/static/gmaj/docs/sample.gmaj

  1#:gmaj
  2
  3#----------------------------------------------------------------
  4# This file specifies input parameters for a Gmaj dataset.
  5# See below for explanatory comments.
  6#----------------------------------------------------------------
  7
  8title = "My favorite genomic region"
  9datapath = /home/cathy/mydata/favreg/
 10alignfile = tba.maf mlagan.maf
 11refseq = any
 12reconorg = none
 13tabext = .gff .gtf .bed .ct .trk
 14nowarn =  maf_version  repeat_type_missing
 15skipotherseq = false
 16
 17seq 0:
 18seqname = human.chr11  hg17.chr11  human
 19exons   = human.exons.bed  chr11
 20repeats = human.repeats
 21links   = human.links
 22underlays    = human.exons.bed  chr11  exons
 23#underlays.1 = human-mouse.underlays
 24#underlays.2 = human-rat.underlays
 25highlights   = human.highlights
 26offset = 4730995
 27
 28seq 1:
 29seqname = mouse.chr7
 30exons   = mouse.exons
 31repeats = mouse.repeats
 32links   = mouse.links
 33underlays    = mouse.underlays
 34#underlays.0 = mouse-human.underlays
 35#underlays.2 = mouse-rat.underlays
 36highlights   = mouse.highlights
 37offset = 0
 38
 39seq 2:
 40seqname = rat.chr1
 41exons   = rat.exons
 42repeats = rat.repeats
 43links   = rat.links
 44underlays    = rat.underlays
 45#underlays.0 = rat-human.underlays
 46#underlays.1 = rat-mouse.underlays
 47highlights   = rat.highlights
 48offset = 0
 49
 50#----------------------------------------------------------------
 51# This file specifies input parameters for Gmaj, including the
 52# names of all data files.  You can omit this file and just give
 53# Gmaj the name of your alignment file directly, but then you
 54# don't get the opportunity to provide annotations, offsets,
 55# additional alignment files, or other optional features.
 56#
 57# Syntax:
 58#
 59# Each key=value(s) pair must reside on its own single, separate
 60# line.  (Note that although the '=' was formerly optional, it
 61# is now required.)  Other than that, the format is fairly loose.
 62# Even the order of lines is arbitrary, except that "seq N:"
 63# defines the current sequence until it is superseded by a new
 64# "seq N:" line.  Values containing spaces must be enclosed in
 65# double quotes.  Embedded quotes in such strings can be escaped
 66# with '\', but there is no way to escape the backslash: quoted
 67# values should not end with '\' (insert a space before the
 68# final quote if necessary).  Lines with missing values are
 69# skipped.  A '#' at the beginning of a line marks a comment
 70# that will be ignored, except for the identifier tag "#:gmaj"
 71# at the top, which is mandatory.
 72#
 73# Required Fields:
 74#
 75# At least one alignfile is required.  You do not have to provide
 76# a section for every sequence (by default they will still be
 77# displayed), but for each sequence you do mention, the "seq N:"
 78# line and the seqname field are also required.  Everything else
 79# is optional.
 80#
 81# File Names and Locations:
 82#
 83# Filenames can be relative or absolute (fully qualified paths).
 84# Gmaj will look for relative names in the following locations:
 85#
 86#   1. the separately specified "bundle" file (if any)
 87#   2. the "datapath" specified here (if any)
 88#   3. the same directory as this parameters file
 89#
 90# If you are using Gmaj's "bundle" feature, you must refer to
 91# the files located in the bundle by their plain filenames,
 92# without any path.
 93#
 94# Title:
 95#
 96# This string will be used as the title for the Gmaj windows.
 97# Typically it describes the alignment data, including the name
 98# of the locus.  It does not control the applet button's label,
 99# however, because the applet has not read this file yet;
100# instead there is a separate applet parameter for that.
101#
102# Reference Sequence:
103#
104# The refseq field identifies the reference sequence used in the
105# alignments.  The default value "any" means that the alignments
106# were generated by a sequence-symmetric program such as TBA, so
107# the user should be allowed to select the reference sequence
108# interactively.  Otherwise, the value must match the appropriate
109# sequence name from the MAF files (including the contig name, if
110# applicable).
111#
112# Reconstructed Sequence:
113#
114# If the alignment files include score rows for an ancestral
115# reconstruction, the reconorg field identifies which organism
116# these scores apply to.  The default value "none" means Gmaj
117# will ignore the scores; otherwise the value must match the
118# species prefix of the appropriate sequence names from the MAF
119# files.  Contig name extensions (e.g. ".chrX") are omitted, as
120# the scores can apply to any contig for that organism.  A score
121# can be supplied only once for each base in the ancestral
122# genome.
