[med-svn] [ncbi-entrez-direct] 05/08: Add man pages for all commands.
Aaron M. Ucko
ucko at moszumanska.debian.org
Wed Jan 25 03:00:00 UTC 2017
This is an automated email from the git hooks/post-receive script.
ucko pushed a commit to branch master
in repository ncbi-entrez-direct.
commit de2895860e638a3b6181330937904f36d9a1eea5
Author: Aaron M. Ucko <ucko at debian.org>
Date: Tue Jan 24 21:12:01 2017 -0500
Add man pages for all commands.
---
debian/changelog | 3 +-
debian/man/amino-acid-composition.1 | 31 +++
debian/man/between-two-genes.1 | 21 ++
debian/man/eaddress.1 | 25 +++
debian/man/ecitmatch.1 | 42 ++++
debian/man/econtact.1 | 30 +++
debian/man/edirect.1 | 86 +++++++
debian/man/edirutil.1 | 52 +++++
debian/man/efetch.1 | 115 ++++++++++
debian/man/efilter.1 | 127 +++++++++++
debian/man/einfo.1 | 54 +++++
debian/man/elink.1 | 85 +++++++
debian/man/enotify.1 | 25 +++
debian/man/entrez-phrase-search.1 | 47 ++++
debian/man/epost.1 | 41 ++++
debian/man/eproxy.1 | 26 +++
debian/man/esearch.1 | 58 +++++
debian/man/espell.1 | 25 +++
debian/man/esummary.1 | 1 +
debian/man/filter-stop-words.1 | 15 ++
debian/man/ftp-cp.1 | 13 ++
debian/man/ftp-ls.1 | 22 ++
debian/man/join-into-groups-of.1 | 12 +
debian/man/nquire.1 | 40 ++++
debian/man/reorder-columns.1 | 18 ++
debian/man/sort-uniq-count-rank.1 | 1 +
debian/man/sort-uniq-count.1 | 48 ++++
debian/man/word-at-a-time.1 | 12 +
debian/man/xtract.1 | 432 ++++++++++++++++++++++++++++++++++++
debian/man/xy-plot.1 | 19 ++
debian/manpages | 1 +
31 files changed, 1526 insertions(+), 1 deletion(-)
diff --git a/debian/changelog b/debian/changelog
index ce3cf6d..8ef483d 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -6,8 +6,9 @@ ncbi-entrez-direct (6.00.20170109+ds-1) UNRELEASED; urgency=medium
their man pages) and deploying wrapper scripts that try to figure out
which implementation the user intended to run. (Proper usage differs
radically, so ambiguity is unlikely to be an issue in practice.)
+ * Add man pages for all commands.
- -- Aaron M. Ucko <ucko at debian.org> Mon, 16 Jan 2017 22:49:45 -0500
+ -- Aaron M. Ucko <ucko at debian.org> Tue, 24 Jan 2017 21:11:59 -0500
ncbi-entrez-direct (6.00.20170105+ds-1) unstable; urgency=medium
diff --git a/debian/man/amino-acid-composition.1 b/debian/man/amino-acid-composition.1
new file mode 100644
index 0000000..31df6fd
--- /dev/null
+++ b/debian/man/amino-acid-composition.1
@@ -0,0 +1,31 @@
+.TH AMINO-ACID-COMPOSITION 1 2017-01-24 NCBI "NCBI Entrez Direct User's Manual"
+.SH NAME
+amino\-acid\-composition \- report amino acid composition
+.SH SYNOPSIS
+.B amino\-acid\-composition
+.SH DESCRIPTION
+.B amino\-acid\-composition
+reports on the amino acid composition of protein sequences
+(one case\-insensitive letter per residue)
+it reads from standard input.
+For each line of input, it writes on standard output
+a 26\-line tab\-delimited report using three\-letter symbols,
+in the form
+.RS
+.PD 0
+.IP \fBAla\fP
+.I n
+.IP \fBArg\fP
+.I n
+.IP \fBAsp\fP
+.I n
+.IP ...
+\&...
+.IP \fBVal\fP
+.I n
+.IP \fBXle\fP
+.I n
+.IP \fBXxx\fP
+.I n
+.PD
+.RE
diff --git a/debian/man/between-two-genes.1 b/debian/man/between-two-genes.1
new file mode 100644
index 0000000..3efedde
--- /dev/null
+++ b/debian/man/between-two-genes.1
@@ -0,0 +1,21 @@
+.TH BETWEEN-TWO-GENES 1 2017-01-24 NCBI "NCBI Entrez Direct User's Manual"
+.SH NAME
+between\-two\-genes \- select a range of tab-delimited lines
+.SH SYNOPSIS
+.B between\-two\-genes
+.I key1
+.I key2
+.SH DESCRIPTION
+\fBbetween\-two\-genes\fP reads a tab\-delimited file
+(as produced by \fBxtract\fP(1), perhaps)
+on standard input
+and writes to standard output a consecutive subset of its lines,
+from the (first) line whose first field is
+.I key1
+up to (but \fBnot\fP including) the next line whose first field is
+.IR key2 .
+Both keys are expected to be alphanumeric (gene symbols or the like);
+using other characters can yield undefined behavior.
+.SH SEE ALSO
+.BR reorder\-columns (1),
+.BR xtract (1).
diff --git a/debian/man/eaddress.1 b/debian/man/eaddress.1
new file mode 100644
index 0000000..a68682a
--- /dev/null
+++ b/debian/man/eaddress.1
@@ -0,0 +1,25 @@
+.TH EADDRESS 1 2017-01-24 NCBI "NCBI Entrez Direct User's Manual"
+.SH NAME
+eaddress \- check edirect's notion of your e\-mail address
+.SH SYNOPSIS
+.B eaddress
+
+.B edirect -address
+.SH DESCRIPTION
+\fBeaddress\fP prints (to standard output) the e\-mail address
+that other \fBedirect\fP(1) subcommands will send by default
+to have someone to notify in case
+a runaway script causes problems with an NCBI Entrez server.
+If the \fBEMAIL\fP environment variable is set,
+\fBedirect\fP will honor it.
+Otherwise, it will combine a username
+from the \fBUSER\fP environment variable
+or reported by \fBwhoami\fP(1)
+with a hostname from \fB/etc/mailname\fP
+or \fBuname\fP(2),
+attempting to obtain a fully qualified form if necessary.
+.SH SEE ALSO
+.BR econtact (1),
+.BR edirect (1),
+.BR whoami (1).
+
diff --git a/debian/man/ecitmatch.1 b/debian/man/ecitmatch.1
new file mode 100644
index 0000000..1b99aeb
--- /dev/null
+++ b/debian/man/ecitmatch.1
@@ -0,0 +1,42 @@
+.TH ECITMATCH 1 2017-01-24 NCBI "NCBI Entrez Direct User's Manual"
+.SH NAME
+ecitmatch \- look up a citation's PubMed ID
+.SH SYNOPSIS
+\fBecitmatch\fP (\fBedirect\ \-citmatch\fP)
+[\|\fB\-help\fP\|]
+[\|\fB\-journal\fP\ \fItitle\fP\|]
+[\|\fB\-year\fP\ \fIyear\fP\|]
+[\|\fB\-volume\fP\ \fIN\fP\|]
+[\|\fB\-page\fP\ \fIN\fP\|]
+[\|\fB\-author\fP\ \fIname\fP\|]
+.SH DESCRIPTION
+\fBecitmatch\fP prints (to standard output)
+the numeric PubMed identifier for a specified article.
+If there were multiple matches, it substitutes
+a parenthesized expression of the form
+\fB(\fP\fIn\fP\fB\ citations)\fP.
+If there were no matches, it prints nothing at all.
+.SH OPTIONS
+.TP
+\fB\-help\fP
+Print a summary of available options.
+.TP
+\fB\-journal\fP\ \fItitle\fP
+Match only articles whose journal has the given title
+(which may be specified as a standard abbreviation).
+.TP
+\fB\-year\fP\ \fIyear\fP
+Match only articles published in the given year.
+.TP
+\fB\-volume\fP\ \fIN\fP
+Match only articles with the given volume number.
+.TP
+\fB\-page\fP\ \fIN\fP
+Match only articles starting on the given page number.
+.TP
+\fB\-author\fP\ \fIname
+Match only articles with the given author name
+(may be partial; may not be repeated).
+.SH SEE ALSO
+.BR edirect (1).
