[med-svn] [fsa] 02/03: rename translate to fas-translate, complete manpages
Andreas Tille
tille at debian.org
Mon Dec 21 20:16:28 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository fsa.
commit 8014cf7e50a06462b3a3a82221669814d6cad54e
Author: Andreas Tille <tille at debian.org>
Date: Mon Dec 21 21:07:53 2015 +0100
rename translate to fas-translate, complete manpages
---
debian/control | 5 ++-
debian/links | 2 +
debian/manpages | 1 +
debian/mans/fsa-translate.1 | 16 ++++++++
debian/mans/fsa.1 | 15 ++++++++
debian/mans/gapcleaner.1 | 17 +++++++++
debian/mans/isect_mercator_alignment_gff.1 | 60 ++++++++++++++++++++++++++++++
debian/mans/map_coords.1 | 38 +++++++++++++++++++
debian/mans/map_gff_coords.1 | 58 +++++++++++++++++++++++++++++
debian/mans/percentid.1 | 15 ++++++++
debian/mans/prot2codon.1 | 16 ++++++++
debian/mans/slice_fasta.1 | 16 ++++++++
debian/mans/slice_fasta_gff.1 | 22 +++++++++++
debian/mans/slice_mercator_alignment.1 | 50 +++++++++++++++++++++++++
debian/rules | 28 ++------------
15 files changed, 333 insertions(+), 26 deletions(-)
diff --git a/debian/control b/debian/control
index d4845da..48e6451 100644
--- a/debian/control
+++ b/debian/control
@@ -17,7 +17,10 @@ Homepage: http://fsa.sourceforge.net/
Package: fsa
Architecture: any
Depends: ${shlibs:Depends},
- ${misc:Depends}
+ ${misc:Depends},
+ mummer,
+ exonerate
+Recommends: med-config (>= 2.1)
Description: Fast Statistical Alignment of protein, RNA or DNA sequences
FSA is a probabilistic multiple sequence alignment algorithm which uses
a "distance-based" approach to aligning homologous protein, RNA or DNA
diff --git a/debian/links b/debian/links
new file mode 100644
index 0000000..e9d435b
--- /dev/null
+++ b/debian/links
@@ -0,0 +1,2 @@
+usr/bin/fsa-translate usr/lib/debian-med/bin/tranlate
+usr/share/man/man1/fsa-translate.1.gz usr/lib/debian-med/share/man/man1/translate.1.gz
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/fsa-translate.1 b/debian/mans/fsa-translate.1
new file mode 100644
index 0000000..e9e5ef5
--- /dev/null
+++ b/debian/mans/fsa-translate.1
@@ -0,0 +1,16 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.3.
+.TH FSA-TRANSLATE "1" "December 2015" "fsa-translate 1.15.9" "User Commands"
+.SH NAME
+fsa-translate \- Translate input nucleotide sequences into protein sequence
+.SH SYNOPSIS
+.B translate
+\fI\,<FASTA file>\/\fR
+.SH DESCRIPTION
+translate from FSA 1.15.9
+.PP
+Translate input nucleotide sequences into protein sequence.
+.PP
+Input nucleotide sequences must be in FASTA format.
+Uses the first reading frame and drops incomplete codons at ends of sequences.
+.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/fsa.1 b/debian/mans/fsa.1
new file mode 100644
index 0000000..7268985
--- /dev/null
+++ b/debian/mans/fsa.1
@@ -0,0 +1,15 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.3.
+.TH FSA "1" "December 2015" "fsa 1.15.9" "User Commands"
+.SH NAME
+fsa \- Distance-based alignment of DNA, RNA and proteins
+.SH SYNOPSIS
+.B fsa
+[\fI\,options\/\fR] \fI\,<sequence file(s)>\/\fR
+.SH DESCRIPTION
+fsa \- Distance\-based alignment of DNA, RNA and proteins.
+.PP
+Type 'fsa \fB\-\-help\fR' for command\-line options.
+.PP
+ERROR: Please specify at least one sequence file.
