mirror of
https://github.com/galaxyproject/galaxy.git
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Add Genetrack tools and display site
This commit is contained in:
Nate Coraor
@@ -20,26 +20,26 @@ log = logging.getLogger(__name__)
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class GeneTrack( data.Binary ):
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file_ext = "genetrack"
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MetadataElement( name="hdf", default="data.hdf", desc="HDF DB", readonly=True, visible=True, no_value=0 )
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MetadataElement( name="sqlite", default="features.sqlite", desc="SQLite Features DB", readonly=True, visible=True, no_value=0 )
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MetadataElement( name="genetrack", default="data.genetrack", desc="HDF index", readonly=True, visible=True, no_value=0 )
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MetadataElement( name="label", default="Custom", desc="Track Label", readonly=True, visible=True, no_value="Custom" )
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def __init__(self, **kwargs):
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super( GeneTrack, self ).__init__( **kwargs )
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self.add_display_app( 'genetrack', 'View in GeneTrack', '', 'genetrack_link' )
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self.add_display_app( 'genetrack', 'View in', '', 'genetrack_link' )
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def get_display_links( self, dataset, type, app, base_url, target_frame='galaxy_main', **kwd ):
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return data.Binary.get_display_links( self, dataset, type, app, base_url, target_frame=target_frame, **kwd )
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def genetrack_link( self, hda, type, app, base_url ):
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ret_val = []
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if hda.has_data:
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# Get the disk file name
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# Get the disk file name and data id
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file_name = hda.dataset.get_file_name()
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data_id = hda.dataset.id
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# Make it secure
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a = hmac_new( app.config.tool_secret, file_name )
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b = binascii.hexlify( file_name )
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encoded_file_name = "%s:%s" % ( a, b )
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for site_name, site_url in util.get_genetrack_sites():
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if site_name in app.config.genetrack_display_sites:
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link = "%s?filename=%s" % ( site_url, encoded_file_name )
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ret_val.append( ( site_name, link ) )
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hashkey = hmac_new( app.config.tool_secret, file_name )
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encoded = binascii.hexlify( file_name )
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for name, url in util.get_genetrack_sites():
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if name.lower() in app.config.genetrack_display_sites:
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# send both parameters filename and hashkey
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link = "%s?filename=%s&hashkey=%s&id=%s&GALAXY_URL=%s" % ( url, encoded, hashkey, data_id, base_url )
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ret_val.append( ( name, link ) )
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return ret_val
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@@ -1,293 +0,0 @@
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import time, glob, os, sys
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from itertools import cycle
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from mako import exceptions
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from mako.template import Template
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from mako.lookup import TemplateLookup
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from galaxy.web.base.controller import *
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from galaxy.util.hash_util import *
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try:
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import pkg_resources
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pkg_resources.require("GeneTrack")
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import atlas
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from atlas import sql
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from atlas import hdf
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from atlas import util as atlas_utils
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from atlas.web import formlib, feature_query, feature_filter
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from atlas.web import label_cache as atlas_label_cache
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from atlas.plotting.const import *
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from atlas.plotting.tracks import prefab
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from atlas.plotting.tracks import chart
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from atlas.plotting import tracks
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except Exception, exc:
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raise ControllerUnavailable("GeneTrack could not import a required dependency: %s" % str(exc))
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pkg_resources.require( "Paste" )
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import paste.httpexceptions
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# Database helpers
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SHOW_LABEL_LIMIT = 10000
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def list_labels(session):
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"""
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Returns a list of labels that will be plotted in order.
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"""
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labels = sql.Label
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query = session.query(labels).order_by("-id")
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return query
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def open_databases( conf ):
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"""
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A helper function that returns handles to the hdf and sql databases
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"""
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db = hdf.hdf_open( conf.HDF_DATABASE, mode='r' )
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session = sql.get_session( conf.SQL_URI )
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return db, session
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def hdf_query(db, name, param, autosize=False ):
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"""
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Schema specific hdf query.
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Note that returns data as columns not rows.