+
diff --git a/debian/man/econtact.1 b/debian/man/econtact.1
new file mode 100644
index 0000000..7ff4c29
--- /dev/null
+++ b/debian/man/econtact.1
@@ -0,0 +1,30 @@
+.TH ECONTACT 1 2017-01-24 NCBI "NCBI Entrez Direct User's Manual"
+.SH NAME
+econtact \- adjust contact information for an edirect pipeline
+.SH SYNOPSIS
+\fBecontact\fP (\fBedirect\ \-contact\fP)
+[\|\fB\-help\fP\|]
+[\|\fB\-email\fP\ \fIaddress\fP\|]
+[\|\fB\-tool\fP\ \fIname\fP\|]
+.SH DESCRIPTION
+\fBecontact\fP adjusts the e\-mail address and/or client name
+that subsequent \fBedirect\fP(1) pipeline stages will send
+to have someone to notify in case
+a runaway script causes problems with an NCBI Entrez server.
+.SH OPTIONS
+.TP
+\fB\-help\fP
+Print usage information.
+.TP
+\fB\-email\fP\ \fIaddress\fP
+Send the given e\-mail address.
+.TP
+\fB\-tool\fP\ \fIname
+Send the given client name.
+.SH SEE ALSO
+.BR eaddress (1),
+.BR edirect (1),
+.BR edirutil (1),
+.BR enotify (1),
+.BR eproxy (1).
+
diff --git a/debian/man/edirect.1 b/debian/man/edirect.1
new file mode 100644
index 0000000..cb5de30
--- /dev/null
+++ b/debian/man/edirect.1
@@ -0,0 +1,86 @@
+.TH EDIRECT 1 2017-01-24 NCBI "NCBI Entrez Direct User's Manual"
+.SH NAME
+edirect \- access NCBI Entrez from the command line
+.SH SYNOPSIS
+.B edirect\ \-version
+
+\fBesearch\fP (\fBedirect\ \-search\fP) \fIoptions\fP
+
+\fBelink\fP (\fBedirect\ \-link\fP) \fIoptions\fP
+
+\fBefilter\fP (\fBedirect\ \-filter\fP) \fIoptions\fP
+
+\fBesummary\fP (\fBedirect\ \-summary\fP) \fIoptions\fP
+
+\fBefetch\fP (\fBedirect\ \-fetch\fP) \fIoptions\fP
+
+\fBeinfo\fP (\fBedirect\ \-info\fP) \fIoptions\fP
+
+\fBepost\fP (\fBedirect\ \-post\fP) \fIoptions\fP
+
+\fBespell\fP (\fBedirect\ \-spell\fP) \fIoptions\fP
+
+\fBecitmatch\fP (\fBedirect\ \-citmatch\fP) \fIoptions\fP
+
+\fBeproxy\fP (\fBedirect\ \-proxy\fP) \fIoptions\fP
+
+\fBecontact\fP (\fBedirect\ \-contact\fP) \fIoptions\fP
+
+\fBenotify\fP (\fBedirect\ \-notify\fP) \fIoptions\fP
+
+\fBeaddress\fP (\fBedirect\ \-address\fP) \fIoptions\fP
+.SH DESCRIPTION
+\fBedirect\fP (Entrez Direct) is a command\-line utility
+for consulting NCBI's set of interconnected databases
+(publication, sequence, structure, gene, variation, expression, etc.)
+in a variety of fashions,
+each of which is documented individually in a dedicated man page.
+.SH COMMON OPTIONS
+Most subcommands accept the following options,
+in addition to command\-specific options.
+.TP
+\fB\-help\fP
+Print usage information.
+.TP
+\fB\-email\fP\ \fIaddress\fP
+Send the given e\-mail address to have someone to notify
+in case a runaway script causes problems
+with an NCBI Entrez server.
+.TP
+\fB\-tool\fP\ \fIname
+Send the given client name.
+.TP
+\fB\-http\fP[\fBs\fP]\ \fBget\fP
+Force the use of \fBGET\fP rather than \fBPOST\fP HTTPS requests.
+.TP
+\fB-alias\fP\ \fIfilename\fP
+Specify a file of shortcut keywords and query strings or URL sections.
+.TP
+\fB\-silent\fP
+Suppress connection failure retry messages.
+.TP
+\fB\-verbose\fP
+Display the \fBENTREZ_DIRECT\fP XML field values at each step.
+.TP
+\fB\-debug\fP
+Print the internal URL query and XML results of each step.
+.TP
+\fB\-base\fP\ \fIURL\fP
+Specify a particular server for quality assurance testing.
+.SH SEE ALSO
+.BR eaddress (1),
+.BR ecitmatch (1),
+.BR econtact (1),
+.BR efetch (1),
+.BR efilter (1),
+.BR einfo (1),
+.BR elink (1),
+.BR enotify (1),
+.BR entrez\-phrase\-search (1),
+.BR epost (1),
+.BR eproxy (1),
+.BR esearch (1),
+.BR espell (1),
+.BR esummary (1),
+.BR nquire (1),
+.BR xtract (1).
diff --git a/debian/man/edirutil.1 b/debian/man/edirutil.1
new file mode 100644
index 0000000..9f78c78
--- /dev/null
+++ b/debian/man/edirutil.1
@@ -0,0 +1,52 @@
+.TH EDIRUTIL 1 2017-01-24 NCBI "NCBI Entrez Direct User's Manual"
+.SH NAME
+edirutil \- synthesize NCBI ENTREZ_DIRECT XML (edirect pipeline state)
+.SH SYNOPSIS
+.B edirutil
+[\|\fB\-db\fP\ \fIname\fP\|]
+[\|\fB\-web\fP\ \fIwebenv\fP\|]
+[\|\fB\-key\fP\ \fIN\fP\|]
+[\|\fB\-count\fP\ \fIN\fP\|]
+[\|\fB\-step\fP\ \fIN\fP\|]
+.\"[\|\fB\-seconds\fP\ \fIX\fP\|] \" ignored
+.\"[\|\fB\-version\fP\ \fIver\fP\|] \" ignored
+[\|\fB\-silent\fP\|]
+[\|\fB\-verbose\fP\|]
+[\|\fB\-debug\fP\|]
+.SH DESCRIPTION
+\fBedirutil\fP synthesizes \fBENTREZ_DIRECT\fP XML records,
+which several \fBedirect\fP commands read, write, or both,
+to allow for server\-side transformation or filtering of results
+prior to presenting them.
+\fBedirutil\fP makes it possible to bypass
+one or more \fBedirect\fP pipeline stages
+on the basis of state observed in browsers or other tools
+that don't natively produce \fBENTREZ_DIRECT\fP XML.
+.SH OPTIONS
+.TP
+\fB\-db\fP\ \fIname\fP
+Work with the named Entrez database.
+.TP
+\fB\-web\fP\ \fIwebenv\fP
+Pass the specified \fBWebEnv\fP cookie.
+.TP
+\fB\-key\fP\ \fIN\fP
+Work with the \fIN\fPth result set associated with the specified \fBWebEnv\fP.
+.TP
+\fB\-count\fP\ \fIN\fP
+Expect \fIN\fP results.
+.TP
+\fB\-step\fP\ \fIN\fP
+Indicate the current pipeline depth.
+.TP
+\fB\-silent\fP
+Suppress connection failure retry messages.
+.TP
+\fB\-verbose\fP
+Display the \fBENTREZ_DIRECT\fP XML field values at each step.
+.TP
+\fB\-debug\fP
+Print the internal URL query and XML results of each step.
+.SH SEE ALSO
+.BR econtact (1),
+.BR edirect (1).
diff --git a/debian/man/efetch.1 b/debian/man/efetch.1
new file mode 100644
index 0000000..413028f
--- /dev/null
+++ b/debian/man/efetch.1
@@ -0,0 +1,115 @@
+.TH EFETCH 1 2017-01-24 NCBI "NCBI Entrez Direct User's Manual"
+.SH NAME
+efetch, esummary \- retrieve results from an NCBI Entrez search
+.SH SYNOPSIS
+\fBefetch\fP (\fBedirect\ \-fetch\fP)
+[\|\fB\-help\fP\|]
+[\|\fB\-format\fP\ \fIfmt\fP\|]
+[\|\fB\-mode\fP\ \fImode\fP\|]
+[\|\fB\-db\fP\ \fIname\fP\|]
+[\|\fB\-id\fP\ \fIID\fP\|]
+[\|\fB\-seq_start\fP\ \fIN\fP\|]
+[\|\fB\-seq_stop\fP\ \fIN\fP\|]
+[\|\fB\-strand\fP\ \fIN\fP\|]
+[\|\fB\-chr_start\fP\ \fIN\fP\|]
+[\|\fB\-chr_stop\fP\ \fIN\fP\|]
+[\|\fB\-complexity\fP\ \fIN\fP\|]
+[\|\fB\-extend\fP\ \fIN\fP\|]
+[\|\fB\-extrafeat\fP\ \fIN\fP\|]
+
+\fBesummary\fP (\fBedirect\ \-summary\fP)
+[\|\fB\-help\fP\|]
+[\|\fB\-mode\fP\ \fImode\fP\|]
+[\|\fB\-db\fP\ \fIname\fP\|]
+[\|\fB\-id\fP\ \fIID\fP\|]
+[\|\fB\-seq_start\fP\ \fIN\fP\|]
+[\|\fB\-seq_stop\fP\ \fIN\fP\|]
+[\|\fB\-strand\fP\ \fIN\fP\|]
+[\|\fB\-chr_start\fP\ \fIN\fP\|]
+[\|\fB\-chr_stop\fP\ \fIN\fP\|]
+[\|\fB\-complexity\fP\ \fIN\fP\|]
+[\|\fB\-extend\fP\ \fIN\fP\|]
+[\|\fB\-extrafeat\fP\ \fIN\fP\|]
+.SH DESCRIPTION
+\fBefetch\fP and \fBesummary\fP retrieve results
+from either an \fBedirect\fP(1) pipeline
+or an immediate lookup (via \fB\-db\fP and \fB\-id\fP).