+.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/gapcleaner.1 b/debian/mans/gapcleaner.1
new file mode 100644
index 0000000..ba7d0e7
--- /dev/null
+++ b/debian/mans/gapcleaner.1
@@ -0,0 +1,17 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.3.
+.TH GAPCLEANER "1" "December 2015" "gapcleaner 1.15.9" "User Commands"
+.SH NAME
+gapcleaner \- Find the most-parsimonious ordering of indels
+.SH SYNOPSIS
+.B gapcleaner
+\fI\,<multi-FASTA or Stockholm alignment>\/\fR
+.SH DESCRIPTION
+gapcleaner from FSA 1.15.9
+.PP
+Find the most\-parsimonious ordering of indels.
+Finds the minimal chain decomposition of the POSET of the alignment;
+this corresponds to minimizing the number of gap\-openings across the sequences.
+.PP
+Input protein alignment must be in multi\-FASTA or Stockholm format.
+.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/isect_mercator_alignment_gff.1 b/debian/mans/isect_mercator_alignment_gff.1
new file mode 100644
index 0000000..a1e7bef
--- /dev/null
+++ b/debian/mans/isect_mercator_alignment_gff.1
@@ -0,0 +1,60 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.3.
+.TH ISECT_MERCATOR_ALIGNMENT_GFF "1" "December 2015" "isect_mercator_alignment_gff 1.15.9" "User Commands"
+.SH NAME
+isect_mercator_alignment_gff \- Extracts subalignments from a Mercator multiple alignment for the features in the GFF file
+.SH SYNOPSIS
+.B isect_mercator_alignment_gff
+[\fI\,options\/\fR] \fI\,<genome> <GFF file>\/\fR
+.SH DESCRIPTION
+isect_mercator_alignment_gff from FSA 1.15.9
+.PP
+Extracts subalignments from a Mercator multiple alignment for the features in the GFF file.
+.SH OPTIONS
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this message
+.TP
+\fB\-v\fR, \fB\-\-version\fR
+show version information
+.TP
+\fB\-t\fR, \fB\-\-type\fR <string>
+only look at features of particular type
+.TP
+\fB\-D\fR, \fB\-\-data\fR <directory>
+path to map, genome and alignment files
+.TP
+\fB\-M\fR, \fB\-\-map\fR <directory>
+path to map and genome files
+.TP
+\fB\-A\fR, \fB\-\-align\fR <directory>
+path to alignment files
+.TP
+\fB\-L\fR, \fB\-\-lazy\fR
+warn, rather than die, if the subalignment can't be obtained
+.TP
+\fB\-U\fR, \fB\-\-truncate\fR
+truncate unmappable sequence (rather than skipping) and show truncated subalignment
+.TP
+\fB\-s\fR, \fB\-\-stockholm\fR
+use and display Stockholm\-format alignments with conservation statistics (default is multi\-FASTA)
+.TP
+\fB\-e\fR, \fB\-\-verbose\fR
+report progress
+.PP
+PLEASE NOTE: While this program is reasonably fast if the GFF is properly
+ordered by chromosome and the start and end coordinates of features, it
+will be *very slow* if the GFF is not sorted.
+Assumes that the "seqid" or "name" field (the first field) of the GFF entries
+holds the chromosome name.
+.PP
+Note that the GFF specification defines coordinates to be 1\-based
+and fully\-closed, therefore representing the interval [start, end].
+Conformance to this specification is assumed internally.
+.PP
+If requested, unmappable sequence will be truncated to the mappable portion;
+note that the truncation will favor the beginning of the requested sequence.
+.PP
+If a GFF feature is on the \- strand, then the corresponding
+subalignment will be reverse\-complemented.
+.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_coords.1 b/debian/mans/map_coords.1
new file mode 100644
index 0000000..6aba537
--- /dev/null
+++ b/debian/mans/map_coords.1
@@ -0,0 +1,38 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.3.