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"""
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if not hdf.has_node(db=db, name=name):
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atlas.warn( 'missing label %s' % name )
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return [], [], [], []
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data = hdf.GroupData( db=db, name=name)
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istart, iend = data.get_indices(label=param.chrom, start=param.start, stop=param.end)
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table = data.get_table(label=param.chrom)
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if autosize:
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# attempts to reduce the number of points
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size = len( table.cols.ix[istart:iend] )
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step = max( [1, size/1200] )
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else:
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step = 1
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ix = table.cols.ix[istart:iend:step].tolist()
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wx = table.cols.wx[istart:iend:step].tolist()
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cx = table.cols.cx[istart:iend:step].tolist()
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ax = table.cols.ax[istart:iend:step].tolist()
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return ix, wx, cx, ax
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# Chart helpers
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def build_tracks( param, conf, data_label, fit_label, pred_label, strand, show=False ):
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"""
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Builds tracks
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"""
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# gets all the labels for a fast lookup
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label_cache = atlas_label_cache( conf )
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# get database handles for hdf and sql
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db, session = open_databases( conf )
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# fetching x and y coordinates for bar and fit (line) for
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# each strand plus (p), minus (m), all (a)
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bix, bpy, bmy, bay = hdf_query( db=db, name=data_label, param=param )
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fix, fpy, fmy, fay = hdf_query( db=db, name=fit_label, param=param )
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# close the hdf database
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db.close()
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# get all features within the range
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all = feature_query( session=session, param=param )
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# draws the barchart and the nucleosome chart below it
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if strand == 'composite':
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bar = prefab.composite_bartrack( fix=fix, fay=fay, bix=bix, bay=bay, param=param)
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else:
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bar = prefab.twostrand_bartrack( fix=fix, fmy=fmy, fpy=fpy, bix=bix, bmy=bmy, bpy=bpy, param=param)
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charts = list()
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charts.append( bar )
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return charts
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def feature_chart(param=None, session=None, label=None, label_dict={}, color=cycle( [LIGHT, WHITE] ) ):
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all = feature_filter(feature_query(session=session, param=param), name=label, kdict=label_dict)
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flipped = []
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for feature in all:
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if feature.strand == "-":
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feature.start, feature.end = feature.end, feature.start
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flipped.append(feature)
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opts = track_options(
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xscale=param.xscale, w=param.width, fgColor=PURPLE,
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show_labels=param.show_labels, ylabel=str(label),
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bgColor=color.next()
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)
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return [
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tracks.split_tracks(features=flipped, options=opts, split=param.show_labels, track_type='vector')
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]
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def consolidate_charts( charts, param ):
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# create the multiplot
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opt = chart_options( w=param.width )
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multi = chart.MultiChart(options=opt, charts=charts)
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return multi
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# SETUP Track Builders
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import functools
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def twostrand_tracks( param=None, conf=None ):
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return build_tracks( data_label=conf.LABEL, fit_label=conf.FIT_LABEL, pred_label=conf.PRED_LABEL, param=param, conf=conf, strand='twostrand')
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def composite_tracks( param=None, conf=None ):
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return build_tracks( data_label=conf.LABEL, fit_label=conf.FIT_LABEL, pred_label=conf.PRED_LABEL, param=param, conf=conf, strand='composite')
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class BaseConf( object ):
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"""
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Fake web_conf for atlas.
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"""
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IMAGE_DIR = "static/genetrack/plots/"
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LEVELS = [str(x) for x in [ 50, 100, 250, 500, 1000, 2500, 5000, 10000, 20000, 50000, 100000, 200000 ]]
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ZOOM_LEVELS = zip(LEVELS, LEVELS)
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PLOT_SETUP = [
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('comp-id', 'Composite' , 'genetrack/index.html', composite_tracks ),
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('two-id' , 'Two Strand', 'genetrack/index.html', twostrand_tracks ),
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]
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PLOT_CHOICES = [ (id, name) for (id, name, page, func) in PLOT_SETUP ]
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PLOT_MAPPER = dict( [ (id, (page, func)) for (id, name, page, func) in PLOT_SETUP ] )
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def __init__(self, **kwds):
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for key,value in kwds.items():
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setattr( self, key, value)
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class WebRoot(BaseController):
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@web.expose
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def search(self, trans, word='', dataset_id=None, submit=''):
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"""
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Default search page
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"""
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data = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( dataset_id )
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if not data:
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raise paste.httpexceptions.HTTPRequestRangeNotSatisfiable( "Invalid reference dataset id: %s." % str( dataset_id ) )
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# the main configuration file
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conf = BaseConf(
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TITLE = "<i>%s</i>: %s" % (data.metadata.dbkey, data.metadata.label),
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HDF_DATABASE = os.path.join( data.extra_files_path, data.metadata.hdf ),
