debian/createmanpages

@@ -3,7 +3,7 @@ MANDIR=debian/mans
 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: *//'`
+NAME=`grep "^Description:" debian/control | sed 's/^Description: *//' | head -n1`
 PROGNAME=`grep "^Package:" debian/control | sed 's/^Package: *//'`
 
 AUTHOR=".SH AUTHOR\nThis manpage was written by $DEBFULLNAME for the Debian distribution and
@@ -72,6 +72,36 @@ help2man --no-info --no-discard-stderr \
             --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
 echo $AUTHOR >> $MANDIR/${progname}.1
 
+progname=fetch_refseq_bacterial_genomes_by_name
+help2man --no-info --no-discard-stderr \
+         --name="$NAME" \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=ncbi_search
+help2man --no-info --no-discard-stderr \
+         --name="$NAME" \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=redraw_maps
+help2man --no-info --no-discard-stderr \
+         --name="$NAME" \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=remove_long_seqs
+help2man --no-info --no-discard-stderr \
+         --name="$NAME" \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=remove_short_seqs
+help2man --no-info --no-discard-stderr \
+         --name="$NAME" \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
 sed -i -e 's/perl \([^ ]\+\)\.pl/\1/' -e 's/\.pl / /' -e 's/\.sh / /' $MANDIR/*
 
 echo "$MANDIR/*.1" > debian/cct.manpages

debian/mans/fetch_all_refseq_chloroplast_genomes.1

@@ -3,7 +3,24 @@
 .SH NAME
 fetch_all_refseq_chloroplast_genomes \- visually comparing bacterial, plasmid, chloroplast, or mitochondrial sequences
 .SH DESCRIPTION
+.SS "USAGE:"
 .IP
-ncbi_.
+fetch_all_refseq_chloroplast_genomes \fB\-o\fR DIR
+.SS "DESCRIPTION:"
+.IP
+Downloads all chloroplast RefSeq sequences form NCBI in GenBank format.
+.SS "REQUIRED ARGUMENTS:"
+.HP
+\fB\-o\fR, \fB\-\-output\fR DIR
+.IP
+The output directory to contain the downloaded GenBank files.
+.SS "OPTIONAL ARGUMENTS:"
+.HP
+\fB\-h\fR, \fB\-\-help\fR
+.IP
+Show this message.
+.SS "EXAMPLE:"
+.IP
+fetch_all_refseq_chloroplast_genomes \fB\-o\fR my_project/comparison_genomes
 .SH AUTHOR
 This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

debian/mans/fetch_refseq_bacterial_genomes_by_name.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH FETCH_REFSEQ_BACTERIAL_GENOMES_BY_NAME "1" "August 2018" "fetch_refseq_bacterial_genomes_by_name 20170919" "User Commands"
+.SH NAME
+fetch_refseq_bacterial_genomes_by_name \- visually comparing bacterial, plasmid, chloroplast, or mitochondrial sequences
+.SH DESCRIPTION
+.SS "USAGE:"
+.IP
+fetch_refseq_bacterial_genomes_by_name \fB\-n\fR STRING \fB\-o\fR DIR
+.SS "DESCRIPTION:"
+.IP
+Downloads a GenBank record using a partial or complete bacterial species name.
+The \fB\-\-min\fR and \fB\-\-max\fR options can be used to restrict the size of the
+returned sequences.
+.SS "REQUIRED ARGUMENTS:"
+.HP
+\fB\-n\fR, \fB\-\-name\fR STRING
+.IP
+Complete or partial name of the bacterial species.
+.HP
+\fB\-m\fR, \fB\-\-min\fR INTEGER
+.IP
+Records with a sequence length shorter than this value will be ignored.
+.HP
+\fB\-x\fR, \fB\-\-max\fR INTEGER
+.IP
+Records with a sequence length longer than this value will be ignored.
+.HP
+\fB\-o\fR, \fB\-\-output\fR DIR
+.IP
+The output directory to download the GenBank file into.
+.SS "OPTIONAL ARGUMENTS:"
+.HP
+\fB\-h\fR, \fB\-\-help\fR
+.IP
+Show this message.
+.SS "EXAMPLE:"
+.IP
+fetch_refseq_bacterial_genomes_by_name \fB\-n\fR 'Escherichia*' \fB\-o\fR my_project/comparison_genomes
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