+.TH MAP_COORDS "1" "December 2015" "map_coords 1.15.9" "User Commands"
+.SH NAME
+map_coords \- Map coordinates from one genome to another using a Mercator multiple alignment
+.SH SYNOPSIS
+.B map_coords
+[\fI\,options\/\fR] \fI\,<source genome> <chromosome> <start> <end> <strand> <target genome>\/\fR
+.SH DESCRIPTION
+map_coords from FSA 1.15.9
+.PP
+Map coordinates from one genome to another using a Mercator multiple alignment.
+.SH OPTIONS
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this message
+.TP
+\fB\-D\fR, \fB\-\-data\fR <directory>
+path to map, genome and alignment files
+.TP
+\fB\-M\fR, \fB\-\-map\fR <directory>
+path to map and genome files
+.TP
+\fB\-A\fR, \fB\-\-align\fR <directory>
+path to alignment files
+.TP
+\fB\-L\fR, \fB\-\-lazy\fR
+warn, rather than die, if the subalignment can't be obtained
+.TP
+\fB\-U\fR, \fB\-\-truncate\fR
+truncate unmappable sequence (rather than skipping) and show truncated subalignment
+.PP
+Assumes that coordinates are 1\-based and fully\-closed,
+therefore representing the interval [start, end].
+.PP
+If requested, unmappable sequence will be truncated to the mappable portion;
+note that the truncation will favor the beginning of the requested sequence.
+.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_gff_coords.1 b/debian/mans/map_gff_coords.1
new file mode 100644
index 0000000..aa6f1cf
--- /dev/null
+++ b/debian/mans/map_gff_coords.1
@@ -0,0 +1,58 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.3.
+.TH MAP_GFF_COORDS "1" "December 2015" "map_gff_coords 1.15.9" "User Commands"
+.SH NAME
+map_gff_coords \- Map coordinates of GFF features from one genome to another using a Mercator multiple alignment
+.SH SYNOPSIS
+.B map_gff_coords
+[\fI\,options\/\fR] \fI\,<source genome> <source GFF file> <target genome>\/\fR
+.SH DESCRIPTION
+map_gff_coords from FSA 1.15.9
+.PP
+Map coordinates of GFF features from one genome to another using a Mercator multiple alignment.
+.SH OPTIONS
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this message
+.TP
+\fB\-t\fR, \fB\-\-type\fR <string>
+only look at features of particular type
+.TP
+\fB\-D\fR, \fB\-\-data\fR <directory>
+path to map, genome and alignment files
+.TP
+\fB\-M\fR, \fB\-\-map\fR <directory>
+path to map and genome files
+.TP
+\fB\-A\fR, \fB\-\-align\fR <directory>
+path to alignment files
+.TP
+\fB\-L\fR, \fB\-\-lazy\fR
+warn, rather than die, if the subalignment can't be obtained
+.TP
+\fB\-U\fR, \fB\-\-truncate\fR
+truncate unmappable sequence (rather than skipping) and show truncated subalignment
+.TP
+\fB\-f\fR, \fB\-\-force\-entry\fR
+if a feature can't be mapped, then add an empty entry to the GFF file (rather than skipping it entirely); implies \fB\-\-lazy\fR
+.TP
+\fB\-e\fR, \fB\-\-verbose\fR
+report progress
+.PP
+PLEASE NOTE: While this program is reasonably fast if the GFF is properly
+ordered by chromosome and the start and end coordinates of features, it
+will be *very slow* if the GFF is not sorted.
+Assumes that the "seqid" or "name" field (the first field) of the GFF entries
+holds the chromosome name.
+.PP
+Note that the GFF specification defines coordinates to be 1\-based
+and fully\-closed, therefore representing the interval [start, end].
+Conformance to this specification is assumed internally.
+.PP
+If requested, unmappable sequence will be truncated to the mappable portion;
+note that the truncation will favor the beginning of the requested sequence.
+.PP
+If a GFF feature is on the + strand for the source genome but
+the corresponding homologous region in the target genome is on the \- strand,
+then the mapped GFF feature will be reported as on the \- strand.