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SQL_URI = "sqlite:///%s" % os.path.join( data.extra_files_path, data.metadata.sqlite ),
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LABEL = data.metadata.label,
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FIT_LABEL = "%s-SIGMA-%d" % (data.metadata.label, 20),
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PRED_LABEL = "PRED-%s-SIGMA-%d" % (data.metadata.label, 20),
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)
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param = atlas.Param( word=word )
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# search for a given
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try:
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session = sql.get_session( conf.SQL_URI )
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except:
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return trans.fill_template_mako('genetrack/invalid.html', dataset_id=dataset_id)
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if param.word:
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def search_query( word, text ):
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query = session.query(sql.Feature).filter( "name LIKE :word or freetext LIKE :text" ).params(word=word, text=text)
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query = list(query[:20])
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return query
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# a little heuristics to match most likely target
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targets = [
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(param.word+'%', 'No match'), # match beginning
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('%'+param.word+'%', 'No match'), # match name anywhere
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('%'+param.word+'%', '%'+param.word+'%'), # match json anywhere
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]
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for word, text in targets:
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query = search_query( word=word, text=text)
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if query:
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break
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else:
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query = []
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return trans.fill_template_mako('genetrack/search.html', param=param, query=query, dataset_id=dataset_id)
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@web.expose
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def index(self, trans, dataset_id=None, **kwds):
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"""
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Main request handler
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"""
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color = cycle( [LIGHT, WHITE] )
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data = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( dataset_id )
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if not data:
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raise paste.httpexceptions.HTTPRequestRangeNotSatisfiable( "Invalid reference dataset id: %s." % str( dataset_id ) )
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# the main configuration file
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conf = BaseConf(
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TITLE = "<i>%s</i>: %s" % (data.metadata.dbkey, data.metadata.label),
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HDF_DATABASE = os.path.join( data.extra_files_path, data.metadata.hdf ),
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SQL_URI = "sqlite:///%s" % os.path.join( data.extra_files_path, data.metadata.sqlite ),
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LABEL = data.metadata.label,
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FIT_LABEL = "%s-SIGMA-%d" % (data.metadata.label, 20),
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PRED_LABEL = "PRED-%s-SIGMA-%d" % (data.metadata.label, 20),
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)
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try:
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session = sql.get_session( conf.SQL_URI )
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except:
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return trans.fill_template_mako('genetrack/invalid.html', dataset_id=dataset_id)
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if os.path.exists( conf.HDF_DATABASE ):
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db = hdf.hdf_open( conf.HDF_DATABASE, mode='r' )
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conf.CHROM_FIELDS = [(x,x) for x in hdf.GroupData(db=db, name=conf.LABEL).labels]
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db.close()
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else:
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query = session.execute(sql.select([sql.feature_table.c.chrom]).distinct())
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conf.CHROM_FIELDS = [(x.chrom,x.chrom) for x in query]
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# generate a new form based on the configuration
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form = formlib.main_form( conf )
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# clear the tempdir every once in a while
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atlas_utils.clear_tempdir( dir=conf.IMAGE_DIR, days=1, chance=10)
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incoming = form.defaults()
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incoming.update( kwds )
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# manage the zoom and pan requests
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incoming = formlib.zoom_change( kdict=incoming, levels=conf.LEVELS)
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incoming = formlib.pan_view( kdict=incoming )
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# process the form
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param = atlas.Param( **incoming )
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form.process( incoming )
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if kwds and form.isSuccessful():
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# adds the sucessfull parameters
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param.update( form.values() )
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# if it was a search word not a number go to search page
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try:
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center = int( param.feature )
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except ValueError:
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# go and search for these
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return trans.response.send_redirect( web.url_for( controller='genetrack', action='search', word=param.feature, dataset_id=dataset_id ) )
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param.width = min( [2000, int(param.img_size)] )
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param.xscale = [ param.start, param.end ]
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param.show_labels = ( param.end - param.start ) <= SHOW_LABEL_LIMIT
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# get the template and the function used to generate the tracks
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tmpl_name, track_maker = conf.PLOT_MAPPER[param.plot]
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# check against a hash, display an image that already exists if it was previously created.
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hash = new_secure_hash()
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hash.update(str(dataset_id))
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for key in sorted(kwds.keys()):
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hash.update(str(kwds[key]))
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fname = "%s.png" % hash.hexdigest()
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fpath = os.path.join(conf.IMAGE_DIR, fname)
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charts = []
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param.fname = fname
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# The SHA1 hash should uniquely identify the qs that created the plot...
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if os.path.exists(fpath):
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os.utime(fpath, (time.time(), time.time()))
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return trans.fill_template_mako(tmpl_name, conf=conf, form=form, param=param, dataset_id=dataset_id)
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# If the hashed filename doesn't exist, create it.