+\fBesummary\fP is equivalent to \fBefetch -format docsum\fP.
+
+\fBefetch\fP is also the name of an AceDB tool
+for consulting local sequence databases.
+To resolve this ambiguity,
+Debian systems with both AceDB tools and Entrez Direct installed
+arrange for AceDB's executable to have the name \fBefetch.acedb\fP(1)
+and for \fBefetch\fP to be a wrapper script
+that examines its usage and proceeds to run whichever of
+\fBedirect \-fetch\fP or \fBefetch.acedb\fP(1)
+looks like a better fit.
+.SH OPTIONS
+.SS Format Selection
+.TP
+\fB\-format\fP\ \fIfmt\fP
+Format of record or report.
+(See \fB-help\fP output for examples.)
+.TP
+\fB\-mode\fP\ \fImode\fP
+.BR text ,
+.BR xml ,
+.BR asn.1 ,
+or
+.BR json .
+.SS Direct Record Selection
+.TP
+\fB\-db\fP\ \fIname\fP
+Entrez database name for immediate lookups.
+.TP
+\fB\-id\fP\ \fIID\fP
+Unique identifier or accession for immediate lookups.
+.SS Sequence Range
+.TP
+\fB\-seq_start\fP\ \fIN\fP
+First sequence position to retrieve (1\-based).
+.TP
+\fB\-seq_stop\fP\ \fIN\fP
+Last sequence position to retrieve (1\-based).
+.TP
+\fB\-strand\fP\ \fIN\fP
+Strand of DNA to retrieve:
+\fB1\fP for plus, \fB2\fP for minus.
+.SS Gene Range
+.TP
+\fB\-chr_start\fP\ \fIN\fP
+First sequence position to retrieve (0\-based).
+.TP
+\fB\-chr_stop\fP\ \fIN\fP
+Last sequence position to retrieve (1\-based).
+.SS Miscellaneous
+.TP
+\fB\-help\fP
+Print usage information, complete with examples of notable
+.BR \-db / \-format / \-mode
+combinations.
+.TP
+\fB\-complexity\fP\ \fIN\fP
+How much context to fetch:
+.RS
+.PD 0
+.IP \fB0\fP
+default
+.IP \fB1\fP
+Bioseq
+.IP \fB3\fP
+Nuc\-prot set
+.PD
+.RE
+.TP
+\fB\-extend\fP\ \fIN\fP
+Extend sequence retrieval by \fIN\fP residues in both directions.
+.TP
+\fB\-extrafeat\fP\ \fIN\fP
+Bit flag specifying extra features.
+.SH SEE ALSO
+.BR edirect (1),
+.BR efetch.acedb (1),
+.BR esearch (1),
+.BR xtract (1).
diff --git a/debian/man/efilter.1 b/debian/man/efilter.1
new file mode 100644
index 0000000..5bb3461
--- /dev/null
+++ b/debian/man/efilter.1
@@ -0,0 +1,127 @@
+.TH EFILTER 1 2017-01-24 NCBI "NCBI Entrez Direct User's Manual"
+.SH NAME
+efilter \- filter and/or sort NCBI Entrez search results
+.SH SYNOPSIS
+\fBefilter\fP (\fBefetch \-filter\fP)
+[\|\fB\-help\fP\|]
+[\|\fB\-query\fP\ \fIstr\fP\|]
+[\|\fB\-sort\fP\ \fIfield\fP\|]
+[\|\fB\-days\fP\ \fIN\fP\|]
+[\|\fB\-datetype\fP\ \fIfield\fP\|]
+[\|\fB\-mindate\fP\ \fIdate\fP\|]
+[\|\fB\-maxdate\fP\ \fIdate\fP\|]
+[\|\fB\-spell\fP\|]
+[\|\fB\-pub\fP\ \fItype\fP\|]
+[\|\fB\-feature\fP\ \fItype\fP\|]
+[\|\fB\-location\fP\ \fItype\fP\|]
+[\|\fB\-molecule\fP\ \fItype\fP\|]
+[\|\fB\-organism\fP\ \fItype\fP\|]
+[\|\fB\-source\fP\ \fItype\fP\|]
+[\|\fB\-status\ alive\fP\|]
+[\|\fB\-type\fP\ \fItype\fP\|]
+[\|\fB\-label\fP\ \fIname\fP\|]
+.SH DESCRIPTION
+\fBefilter\fP filters and/or sorts results
+from a previous \fBedirect\fP(1) search.
+.SH OPTIONS
+.SS Query Specification
+.TP
+\fB\-query\fP\ \fIstr\fP
+Limit results to those matching the given query string.
+.SS Document Order
+.TP
+\fB\-sort\fP\ \fIfield\fP
+Sort results by the given field.
+.SS Date Constraint
+.TP
+\fB\-days\fP\ \fIN\fP
+Keep only results from the past \fIN\fP days.
+.TP
+\fB\-datetype\fP\ \fIfield\fP
+Which date field (in abbreviated form) to consider.
+.TP
+\fB\-mindate\fP\ \fIdate\fP
+Start of date range.
+.TP
+\fB\-maxdate\fP\ \fIdate\fP
+End of date range.
+.SS Spell Check
+.TP
+\fB\-spell\fP
+Correct misspellings in query.
+.SS Publication Filters
+.TP
+\fB\-pub\fP\ \fItype\fP
+.BR abstract ,
+.BR clinical ,
+.BR english ,
+.BR free ,
+.BR historical ,
+.BR journal ,
+.BR last_week ,
+.BR last_month ,
+.BR last_year ,
+.BR preprint ,
+.BR review ,
+.BR structured .
+.SS Sequence Filters
+.TP
+\fB\-feature\fP\ \fItype\fP
+.BR gene ,
+.BR mrna ,
+.BR cds ,
+.BR mat_peptide ,
+\&...
+.TP
+\fB\-location\fP\ \fItype\fP
+.BR mitochondrion ,
+.BR chloroplast ,
+.BR plasmid ,
+.BR plastid .
+.TP
+\fB\-molecule\fP\ \fItype\fP
+.BR genomic ,
+.BR mrna ,
+.BR trna ,
+.BR rrna ,
+.BR ncrna .
+.TP
+\fB\-organism\fP\ \fItype\fP
+.BR animals ,
+.BR archaea ,
+.BR bacteria ,
+.BR eukaryotes ,
+.BR fungi ,
+.BR human ,
+.BR insects ,
+.BR mammals ,
+.BR plants ,
+.BR prokaryotes ,
+.BR protists ,
+.BR rodents ,
+.BR viruses .
+.TP
+\fB\-source\fP\ \fItype\fP
+.BR genbank ,
+.BR insd ,
+.BR pdb ,
+.BR pir ,
+.BR refseq ,
+.BR swissprot ,
+.BR tpa
+.SS Gene Filters
+.TP
+\fB\-status\ alive\fP
+.TP
+\fB\-type\fP\ \fItype\fP
+.BR coding ,
+.BR pseudo .
+.SS Miscellaneous Arguments
+.TP
+\fB\-help\fP
+Print usage information.
+.TP
+\fB\-label\fP\ \fIname\fP
+Alias for query step.