+.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/percentid.1 b/debian/mans/percentid.1
new file mode 100644
index 0000000..0470a08
--- /dev/null
+++ b/debian/mans/percentid.1
@@ -0,0 +1,15 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.3.
+.TH PERCENTID "1" "December 2015" "percentid 1.15.9" "User Commands"
+.SH NAME
+percentid \- Calculate the percentage identity of the passed alignment
+.SH SYNOPSIS
+.B percentid
+\fI\,<multi-FASTA or Stockholm alignment>\/\fR
+.SH DESCRIPTION
+percentid from FSA 1.15.9
+.PP
+Calculate the percentage identity of the passed alignment.
+.PP
+Input protein alignment must be in multi\-FASTA or Stockholm format.
+.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/prot2codon.1 b/debian/mans/prot2codon.1
new file mode 100644
index 0000000..5987695
--- /dev/null
+++ b/debian/mans/prot2codon.1
@@ -0,0 +1,16 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.3.
+.TH PROT2CODON "1" "December 2015" "prot2codon 1.15.9" "User Commands"
+.SH NAME
+prot2codon \- Find the codon alignment corresponding to the given protein alignment
+.SH SYNOPSIS
+.B prot2codon
+\fI\,<multi-FASTA or Stockholm alignment> <FASTA file>\/\fR
+.SH DESCRIPTION
+prot2codon from FSA 1.15.9
+.PP
+Find the codon alignment corresponding to the given protein alignment.
+.PP
+Input protein alignment must be in multi\-FASTA or Stockholm format.
+Input nucleotide sequences must be in FASTA format.
+.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/slice_fasta.1 b/debian/mans/slice_fasta.1
new file mode 100644
index 0000000..5a3cad9
--- /dev/null
+++ b/debian/mans/slice_fasta.1
@@ -0,0 +1,16 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.3.
+.TH SLICE_FASTA "1" "December 2015" "slice_fasta 1.15.9" "User Commands"
+.SH NAME
+slice_fasta \- Slice a subsequence from an input FASTA file
+.SH SYNOPSIS
+.B slice_fasta
+\fI\,<FASTA file> <sequence name> <start> <end> <strand>\/\fR
+.SH DESCRIPTION
+slice_fasta from FSA 1.15.9
+.PP
+Slice a subsequence from an input FASTA file.
+Assumes 1\-based, fully\-closed coordinates.
+If <strand> is omitted, then the + strand is assumed.
+If the \- strand is requested, then the subsequence is pulled out and then reverse\-complemented.
+.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/slice_fasta_gff.1 b/debian/mans/slice_fasta_gff.1
new file mode 100644
index 0000000..523949f
--- /dev/null
+++ b/debian/mans/slice_fasta_gff.1
@@ -0,0 +1,22 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.3.
+.TH SLICE_FASTA_GFF "1" "December 2015" "slice_fasta_gff 1.15.9" "User Commands"
+.SH NAME
+slice_fasta_gff \- Slice subsequences from an input FASTA file
+.SH SYNOPSIS
+.B slice_fasta
+[\fI\,options\/\fR] \fI\,<FASTA file> <GFF file>\/\fR
+.SH DESCRIPTION
+slice_fasta from FSA 1.15.9
+.SH OPTIONS
+.TP
+\fB\-t\fR, \fB\-\-type\fR <string>
+only look at features of particular type
+.PP
+Slice subsequences from an input FASTA file.
+Assumes 1\-based, fully\-closed coordinates.
+If no strand information is available, then the + strand is assumed.
+If the \- strand is requested, then the subsequence is pulled out and then reverse\-complemented.
+.PP
+Assumes a DNA alphabet.
+.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/slice_mercator_alignment.1 b/debian/mans/slice_mercator_alignment.1
new file mode 100644
index 0000000..101a8c4
--- /dev/null
+++ b/debian/mans/slice_mercator_alignment.1
@@ -0,0 +1,50 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.3.