debian/mans/ncbi_search.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH NCBI_SEARCH "1" "August 2018" "ncbi_search 20170919" "User Commands"
+.SH NAME
+ncbi_search \- visually comparing bacterial, plasmid, chloroplast, or mitochondrial sequences
+.SH DESCRIPTION
+.SS "USAGE:"
+.IP
+ncbi_search \fB\-q\fR STRING \fB\-o\fR FILE \fB\-d\fR STRING \fB\-r\fR STRING [Options]
+.SS "DESCRIPTION:"
+.IP
+Uses NCBI's eSearch to download collections of sequences.
+.SS "REQUIRED ARGUMENTS:"
+.HP
+\fB\-q\fR, \fB\-\-query\fR [STRING]
+.IP
+Raw query text.
+.HP
+\fB\-o\fR, \fB\-\-output\fR [FILE]
+.IP
+Output file to create. If the split option is given, this should be a
+directory, where the returned records will be written. If the directory
+does not exist it will be created.
+.HP
+\fB\-d\fR, \fB\-\-database\fR [STRING]
+.IP
+Name of the NCBI database to search, such as 'nucleotide', 'protein',
+or 'gene'.
+.HP
+\fB\-r\fR, \fB\-\-return_type\fR [STRING]
+.IP
+The type of information requested. For sequences 'fasta' is often used.
+The accepted formats vary depending on the database being queried.
+.HP
+\fB\-s\fR, \fB\-\-split\fR
+.IP
+Return each record as a separate file where the file name will will be
+the accesssion id of the record. This option only works if the
+return_type is 'gb' or 'gbwithparts'.
+.HP
+\fB\-m\fR, \fB\-\-max_records\fR [INTEGER]
+.IP
+The maximum number of records to return (default is to return all matches
+satisfying the query).
+.HP
+\fB\-v\fR, \fB\-\-verbose\fR
+.IP
+Provide progress messages.
+.HP
+\fB\-h\fR, \fB\-\-help\fR
+.IP
+Show this message.
+.SS "EXAMPLE:"
+.IP
+ncbi_search \fB\-q\fR 'dysphagia AND homo sapiens[ORGN]' \e
+.HP
+\fB\-o\fR results.txt \fB\-d\fR pubmed \fB\-r\fR uilist \fB\-m\fR 100
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

debian/mans/redraw_maps.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH REDRAW_MAPS "1" "August 2018" "redraw_maps 20170919" "User Commands"
+.SH NAME
+redraw_maps \- visually comparing bacterial, plasmid, chloroplast, or mitochondrial sequences
+.SH DESCRIPTION
+.SS "USAGE:"
+.IP
+redraw_maps \fB\-p\fR DIR [Options]
+.SS "DESCRIPTION:"
+.IP
+Used to redraw the maps. This can be used after editing the CGView XML file
+or to change the output image formats.
+.SS "REQUIRED ARGUMENTS:"
+.HP
+\fB\-p\fR, \fB\-\-project\fR DIR
+.IP
+Path to a completed CCT project.
+.SS "OPTIONAL ARGUMENTS:"
+.HP
+\fB\-f\fR, \fB\-\-format\fR STRING
+.IP
+Image format for output map. Options are png, jpg, svg, svgz.
+(Default: png)
+.HP
+\fB\-m\fR, \fB\-\-memory\fR STRING
+.IP
+Memory value for Java's \fB\-Xmx\fR option (Default: 1500m).
+.HP
+\fB\-h\fR, \fB\-\-help\fR
+.IP
+Show this message
+.SS "EXAMPLE:"
+.IP
+redraw_maps \fB\-p\fR my_project \fB\-f\fR svg
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

debian/mans/remove_long_seqs.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH REMOVE_LONG_SEQS "1" "August 2018" "remove_long_seqs 20170919" "User Commands"
+.SH NAME
+remove_long_seqs \- visually comparing bacterial, plasmid, chloroplast, or mitochondrial sequences
+.SH DESCRIPTION
+.SS "USAGE:"
+.IP
+remove_long_seqs \fB\-i\fR DIR \fB\-l\fR INTEGER
+.SS "DESCRIPTION:"
+.IP
+Removes GenBank files that are longer than the specified length from the
+provided directory.
+.SS "REQUIRED ARGUMENTS:"
+.HP
+\fB\-i\fR, \fB\-\-input\fR DIR
+.IP
+Input directory of GenBank files with .gbk extensions.
+.HP
+\fB\-l\fR, \fB\-\-length\fR INTEGER
+.IP
+Remove GenBank files that describe sequences longer than this length.
+.SS "OPTIONAL ARGUMENTS:"
+.HP
+\fB\-h\fR, \fB\-\-help\fR
+.IP
+Show this message
+.SS "EXAMPLE:"
+.IP
+remove_long_seqs \fB\-i\fR my_project/comparison_genomes \fB\-l\fR 100000
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

debian/mans/remove_short_seqs.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH REMOVE_SHORT_SEQS "1" "August 2018" "remove_short_seqs 20170919" "User Commands"
+.SH NAME
+remove_short_seqs \- visually comparing bacterial, plasmid, chloroplast, or mitochondrial sequences
+.SH DESCRIPTION
+usage: remove_short_seqs [[\-i input] [\-l length] | [\-h]]
+\fB\-i\fR DIRECTORY the input directory of GenBank files with .gbk extensions
+\fB\-l\fR INTEGER remove GenBank files that describe sequences shorter than this length
+.SS "USAGE:"
+.IP
+remove_short_seqs \fB\-i\fR DIR \fB\-l\fR INTEGER
+.SS "DESCRIPTION:"
+.IP
+Removes GenBank files that are shorter than the specified length from the
+provided directory.
+.SS "REQUIRED ARGUMENTS:"
+.HP
+\fB\-i\fR, \fB\-\-input\fR DIR
+.IP
+Input directory of GenBank files with .gbk extensions.
+.HP
+\fB\-l\fR, \fB\-\-length\fR INTEGER
+.IP
+Remove GenBank files that describe sequences shorter than this length.
+.SS "OPTIONAL ARGUMENTS:"
+.HP
+\fB\-h\fR, \fB\-\-help\fR
+.IP
+Show this message
+.SS "EXAMPLE:"
+.IP
+remove_short_seqs \fB\-i\fR my_project/comparison_genomes \fB\-l\fR 100000
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.