+.SH SEE ALSO
+.BR edirect (1).
diff --git a/debian/man/einfo.1 b/debian/man/einfo.1
new file mode 100644
index 0000000..5f56bc5
--- /dev/null
+++ b/debian/man/einfo.1
@@ -0,0 +1,54 @@
+.TH EINFO 1 2017-01-24 NCBI "NCBI Entrez Direct User's Manual"
+.SH NAME
+einfo \- look up general NCBI Entrez database information
+.SH SYNOPSIS
+\fBeinfo\fP (\fBedirect\ \-info\fP)
+[\|\fB\-help\fP\|]
+[\|\fB\-db\fP\ \fIname\fP\|]
+[\|\fB\-dbs\fP\|]
+[\|\fB\-fields\fP\|]
+[\|\fB\-links\fP\|]
+.SH DESCRIPTION
+\fBeinfo\fP looks up general information about
+either an individual NCBI Entrez database
+with which other \fBedirect\fP(1) commands can work
+or the set of available databases as a whole.
+
+\fBeinfo\fP is also the name of an tool
+for accessing contents of local EPUB files.
+To resolve this ambiguity,
+Debian systems with both EPUB utilities and Entrez Direct installed
+arrange for the EPUB\-related executable
+to have the name \fBeinfo.epub\fP(1)
+and for \fBeinfo\fP to be a wrapper script
+that examines its usage and proceeds to run whichever of
+\fBedirect \-info\fP or \fBeinfo.epub\fP(1)
+looks like a better fit.
+.SH OPTIONS
+.SS Database Selection
+.TP
+\fB\-db\fP\ \fIname\fP
+Print information on the specified Entrez database,
+as an XML \fBeInfoResult\fP document.
+.TP
+\fB\-dbs\fP
+Print a plain\-text list of all available Entrez databases.
+.SS Data Summaries
+.TP
+\fB\-fields\fP
+Print just an XML\-structured summary of fields
+in the specified database.
+.TP
+\fB\-links\fP
+Print just an XML\-structured summary of links
+to and from the specified database.
+.SS Miscellaneous
+.TP
+\fB\-help\fP
+Print usage information,
+complete with samples of
+\fB\-fields\fP and \fB\-links\fP XML output.
+.SH SEE ALSO
+.BR edirect (1),
+.BR einfo.epub (1),
+.BR elink (1).
diff --git a/debian/man/elink.1 b/debian/man/elink.1
new file mode 100644
index 0000000..9443bd9
--- /dev/null
+++ b/debian/man/elink.1
@@ -0,0 +1,85 @@
+.TH ELINK 1 2017-01-24 NCBI "NCBI Entrez Direct User's Manual"
+.SH NAME
+elink \- look up related NCBI Entrez records
+.SH SYNOPSIS
+\fBelink\fP (\fBedirect\ \-link\fP)
+[\|\fB\-help\fP\|]
+[\|\fB\-related\fP\|]
+[\|\fB\-target\fP\ \fIdbname\fP\|]
+[\|\fB\-name\fP\ \fIname\fP\|]
+[\|\fB\-db\fP\ \fIname\fP\|]
+[\|\fB\-id\fP\ \fIID(s)\fP\|]
+[\|\fB\-cmd\fP\ \fIcommand\fP\|]
+[\|\fB\-mode\ ref\fP\|]
+[\|\fB\-holding\fP\ \fIprovider\fP\|]
+[\|\fB\-batch\fP\|]
+[\|\fB\-label\fP\ \fIname\fP\|]
+.SH DESCRIPTION
+\fBelink\fP follows links between Entrez databases,
+either extending an existing \fBedirect\fP(1) pipeline
+or honoring explicit \fB\-db\fP and \fB\-id\fP options.
+.SH OPTIONS
+.SS Destination Database
+.TP
+\fB\-related\fP
+Look up neighbors in the same database.
+.TP
+\fB\-target\fP\ \fIdbname\fP
+Follow links to another database.
+.TP
+\fB\-name\fP\ \fIname\fP
+Follow an explicit link name such as
+.BR pubmed_protein_refseq .
+.SS Direct Record Selection
+.TP
+\fB\-db\fP\ \fIname\fP
+Entrez database name for immediate lookups.
+.TP
+\fB\-id\fP\ \fIID(s)\fP
+Unique identifier(s) for immediate lookups.
+.SS Advanced Control
+.TP
+\fB\-cmd\fP\ \fIcommand\fP
+Command type (returns \fBeLinkResult\fP XML):
+.RS
+.PD 0
+.IP \fBneighbor\fP
+Neighbors or links
+.IP \fBneighbor_score\fP
+Neighbors with computed similarity scores
+.IP \fBacheck\fP
+All links available
+.IP \fBncheck\fP
+Existence of neighbors
+.IP \fBlcheck\fP
+Existence of external links (LinkOuts)
+.IP \fBllinks\fP
+Non-library LinkOut providers
+.IP \fBllinkslib\fP
+All LinkOut providers
+.IP \fBprlinks\fP
+Primary LinkOut provider,
+or URL for single UID with \fB-mode\ ref\fP.
+.PD
+.RE
+.TP
+\fB\-mode\ ref\fP
+Use LinkOut provider's web site.
+.TP
+\fB\-holding\fP\ \fIprovider\fP
+Name of LinkOut provider.
+.SS Batch Processing
+.TP
+\fB\-batch\fP
+Bypass Entrez history mechanism.
+.SS Miscellaneous Arguments
+.TP
+\fB\-help\fP
+Print usage information.
+.TP
+\fB\-label\fP\ \fIname\fP
+Alias for query step.
+.SH SEE ALSO
+.BR edirect (1),
+.BR einfo (1),
+.BR epost (1).
diff --git a/debian/man/enotify.1 b/debian/man/enotify.1
new file mode 100644
index 0000000..a19d189
--- /dev/null
+++ b/debian/man/enotify.1
@@ -0,0 +1,25 @@
+.TH ENOTIFY 1 2017-01-24 NCBI "NCBI Entrez Direct User's Manual"
+.SH NAME
+enotify \- send e\-mail with NCBI Entrez search results
+.SH SYNOPSIS
+\fBenotify\fP (\fBedirect\ \-notify\fP)
+[\|\fB\-help\fP\|]
+[\|\fB\-email\fP\ \fIaddress\fP\|]
+[\|\fB\-tool\fP\ \fIname\fP\|]
+.SH DESCRIPTION
+\fBenotify\fP sends e\-mail with results
+of an \fBedirect\fP(1) search.
+.SH OPTIONS
+.TP
+\fB\-help\fP
+Print a summary of available options.
+.TP
+\fB\-email\fP\ \fIaddress\fP
+Use the given e\-mail address.
+.TP
+\fB\-tool\fP\ \fIname
+Identify to Entrez with the given client name.
+.SH SEE ALSO
+.BR eaddress (1),
+.BR econtact (1),
+.BR edirect (1).
diff --git a/debian/man/entrez-phrase-search.1 b/debian/man/entrez-phrase-search.1
new file mode 100644
index 0000000..767f28f
--- /dev/null
+++ b/debian/man/entrez-phrase-search.1
@@ -0,0 +1,47 @@
+.TH ENTREZ-PHRASE-SEARCH 1 2017-01-24 NCBI "NCBI Entrez Direct User's Manual"
+.SH NAME
+entrez\-phrase\-search \- search NCBI Entrez for phrases
+.SH SYNOPSIS
+\fBentrez\-phrase\-search\fP
+[\|\fB\-help\fP\|]
+[\|\fB\-count\fP[\fBs\fP]\|]
+[\|\fB\-string\fP\|]
+[\|\fB\-db\fP\ \fIname\fP\|]
+[\|\fB\-database\fP\ \fIname\fP\|]
+[\|\fB\-field\fP\ \fIname\fP\|]
+\fIquery\fP
+.SH DESCRIPTION
+\fBentrez\-phrase\-search\fP
+is an \fBedirect\fP(1) \fBesearch\fP(1) wrapper script
+that searches an NCBI Entrez database for a phrase
+rather than discrete keywords.
+It works by breaking the query up into pairs of adjacent words
+(disregarding connecting words like "the")
+and intersecting searches
+for word pairs that appear reasonably often.
+.SH OPTIONS
+.TP
+\fB\-help\fP
+Print usage information.
+.TP
+\fB\-count\fP[\fBs\fP]
+Just print counts for individual word pairs.
+.TP
+\fB\-string\fP
+Just print the final query string.
+.TP
+\fB\-db\fP\ \fIname\fP (\fB\-database\fP\ \fIname\fP)
+Search the specified Entrez database
+(default: \fBpubmed\fP).
+.TP
+\fB\-field\fP\ \fIname\fP
+Search the specified field
+(default: \fBTIAB\fP, titles + abstracts).
+.TP
+\fIquery\fP
+Phrase to search for.
+(Quotes optional.)