123#
124# Tabular File Extensions:
125# 
126# The tabext field specifies which filename extensions should
127# be treated as generic, tab-delimited formats (GFF/GTF/BED)
128# instead of the old PipMaker-style formats.  The default list
129# is ".gff .gtf .bed .ct .trk".  Note that it doesn't actually
130# matter which of these is used for a particular file, just
131# whether it is in the list.
132#
133# Warning Suppression:
134#
135# The nowarn field lists keywords for particular warning
136# messages that should not be displayed.  This is especially
137# useful for applets, when the administrator has seen the
138# warning, checked the data, and determined that everything
139# is OK and the end user does not need to see the warning.
140# The keyword for each suppressible message is displayed at
141# the bottom of the message.
142#
143# Ignoring Sequences:
144#
145# The skipotherseq field specifies whether sequences that appear
146# in the MAF files but are not mentioned here should be ignored.
147# If so, these rows are simply skipped; no adjustments are made
148# to remove all-gap columns or join adjacent blocks, and empty
149# blocks are kept to preserve the MAF files' block numbering.
150# This feature is useful for saving memory, and for reducing the
151# number of pips when some species have many aligning contigs.
152# The default value is false, so all sequences are displayed.
153#
154# Sequence Numbers and Sequence Names:
155#
156# The seqname field serves to match up the parameter entries with
157# the sequence name in each row of the MAF alignments (including
158# the contig name, if applicable).  The sequence number assigns
159# the display order, and is also used to identify the secondary
160# sequence for plot-specific underlays (see below).
161#
162# Multiple values can be given for each seqname keyword; in this
163# case the first is the primary name to be used for display, and
164# the rest are aliases for it.  This is useful when two MAF files
165# use different names for the same sequences, or simply for
166# changing the display labels.  Alias resolution is applied to
167# MAF seqnames, the refseq field, and the initzoom parameter, but
168# not to the reconorg field or annotation files.  All primary and
169# alias names must be unique (except in the special case of
170# pairwise self-alignments).
171#
172# Sequence numbers start with 0 and must turn out to be
173# consecutive, after Gmaj fills in any gaps you leave with the
174# MAF sequences you don't mention here.  Thus by default, if
175# the alignment files include ten sequences, the valid sequence
176# numbers would be 0-9, and Gmaj will assign any that you omit
177# (in the order it encounters them, which is affected by file
178# bundling).  However if you set skipotherseq = true, then you
179# must assign consecutive numbers because Gmaj will not assign
180# any.
181#
182# File Specification Modifiers:
183#
184# The generic, tabular annotation formats (GFF/GTF/BED) allow
185# entries for several sequences to be combined in one file,
186# since they can be distinguished by the "seqname" or "chrom"
187# column.  However in this case Gmaj will expect the column
188# value to match the seqname from the MAF alignments.  If it
189# does not (e.g. if the MAF files include a species prefix but
190# the annotation file omits it), you can add a sequence
191# designation after the filename to tell Gmaj what to look for
192# in the annotation file.
193#
194# Gmaj has special support for annotation data that represents
195# exons or repeats (namely adding exon numbers and inferring
196# UTRs, or finding the PipMaker repeat category).  For the exons
197# and repeats panels this is automatic, but you can also invoke
198# it explicitly for files used as linkbars, underlays, or text
199# highlights by adding a type hint of "exons" or "repeats" after
200# the filename.  This only works if the file is in a generic
201# (GFF/GTF/BED) format and contains the appropriate type of data
202# (genes/exons or repeats).
203#
204# Underlays and Highlights:
205#
206# Gmaj allows you to specify color underlays independently for
207# each plot, i.e. for each combination of reference and
208# secondary sequences.  Thus in the "seq 1:" section, the
209# "underlays.0" entry specifies the underlay file to be used
210# when sequence 1 is the reference and sequence 0 is the second
211# sequence.  Note that there is e.g. no "underlays.1" entry in
212# the "seq 1:" section, since we do not usually have plots
213# aligning sequences with themselves.
214#
215# However, specifying a quadratic number of files quickly becomes
216# burdensome as the number of sequences grows.  For the common
217# case where the same underlay file is used for most or all of a
218# particular reference sequence's plots, the plain "underlays"
219# entry (without a number) provides a default for that reference
220# sequence.  This can still be overridden as needed by numbered
221# entries for special plots.
222#
223# The highlights file specifies colors for a particular row of
224# the text display, so there is only one for each sequence.  If
225# you omit it, Gmaj will build default highlights based on the
226# exons file (if you provided one).
227#
228# Offsets:
229#
230# The offset parameter is used for display purposes only.  It
231# specifies an adjustment to be added to all position labels and
232# displayed references for a particular sequence.  For example,
233# this allows positions to be labeled with respect to some larger
234# region.  However, note that all annotations must still be
235# specified relative to the sequences referred to in the MAF
236# files.
237#
238#----------------------------------------------------------------
239# Cathy Riemer, June 2008