH EXAMPLES
+
+.B     coves mymodel.cm seqs.fa
+
+.B     coves -s mymodel.cm seqs.fa
+
+.B     coves -m mymodel.cm seqs.fa
+
+.SH SEE ALSO
+.BR tRNAscan-SE (1),
+/usr/share/doc/trnascan-se/MANUAL.gz
diff --git a/debian/man/eufindtRNA.1 b/debian/man/eufindtRNA.1
new file mode 100644
index 0000000..081cdb2
--- /dev/null
+++ b/debian/man/eufindtRNA.1
@@ -0,0 +1,13 @@
+.TH EUFINDTRNA 1 "October 2015"
+.SH NAME
+eufindtRNA \- detect transfer RNA genes
+.SH DESCRIPTION
+new implementation of tRNA-finding algorithm previously described by
+Pavesi et al.; does step-wise identification of B box, then A box, then
+poly-T termination signal, scored with newly derived log odds score matrix;
+new options included for use with
+.BR tRNAscan-SE (1).
+
+.SH SEE ALSO
+.BR tRNAscan-SE (1),
+/usr/share/doc/trnascan-se/MANUAL.gz
diff --git a/debian/man/trnascan-1.4.1 b/debian/man/trnascan-1.4.1
new file mode 100644
index 0000000..b7717ae
--- /dev/null
+++ b/debian/man/trnascan-1.4.1
@@ -0,0 +1,10 @@
+.TH TRNASCAN-1.4 1 "October 2015"
+.SH NAME
+trnascan-1.4 \- detect transfer RNA genes
+.SH DESCRIPTION
+This program is for internal use by
+.BR tRNAscan-SE (1).
+
+.SH SEE ALSO
+.BR tRNAscan-SE (1),
+/usr/share/doc/trnascan-se/MANUAL.gz
diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..19f429f
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/man/*

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