+.SH SEE ALSO
+.BR edirect (1),
+.BR esearch (1),
+.BR filter\-stop\-words (1).
diff --git a/debian/man/epost.1 b/debian/man/epost.1
new file mode 100644
index 0000000..bddfc55
--- /dev/null
+++ b/debian/man/epost.1
@@ -0,0 +1,41 @@
+.TH EPOST 1 2017-01-24 NCBI "NCBI Entrez Direct User's Manual"
+.SH NAME
+epost \- upload a batch of NCBI Entrez record identifiers
+.SH SYNOPSIS
+\fBepost\fP (\fBedirect\ \-post\fP)
+[\|\fB\-help\fP\|]
+[\|\fB\-db\fP\ \fIname\fP\|]
+[\|\fB\-id\fP\ \fIID(s)\fP\|]
+[\|\fB\-format\fP\ \fIfmt\fP\|]
+[\|\fB\-input\fP\ \fIfilename\fP\|]
+[\|\fB\-label\fP\ \fIname\fP\|]
+.SH DESCRIPTION
+\fBepost\fP uploads a batch of record identifiers
+(textual accessions or numeric UIDs)
+to Entrez history servers for processing
+by other \fBedirect\fP commands.
+By default, it reads these identifiers from standard input.
+.SH OPTIONS
+.TP
+\fB\-help\fP
+Print usage information.
+.TP
+\fB\-db\fP\ \fIname\fP
+Indicate that the identifiers are from the specified database.
+.TP
+\fB\-id\fP\ \fIID(s)\fP
+Specify identifiers directly.
+.TP
+\fB\-format\fP\ \fIfmt\fP
+\fBuid\fP or \fBacc\fP(ession).
+.TP
+\fB\-input\fP\ \fIfilename\fP
+Read from \fIfilename\fP instead of standard input
+(which is then free to receive pipeline state
+from other \fBedirect\fP commands).
+.TP
+\fB\-label\fP\ \fIname\fP
+Alias for query step.
+.SH SEE ALSO
+.BR edirect (1),
+.BR elink (1).
diff --git a/debian/man/eproxy.1 b/debian/man/eproxy.1
new file mode 100644
index 0000000..204ca0f
--- /dev/null
+++ b/debian/man/eproxy.1
@@ -0,0 +1,26 @@
+.TH EPROXY 1 2017-01-24 NCBI "NCBI Entrez Direct User's Manual"
+.SH NAME
+eproxy \- load NCBI Entrez search aliases
+.SH SYNOPSIS
+\fBeproxy\fP (\fBedirect\ \-proxy\fP)
+[\|\fB\-help\fP\|]
+[\|\fB\-alias\fP\ \fIfilename\fP\|]
+[\|\fB\-pipe\fP\|]
+.SH DESCRIPTION
+\fBeproxy\fP loads named search term aliases
+for use in subsequent \fBedirect\fP pipeline stages,
+from a two\-column tab\-delimited text file.
+.SH OPTIONS
+.TP
+\fB\-help\fP
+Print usage information.
+.TP
+\fB\-alias\fP\ \fIfilename\fP
+File of aliases.
+.TP
+\fB\-pipe\fP
+Read aliases from standard input.
+.SH SEE ALSO
+.BR econtact (1),
+.BR edirect (1),
+.BR esearch (1).
diff --git a/debian/man/esearch.1 b/debian/man/esearch.1
new file mode 100644
index 0000000..84db6fa
--- /dev/null
+++ b/debian/man/esearch.1
@@ -0,0 +1,58 @@
+.TH ESEARCH 1 2017-01-24 NCBI "NCBI Entrez Direct User's Manual"
+.SH NAME
+esearch \- search an NCBI Entrez database
+.SH SYNOPSIS
+\fBesearch\fP (\fBedirect\ \-search\fP)
+[\|\fB\-help\fP\|]
+\fB\-db\fP\ \fIname\fP
+\fB\-query\fP\ \fIstr\fP
+[\|\fB\-sort\fP\ \fIfield\fP\|]
+[\|\fB\-days\fP\ \fIN\fP\|]
+[\|\fB\-datetype\fP\ \fIfield\fP\|]
+[\|\fB\-mindate\fP\ \fIdate\fP\|]
+[\|\fB\-maxdate\fP\ \fIdate\fP\|]
+[\|\fB\-spell\fP\|]
+[\|\fB\-label\fP\ \fIname\fP\|]
+.SH DESCRIPTION
+\fBesearch\fP searches an NCBI Entrez database for a given query.
+.SH OPTIONS
+.SS Query Specification
+.TP
+\fB\-db\fP\ \fIname\fP
+Entrez database name.
+.TP
+\fB\-query\fP\ \fIstr\fP
+Query string.
+.SS Document Order
+.TP
+\fB\-sort\fP\ \fIfield\fP
+Sort results by the given field.
+.SS Date Constraint
+.TP
+\fB\-days\fP\ \fIN\fP
+Return only results from the past \fIN\fP days.
+.TP
+\fB\-datetype\fP\ \fIfield\fP
+Which date field (in abbreviated form) to consider.
+.TP
+\fB\-mindate\fP\ \fIdate\fP
+Start of date range.
+.TP
+\fB\-maxdate\fP\ \fIdate\fP
+End of date range.
+.SS Spell Check
+.TP
+\fB\-spell\fP
+Correct misspellings in query.
+.SS Miscellaneous Arguments
+.TP
+\fB\-help\fP
+Print usage information.
+.TP
+\fB\-label\fP\ \fIname\fP
+Alias for query step.
+.SH SEE ALSO
+.BR edirect (1),
+.BR efetch (1),
+.BR eproxy (1),
+.BR espell (1).
diff --git a/debian/man/espell.1 b/debian/man/espell.1
new file mode 100644
index 0000000..f3f6ec5
--- /dev/null
+++ b/debian/man/espell.1
@@ -0,0 +1,25 @@
+.TH ESPELL 1 2017-01-24 NCBI "NCBI Entrez Direct User's Manual"
+.SH NAME
+espell \- spell\-correct an NCBI Entrez query
+.SH SYNOPSIS
+\fBespell\fP (\fBedirect\ \-spell\fP)
+[\|\fB\-help\fP\|]
+\fB\-db\fP\ \fIname\fP
+\fB\-query\fP\ \fIstr\fP
+.SH DESCRIPTION
+\fBespell\fP produces an NCBI \fBeSpellResult\fP XML document
+indicating what changes, if any,
+\fBesearch \-spell\fP would make to the given query.
+.SH OPTIONS
+.TP
+\fB\-help\fP
+Print usage information.
+.TP
+\fB\-db\fP\ \fIname\fP
+Entrez database name.
+.TP
+\fB\-query\fP\ \fIstr\fP
+Query string.
+.SH SEE ALSO
+.BR edirect (1),
+.BR esearch (1).
diff --git a/debian/man/esummary.1 b/debian/man/esummary.1
new file mode 100644
index 0000000..d7ee720
--- /dev/null
+++ b/debian/man/esummary.1
@@ -0,0 +1 @@
+.so man1/efetch.1
diff --git a/debian/man/filter-stop-words.1 b/debian/man/filter-stop-words.1
new file mode 100644
index 0000000..8c2d629
--- /dev/null
+++ b/debian/man/filter-stop-words.1
@@ -0,0 +1,15 @@
+.TH FILTER-STOP-WORDS 1 2017-01-24 NCBI "NCBI Entrez Direct User's Manual"
+.SH NAME
+filter\-stop\-words \- filter out unindexed NCBI Entrez words
+.SH SYNOPSIS
+.B filter\-stop\-words
+.SH DESCRIPTION
+\fBfilter\-stop\-words\fP is a Unix\-style filter
+that lets through only those lines of its input
+that do not consist of words that an Entrez search would ignore.
+Its input is expected to comprise
+one lowercase alphanumeric term per line,
+as produced by \fBword\-at\-a\-time\fP(1).
+.SH SEE ALSO
+.BR edirect (1),
+.BR word-at-a-time (1).
diff --git a/debian/man/ftp-cp.1 b/debian/man/ftp-cp.1
new file mode 100644
index 0000000..da30965
--- /dev/null
+++ b/debian/man/ftp-cp.1
@@ -0,0 +1,13 @@
+.TH FTP-CP 1 2017-01-24 NCBI "NCBI Entrez Direct User's Manual"
+.SH NAME
+ftp\-cp \- download files from an FTP server
+.SH SYNOPSIS
+.B ftp\-cp
+.I server
+.I dir
+.I filename...
+.SH DESCRIPTION
+\fBftp\-cp\fP downloads one or more files from a given directory
+on a specified file server.