+.TH SLICE_MERCATOR_ALIGNMENT "1" "December 2015" "slice_mercator_alignment 1.15.9" "User Commands"
+.SH NAME
+slice_mercator_alignment \- Extracts the corresponding subalignment from a Mercator multiple alignment
+.SH SYNOPSIS
+.B slice_mercator_alignment
+[\fI\,options\/\fR] \fI\,<genome> <chromosome> <start> <end> <strand>\/\fR
+.SH DESCRIPTION
+slice_mercator_alignment from FSA 1.15.9
+.PP
+Extracts the corresponding subalignment from a Mercator multiple alignment.
+.SH OPTIONS
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this message
+.TP
+\fB\-D\fR, \fB\-\-data\fR <directory>
+path to map, genome and alignment files
+.TP
+\fB\-M\fR, \fB\-\-map\fR <directory>
+path to map and genome files
+.TP
+\fB\-A\fR, \fB\-\-align\fR <directory>
+path to alignment files
+.TP
+\fB\-L\fR, \fB\-\-lazy\fR
+warn, rather than die, if the subalignment can't be obtained
+.TP
+\fB\-U\fR, \fB\-\-truncate\fR
+truncate unmappable sequence (rather than skipping) and show truncated subalignment
+.TP
+\fB\-s\fR, \fB\-\-stockholm\fR
+use and display Stockholm\-format alignments with conservation statistics (default is multi\-FASTA)
+.TP
+\fB\-0\fR, \fB\-\-zerobased\fR
+coordinates are 0\-based (default is 1\-based)
+.TP
+\fB\-o\fR, \fB\-\-halfopen\fR
+end coordinate is open, i.e., [start, end)
+.PP
+Assumes that coordinates are 1\-based and fully\-closed,
+therefore representing the interval [start, end].
+.PP
+If requested, unmappable sequence will be truncated to the mappable portion;
+note that the truncation will favor the beginning of the requested sequence.
+.PP
+If the requested sequence is on the \- strand, then the corresponding
+subalignment will be reverse\-complemented.
+.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/rules b/debian/rules
index 0f06fdf..a00ab1e 100755
--- a/debian/rules
+++ b/debian/rules
@@ -22,31 +22,9 @@ override_dh_auto_test:
echo "Tests seem to miss some files:"
echo "make[4]: *** No rule to make target 'apps/isect_d.unmappable.bash', needed by 'apps/isect_d.unmappable.bash.log'. Stop."
-override_dh_installman:
- # try to create man pages whereever possible
- mkdir -p $(mandir)
- $(HELP2MAN) \
- --name='Distance-based alignment of DNA, RNA and proteins' \
- $(bindir)/fsa > $(mandir)/fsa.1
- $(HELP2MAN) \
- --name='Find the most-parsimonious ordering of indels' \
- $(bindir)/gapcleaner > $(mandir)/gapcleaner.1
- $(HELP2MAN) \
- --name='Calculate the percentage identity of the passed alignment' \
- $(bindir)/percentid > $(mandir)/percentid.1
- $(HELP2MAN) \
- --name='Find the codon alignment corresponding to the given protein alignment' \
- $(bindir)/prot2codon > $(mandir)/prot2codon.1
- $(HELP2MAN) \
- --name='Slice a subsequence from an input FASTA file' \
- $(bindir)/slice_fasta > $(mandir)/slice_fasta.1
- $(HELP2MAN) \
- --name='Slice subsequences from an input FASTA file' \
- $(bindir)/slice_fasta_gff > $(mandir)/slice_fasta_gff.1
- $(HELP2MAN) \
- --name='Translate input nucleotide sequences into protein sequence.' \
- $(bindir)/translate > $(mandir)/translate.1
-
+override_dh_install:
+ dh_install
+ mv $(bindir)/translate $(bindir)/fsa-translate
get-orig-source:
uscan --verbose --force-download --repack --compression xz
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/fsa.git
More information about the debian-med-commit
mailing list