+.SH SEE ALSO
+.BR ftp-ls (1).
diff --git a/debian/man/ftp-ls.1 b/debian/man/ftp-ls.1
new file mode 100644
index 0000000..c6d491e
--- /dev/null
+++ b/debian/man/ftp-ls.1
@@ -0,0 +1,22 @@
+.TH FTP-LS 1 2017-01-24 NCBI "NCBI Entrez Direct User's Manual"
+.SH NAME
+ftp\-ls \- list directory entries on an FTP server
+.SH SYNOPSIS
+.B ftp\-ls
+.I server
+.I dir
+.SH DESCRIPTION
+\fBftp\-ls\fP lists the contents of a given directory
+on a specified file server.
+It prints one line per item,
+using a subset of \fBls\ -F\fP's notation:
+.IP * 3
+Regular files' names appear as is.
+.IP * 3
+Subdirectories' names appear with trailing slashes (\fB/\fP).
+.IP * 3
+Symbolic links' names appear with trailing at signs (\fB@\fP),
+whether they refer to files or directories.
+.SH SEE ALSO
+.BR ftp-cp (1),
+.BR ls (1).
diff --git a/debian/man/join-into-groups-of.1 b/debian/man/join-into-groups-of.1
new file mode 100644
index 0000000..532c293
--- /dev/null
+++ b/debian/man/join-into-groups-of.1
@@ -0,0 +1,12 @@
+.TH JOIN-INTO-GROUPS-OF 1 2017-01-24 NCBI "NCBI Entrez Direct User's Manual"
+.SH NAME
+join\-into\-groups\-of \- join input words into N\-word groups
+.SH SYNOPSIS
+.B join\-into\-groups\-of
+.I N
+.SH DESCRIPTION
+\fBjoin\-into\-groups\-of\fP is a Unix-style filter
+that splits its input into groups of \fIN\fP words
+(the last group possibly being partial)
+with each group appearing on its own line
+and delimited internally by commas.
diff --git a/debian/man/nquire.1 b/debian/man/nquire.1
new file mode 100644
index 0000000..aa115c2
--- /dev/null
+++ b/debian/man/nquire.1
@@ -0,0 +1,40 @@
+.TH NQUIRE 1 2017-01-24 NCBI "NCBI Entrez Direct User's Manual"
+.SH NAME
+nquire \- query NCBI Entrez Utilities or other parameter\-based web services
+.SH SYNOPSIS
+\fBnquire\fP
+[\|\fB\-help\fP\|]
+[\|\fB\-get\fP\|]
+[\|\fB\-url\fP\ \fIURL\fP\|]
+[\|\fB\-eutils\fP\|]
+[\|\fIcomponent\fP ...\|]
+[\|\fB\-\fP\fItag\fP\ \fIvalue\fP ...\|]
+.SH DESCRIPTION
+\fBnquire\fP performs raw HTTP(S) queries
+against web services such as NCBI E\-Utilities
+that take \fBGET\fP or \fBPOST\fP parameters.
+.SH OPTIONS
+.TP
+\fB\-help\fP
+Print usage information, complete with a few examples,
+some additionally illustrating the use of \fBxtract\fP(1).
+.TP
+\fB\-get\fP
+Use HTTP(S) \fBGET\fP instead of \fBPOST\fP.
+.TP
+\fB\-url\fP\ \fIURL\fP
+Base URL for external search.
+.TP
+\fB\-eutils\fP\ \fIname\fP
+Shorthand for \fB\-url\ https://eutils.ncbi.nlm.nih.gov/entrez/eutils\fP.
+.TP
+\fIcomponent\fP
+Add \fB/\fP\fIcomponent\fP to the base URL.
+(Must precede any tag/value pairs.)
+.TP
+\fB\-\fP\fItag\fP\ \fIvalue\fP\ ...
+Add \fB&tag=\fP\fIvalue\fP,... to the base URL.
+(Must follow any simple components.)
+.SH SEE ALSO
+.BR edirect (1),
+.BR xtract (1).
diff --git a/debian/man/reorder-columns.1 b/debian/man/reorder-columns.1
new file mode 100644
index 0000000..7abd0c5
--- /dev/null
+++ b/debian/man/reorder-columns.1
@@ -0,0 +1,18 @@
+.TH REORDER-COLUMNS 1 2017-01-24 NCBI "NCBI Entrez Direct User's Manual"
+.SH NAME
+reorder\-columns \- reorder columns of a tab\-delimited file
+.SH SYNOPSIS
+\fBreorder\-columns\fP
+\fIN\fP ...
+.SH DESCRIPTION
+\fBreorder\-columns\fP is a Unix-style filter
+that reads tab\-delimited data on standard input
+and prints to standard output a modified version
+with all rows in their original order
+but columns reordered and possibly removed or repeated.
+.SH OPTIONS
+\fIN\fP
+Use input column \fIN\fP next on each line.
+.SH SEE ALSO
+.BR between\-two\-genes (1),
+.BR xtract (1).
diff --git a/debian/man/sort-uniq-count-rank.1 b/debian/man/sort-uniq-count-rank.1
new file mode 100644
index 0000000..18cf8a9
--- /dev/null
+++ b/debian/man/sort-uniq-count-rank.1
@@ -0,0 +1 @@
+.so man1/sort-uniq-count.1
diff --git a/debian/man/sort-uniq-count.1 b/debian/man/sort-uniq-count.1
new file mode 100644
index 0000000..19063b4
--- /dev/null
+++ b/debian/man/sort-uniq-count.1
@@ -0,0 +1,48 @@
+.TH SORT\-UNIQ\-COUNT 1 2017-01-24 NCBI "NCBI Entrez Direct User's Manual"
+.SH NAME
+sort\-uniq\-count, sort\-uniq\-count\-rank \- print line frequencies
+.SH SYNOPSIS
+\fBsort\-uniq\-count\fP[\|\fB\-rank\fP\|]
+[\|[\|\fB\-\fP\|]\fBb\fP\|]
+[\|[\|\fB\-\fP\|]\fBf\fP\|]
+[\|[\|\fB\-\fP\|]\fBi\fP\|]
+[\|[\|\fB\-\fP\|]\fBn\fP\|]
+[\|[\|\fB\-\fP\|]\fBr\fP\|]
+[\|[\|\fB\-\fP\|]\fBs\fP\|]
+.SH DESCRIPTION
+\fBsort\-uniq\-count\fP and
+\fBsort\-uniq\-count\-rank\fP each
+read a text file on standard input,
+sort it according to any specified flags
+(\fB-f\fP by default),
+and report to standard output how often
+each input line occurs.
+Each output line consists of a count
+followed by a tab and an input line.
+
+\fBsort\-uniq\-count\fP produces its output
+in the user's choice of sort order.
+\fBsort\-uniq\-count\-rank\fP sorts its output
+primarily from highest to lowest count,
+with the user's sort order as a tiebreaker.
+.SH OPTIONS
+.TP
+[\|\fB\-\fP\|]\fBb\fP
+Ignore leading blanks.
+.TP
+[\|\fB\-\fP\|]\fBf\fP
+Ignore capitalization.
+.TP
+[\|\fB\-\fP\|]\fBi\fP
+Consider only printable characters.
+.TP
+[\|\fB\-\fP\|]\fBn\fP
+Compare according to numerical value.
+.TP
+[\|\fB\-\fP\|]\fBr\fP
+Reverse the result of comparisons.
+.TP
+[\|\fB\-\fP\|]\fBs\fP
+Stabilize sort.
+.SH SEE ALSO
+.BR sort (1).
diff --git a/debian/man/word-at-a-time.1 b/debian/man/word-at-a-time.1
new file mode 100644
index 0000000..2199702
--- /dev/null
+++ b/debian/man/word-at-a-time.1
@@ -0,0 +1,12 @@
+.TH WORD-AT-A-TIME 1 2017-01-24 NCBI "NCBI Entrez Direct User's Manual"
+.SH NAME
+word\-at\-a\-time \- parse an input file into alphanumeric words
+.SH SYNOPSIS
+.B word\-at\-a\-time
+.SH DESCRIPTION
+\fBword\-at\-a\-time\fP reads a text file on standard input,
+extracts all sequences of digits and English letters,
+lowercases any capital letters,
+and prints the resulting terms in order, one per line.
+.SH SEE ALSO
+.BR join\-into\-groups\-of (1).
diff --git a/debian/man/xtract.1 b/debian/man/xtract.1
new file mode 100644
index 0000000..1d6fdef
--- /dev/null
+++ b/debian/man/xtract.1
@@ -0,0 +1,432 @@
+.TH XTRACT 1 2017-01-24 NCBI "NCBI Entrez Direct User's Manual"
+.SH NAME
+xtract \- convert XML into a table of data values
+.SH SYNOPSIS
+\fBxtract\fP
+[\|\fB\-help\fP\|]
+[\|\fB\-cleanup\fP\|]
+[\|\fB\-compress\fP\|]
+[\|\fB\-input\fP\ \fIfilename\fP\|]
+[\|\fB\-pattern\fP\ \fIexpr\fP\|]
+[\|\fB\-group\fP\ \fIexpr\fP\|]
+[\|\fB\-block\fP\ \fIexpr\fP\|]
+[\|\fB\-subset\fP\ \fIexpr\fP\|]
+[\|\fB\-if\fP\ \fIexpr\fP\ [\|\fIconstraint\fP\|]\|]
+[\|\fB\-unless\fP\ \fIexpr\fP\ [\|\fIconstraint\fP\|]\|]
+[\|\fB\-and\fP\ \fIcondition\fP\|]
+[\|\fB\-or\fP\ \fIcondition\fP\|]
+[\|\fB\-else\fP\|]
+[\|\fB\-position\fP\ \fIpos\fP\|]
+[\|\fB\-equals\fP\ \fIstr\fP\|]
+[\|\fB\-contains\fP\ \fIstr\fP\|]
+[\|\fB\-starts\-with\fP\ \fIstr\fP\|]
+[\|\fB\-ends\-with\fP\ \fIstr\fP\|]
+[\|\fB\-is\-not\fP\ \fIstr\fP\|]
+[\|\fB\-gt\fP\ \fIN\fP\|]
+[\|\fB\-ge\fP\ \fIN\fP\|]
+[\|\fB\-lt\fP\ \fIN\fP\|]
+[\|\fB\-le\fP\ \fIN\fP\|]
+[\|\fB\-eq\fP\ \fIN\fP\|]
+[\|\fB\-ne\fP\ \fIN\fP\|]
+[\|\fB\-ret\fP\ \fIstr\fP\|]
+[\|\fB\-tab\fP\ \fIstr\fP\|]
+[\|\fB\-sep\fP\ \fIstr\fP\|]
+[\|\fB\-pfx\fP\ \fIstr\fP\|]
+[\|\fB\-sfx\fP\ \fIstr\fP\|]
+[\|\fB\-clr\fP\|]
+[\|\fB\-pfc\fP\ \fIstr\fP\|]
+[\|\fB\-rst\fP\|]
+[\|\fB\-def\fP\ \fIstr\fP\|]
+[\|\fB\-lbl\fP\ \fIstr\fP\|]
+[\|\fB\-element\fP\ \fIelement\fP\|]
+[\|\fB\-first\fP\ \fIelement\fP\|]
+[\|\fB\-last\fP\ \fIelement\fP\|]
+[\|\fB\-\fP\fINAME\fP\|]
+[\|\fB\-num\fP\ \fIelement\fP\|]
+[\|\fB\-len\fP\ \fIelement\fP\|]
+[\|\fB\-sum\fP\ \fIelement\fP\|]
+[\|\fB\-min\fP\ \fIelement\fP\|]
+[\|\fB\-max\fP\ \fIelement\fP\|]
+[\|\fB\-inc\fP\ \fIelement\fP\|]
+[\|\fB\-dec\fP\ \fIelement\fP\|]
+[\|\fB\-sub\fP\ \fIelement\fP\|]
+[\|\fB\-avg\fP\ \fIelement\fP\|]
+[\|\fB\-dev\fP\ \fIelement\fP\|]
+[\|\fB\-encode\fP\ \fIelement\fP\|]
+[\|\fB\-upper\fP\ \fIelement\fP\|]
+[\|\fB\-lower\fP\ \fIelement\fP\|]
+[\|\fB\-title\fP\ \fIelement\fP\|]
+[\|\fB\-terms\fP\ \fIelement\fP\|]
+[\|\fB\-words\fP\ \fIelement\fP\|]
+[\|\fB\-pairs\fP\ \fIelement\fP\|]
+[\|\fB\-phrase\fP\ \fIelement\fP\|]
+[\|\fB\-0\-based\fP\ \fIelement\fP\|]
+[\|\fB\-1\-based\fP\ \fIelement\fP\|]
+[\|\fB\-ucsc\-based\fP\ \fIelement\fP\|]
+[\|\fB\-insd\fP\ \fIarg\fP\ ...\|]
+[\|\fB\-head\fP\ \fIstr\fP\|]
+[\|\fB\-tail\fP\ \fIstr\fP\|]
+[\|\fB\-hd\fP\ \fIstr\fP\|]
+[\|\fB\-tl\fP\ \fIstr\fP\|]
+[\|\fB\-format\fP\ \fIfmt\fP\|]
+[\|\fB\-filter\fP\ \fIelement\fP \fIaction\fP\ \fItarget\fP\|]
+[\|\fB\-verify\fP\|]
+[\|\fB\-outline\fP\|]
+[\|\fB\-synopsis\fP\|]
+[\|\fB\-examples\fP\|]
+[\|\fB\-version\fP\|]
+.SH DESCRIPTION
+\fBxtract\fP converts an XML document
+into a table of data values
+according to user\-specified rules.
+.SH OPTIONS
+.SS Processing
+.TP
+\fB\-cleanup\fP
+Fix non\-ASCII spaces.
+.TP
+\fB\-compress\fP
+Compress runs of spaces.
+.TP
+\fB\-input\fP\ \fIfilename\fP
+Read from file instead of standard input.
+.SS Exploration Argument Hierarchy
+.PD 0
+.TP
+\fB\-pattern\fP\ \fIexpr\fP
+.TP
+\fB\-group\fP\ \fIexpr\fP
+.TP
+\fB\-block\fP\ \fIexpr\fP
+.TP
+\fB\-subset\fP\ \fIexpr\fP
+Name of record within set.
+Use of different argument names allows
+command-line control of nested looping.
+.PD
+.SS Exploration Constructs
+.PD 0
+.IP Object 15
+\fBDateCreated\fP
+.IP Parent/Child 15
+\fBBook/AuthorList\fP
+.IP Heterogeneous 15
+\fB"PubmedArticleSet/*"\fP
+.IP Nested 15
+\fB"*/Taxon"\fP
+.IP Recursive 15
+\fB"**/Gene-commentary"\fP
+.PD
+.SS Conditional Execution
+.TP
+\fB\-if\fP\ \fIexpr\fP\ [\|\fIconstraint\fP\|]
+Element (or \fB@\fP\fIattribute\fP) must exist
+and satisfy any specified constraint.
+.TP
+\fB\-unless\fP\ \fIexpr\fP\ [\|\fIconstraint\fP\|]
+Skip if element matches.
+.TP
+\fB\-and\fP\ \fIcondition\fP
+Preceding and following tests must both pass.
+.TP
+\fB\-or\fP\ \fIcondition\fP
+Any passing test suffices.
+.TP
+\fB\-else\fP
+Execute if conditional test failed.
+.TP
+\fB\-position\fP\ \fIpos\fP
+Must be at \fBfirst\fP/\fBlast\fP location in list.
+.SS String Constraints
+.TP
+\fB\-equals\fP\ \fIstr\fP
+String must match exactly.
+.TP
+\fB\-contains\fP\ \fIstr\fP
+Substring must be present.
+.TP
+\fB\-starts\-with\fP\ \fIstr\fP
+Substring must be at beginning.
+.TP
+\fB\-ends\-with\fP\ \fIstr\fP
+Substring must be at end.
+.TP
+\fB\-is\-not\fP\ \fIstr\fP
+String must not match.
+.SS Numeric Constraints
+.TP
+\fB\-gt\fP\ \fIN\fP
+Greater than.
+.TP
+\fB\-ge\fP\ \fIN\fP
+Greater than or equal to.
+.TP
+\fB\-lt\fP\ \fIN\fP
+Less than to.
+.TP
+\fB\-le\fP\ \fIN\fP
+Less than or equal to.
+.TP
+\fB\-eq\fP\ \fIN\fP
+Equal to.
+.TP
+\fB\-ne\fP\ \fIN\fP
+Not equal to.
+.SS Format Customization
+.TP
+\fB\-ret\fP\ \fIstr\fP
+Override line break between patterns.
+.TP
+\fB\-tab\fP\ \fIstr\fP
+Replace tab character between fields.
+.TP
+\fB\-sep\fP\ \fIstr\fP
+Separator between group members.
+.TP
+\fB\-pfx\fP\ \fIstr\fP
+Prefix to print before group.
+.TP
+\fB\-sfx\fP\ \fIstr\fP
+Suffix to print after group.
+.TP
+\fB\-clr\fP
+Clear queued tab separator.
+.TP
+\fB\-pfc\fP\ \fIstr\fP
+Preface combines \fB\-clr\fP and \fB\-pfx\fP.
+.TP
+\fB\-rst\fP
+Reset \fB\-sep\fP, \fB\-pfx\fP, and \fB\-sfx\fP.
+.TP
+\fB\-def\fP\ \fIstr\fP
+Default placeholder for missing fields.
+.TP
+\fB\-lbl\fP\ \fIstr\fP
+Insert arbitrary text.
+.SS Element Selection
+.TP
+\fB\-element\fP\ \fIelement\fP
+Print all items that match tag name.
+.TP
+\fB\-first\fP\ \fIelement\fP
+Only print value of first item.
+.TP
+\fB\-last\fP\ \fIelement\fP
+Only print value of last item.
+.TP
+\fB\-\fP\fINAME\fP
+Record value in named variable.
+.SS \-element Constructs
+.PD 0
+.IP Tag 15
+\fBCaption\fP
+.IP Group 15
+\fBInitials,LastName\fP
+.IP Attribute 15
+\fBDescriptorName at MajorTopicYN\fP
+.IP Recursive 15
+\fB"**/Gene-commentary_accession"\fP
+.IP "Object Count" 15
+\fB"#Author"\fP
+.IP "Item Length" 15
+\fB"%Title"\fP
+.IP "Element Depth" 15
+\fB"^PMID"\fP
+.IP Variable 15
+\fB"&NAME"\fP
+.PD
+.SS Special \-element Operations
+.PD 0
+.IP "Parent Index" 15
+\fB"+"\fP
+.IP "XML Subtree" 15
+\fB"*"\fP
+.IP Children 15
+\fB"$"\fP
+.IP Attributes 15
+\fB"@"\fP
+.PD
+.SS Numeric Processing
+.TP
+\fB\-num\fP\ \fIelement\fP
+Count.
+.TP
+\fB\-len\fP\ \fIelement\fP
+Length.
+.TP
+\fB\-sum\fP\ \fIelement\fP
+Sum.
+.TP
+\fB\-min\fP\ \fIelement\fP
+Minimum.
+.TP
+\fB\-max\fP\ \fIelement\fP
+Maximum.
+.TP
+\fB\-inc\fP\ \fIelement\fP
+Increment.
+.TP
+\fB\-dec\fP\ \fIelement\fP
+Decrement.
+.TP
+\fB\-sub\fP\ \fIelement\fP
+Difference.
+.TP
+\fB\-avg\fP\ \fIelement\fP
+Average.
+.TP
+\fB\-dev\fP\ \fIelement\fP
+Deviation.
+.SS String Processing
+.TP
+\fB\-encode\fP\ \fIelement\fP
+URL\-encode \fB<\fP, \fB>\fP, \fB&\fP,
+\fB\(dq\fP, and \fB\[aq]\fP characters.
+.TP
+\fB\-upper\fP\ \fIelement\fP
+Convert text to uppercase.
+.TP
+\fB\-lower\fP\ \fIelement\fP
+Convert text to lowercase.
+.TP
+\fB\-title\fP\ \fIelement\fP
+Capitalize initial letters of words.
+.SS Phrase Processing
+.TP
+\fB\-terms\fP\ \fIelement\fP
+Partition phrase at spaces.
+.TP
+\fB\-words\fP\ \fIelement\fP
+Split at punctuation marks.
+.TP
+\fB\-pairs\fP\ \fIelement\fP
+Adjacent informative words.
+.TP
+\fB\-phrase\fP\ \fIelement\fP
+Experimental index generation.
+.SS Sequence Coordinates
+.TP
+\fB\-0\-based\fP\ \fIelement\fP
+Zero\-based.
+.TP
+\fB\-1\-based\fP\ \fIelement\fP
+One\-based.
+.TP
+\fB\-ucsc\-based\fP\ \fIelement\fP
+Half\-open.
+.SS Command Generator
+.TP
+\fB\-insd\fP\ \fIarg\fP\ ...
+Generate INSDSeq extraction commands.
+Print them if invoked standalone;
+run them if invoked as part of a pipeline.
+Requires one or more arguments,
+which may appear in the following order:
+.RS
+.\".PD 0
+.IP Descriptor(s) 15
+.BR INSDSeq_sequence / INSDSeq_definition / INSDSeq_division "/... [\|...\|]"
+.IP Completeness 15
+.BR complete / partial
+.IP Feature(s) 15
+.BR CDS / mRNA /...[\| , ...\|]
+.IP Qualifier(s)
+.BR INSDFeature_key / \(dq#INSDInterval\(dq / gene / product "/... [\|...\|]"
+.\".PD
+.RE
+.SS Miscellaneous
+.TP
+\fB\-head\fP\ \fIstr\fP
+Print before everything else.
+.TP
+\fB\-tail\fP\ \fIstr\fP
+Print after everything else.
+.TP
+\fB\-hd\fP\ \fIstr\fP
+Print before each record.
+.TP
+\fB\-tl\fP\ \fIstr\fP
+Print after each record.
+.SS Reformatting
+.TP
+\fB\-format\fP\ \fIfmt\fP
+.PD 0
+.RS
+.IP \fBcompact\fP 9
+Compress runs of spaces.
+.IP \fBindent\fP 9
+Indent according to nesting depth.
+.IP \fBexpand\fP 9
+Place each attribute on a separate line.
+.RE
+.PD
+.SS Modification
+.TP
+\fB\-filter\fP\ \fIelement\fP \fIaction\fP\ \fItarget\fP
+Actions:
+.PD 0
+.RS
+.IP \fBretain\fP 12
+Keep matching elements (no\-op).
+.IP \fBremove\fP 12
+Remove matching elements.
+.IP \fBencode\fP 12
+HTML\-escape special characters.
+.IP \fBdecode\fP 12
+Decode HTML esapes.
+.IP \fBshrink\fP 12
+Compress runs of spaces.
+.IP \fBexpand\fP 12
+Place each attribute on a separate line.
+.PD
+.P
+Targets:
+.PD 0
+.IP \fBcontent\fP 12
+Plain\-text content.
+.IP \fBcdata\fP 12
+\fBCDATA\fP blocks.
+.IP \fBcomment\fP 12
+Comments.
+.IP \fBobject\fP 12
+The whole object.
+.IP \fBattributes\fP 12
+Attributes.
+.IP \fBcontainer\fP 12
+Start and end tags.
+.RE
+.PD
+.SS Validation
+.TP
+\fB\-verify\fP
+Report XML data integrity problems.
+.SS Summary
+.TP
+\fB\-outline\fP
+Display outline of XML structure.
+.TP
+\fB\-synopsis\fP
+Display count of unique XML paths.
+.SS Documentation
+.TP
+\fB\-help\fP
+Print usage information and some example argument combinations.
+.TP
+\fB\-examples\fP
+Complete examples of \fBedirect\fP(1) and \fBxtract\fP usage.
+.TP
+\fB-version\fP
+Print version number.
+.SH NOTES
+String constraints use case\-insensitive comparisons.
+
+Numeric constraints and selection arguments use integer values.
+
+\fB\-num\fP and \fB\-len\fP selections are synonyms for
+Object Count (\fB#\fP) and Item Length (\fB%\fP).
+
+\fB\-words\fP, \fB\-pairs\fP, and \fB\-phrase\fP
+convert to lower case.
+.SH SEE ALSO
+.BR edirect (1),
+.BR xy-plot (1).
diff --git a/debian/man/xy-plot.1 b/debian/man/xy-plot.1
new file mode 100644
index 0000000..ac64a2b
--- /dev/null
+++ b/debian/man/xy-plot.1
@@ -0,0 +1,19 @@
+.TH XY-PLOT 1 2017-01-24 NCBI "NCBI Entrez Direct User's Manual"
+.SH NAME
+xy\-plot \- produce and display a line graph
+.SH SYNOPSIS
+\fBxy\-plot\fP
+[\|\fIfilename\fP\|]
+.SH DESCRIPTION
+xy\-plot reads from standard input a two\-column text file
+whose columns contain \fIx\fP and \fIy\fP coordinates respectively,
+generates a corresponding PNG image,
+and (if possible) displays the image to the user.
+.SH OPTIONS
+.TP
+\fIfilename\fP
+Output filename (\fBedirect.png\fP by default).
+Explicitly specifying the \fB.png\fP extension may be helpful.
+.SH SEE ALSO
+.BR xdg-open (1).
+
diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..13cdaf4
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/man/*.1
--
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