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if track_maker is not None and os.path.exists( conf.HDF_DATABASE ):
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# generate the fit track
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charts = track_maker( param=param, conf=conf )
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for label in list_labels( session ):
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charts.extend( feature_chart(param=param, session=session, label=label.name, label_dict={label.name:label.id}, color=color))
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track_chart = consolidate_charts( charts, param )
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track_chart.save(fname=fpath)
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return trans.fill_template_mako(tmpl_name, conf=conf, form=form, param=param, dataset_id=dataset_id)
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@@ -1,3 +1,7 @@
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# GeneTrack sites
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main http://www.genetrack.org/
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test http://www.test.genetrack.org/
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#
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# The key(s) should be added to universe_wsgi.ini as the value of
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# genetrack_display_sites
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#
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# key site url
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psu_galaxy http://genetrack.g2.bx.psu.edu/galaxy
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@@ -125,6 +125,9 @@
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<tool file="visualization/GMAJ.xml" />
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<tool file="visualization/LAJ.xml" />
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<tool file="visualization/build_ucsc_custom_track.xml" />
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<tool file="visualization/genetrack_indexer.xml" />
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<tool file="visualization/genetrack_peak_prediction.xml" />
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</section>
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</section>
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<section name="Regional Variation" id="regVar">
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<tool file="regVariation/windowSplitter.xml" />
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@@ -1,189 +0,0 @@
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#!/usr/bin/env python
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"""
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Run GeneTrack(atlas) with a faked conf file to generate GeneTrack data files.
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usage: %prog
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-l, --label=N: Data label for fit curve/peak plot
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-1, --fits=N/N/N/N/N,...: Data files (interval format) for fit curve/peak plot
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-2, --feats=N:M/N/N/N/N/N,...: Data files (interval format) for features.
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-d, --data=N: Output path for hdf5 and sqlite databases.
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-o, --output=N: Output path for export file.
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"""
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from galaxy import eggs
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import pkg_resources
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pkg_resources.require("GeneTrack")
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pkg_resources.require("bx-python")
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import commands as oscommands
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from atlas import commands
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from atlas import sql
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from bx.cookbook import doc_optparse
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from bx.intervals import io
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import os
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import tempfile
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from functools import partial
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SIGMA = 20
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WIDTH = 5 * SIGMA
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EXCLUSION_ZONE = 147
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def main(label, fit, feats, data_dir, output):
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os.mkdir(data_dir)
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conf = DummyConf(
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__name__=label,
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CLOBBER = True,
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DATA_SIZE = 3*10**6,
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MINIMUM_PEAK_SIZE = 0.1,
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LOADER_ENABLED = False,
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FITTER_ENABLED = False,
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PREDICTOR_ENABLED = False,
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EXPORTER_ENABLED = False,
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LOADER = loader,
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FITTER = fitter,
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PREDICTOR = predictor,
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EXPORTER = partial( commands.exporter, formatter=commands.bed_formatter),
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HDF_DATABASE = os.path.join( data_dir, "data.hdf" ),
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SQL_URI = "sqlite:///%s" % os.path.join( data_dir, "features.sqlite" ),
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SIGMA = SIGMA,
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WIDTH = WIDTH,
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DATA_LABEL = label,
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FIT_LABEL = "%s-SIGMA-%d" % ( label,SIGMA ),
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PEAK_LABEL = "PRED-%s-SIGMA-%d" % ( label,SIGMA ),
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EXCLUSION_ZONE = EXCLUSION_ZONE,
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LEFT_SHIFT = EXCLUSION_ZONE / 2,
|
||||
RIGHT_SHIFT = EXCLUSION_ZONE / 2,
|
||||
EXPORT_LABELS = [ "PRED-%s-SIGMA-%d" % ( label,SIGMA ) ],
|
||||
EXPORT_DIR = os.path.join( data_dir ),
|
||||
DATA_FILE=fit and fit[1] or None,
|
||||
fit=fit,
|
||||
feats=feats,
|
||||
)
|
||||
if fit:
|
||||
# Turn on fit processing.
|
||||
conf.LOADER_ENABLED = True,
|
||||
conf.FITTER_ENABLED = True,
|
||||
conf.PREDICTOR_ENABLED = True,
|
||||
conf.EXPORTER_ENABLED = True,
|
||||
for feat in feats:
|
||||
load_feature_files(conf, feats)
|
||||
commands.execute(conf)
|
||||
outname = "%s.%s.txt" % (conf.__name__, conf.EXPORT_LABELS[0] )
|
||||
if os.path.exists( os.path.join(data_dir, outname) ):
|
||||
os.rename( os.path.join(data_dir, outname), output)
|
||||
|
||||
# mod454 seems to be a module without a package. The necessary funcitons are
|
||||
# stubbed out here until I'm sure of their final home. INS
|
||||
|
||||
def loader( conf ):
|
||||
from atlas import hdf
|
||||
from mod454.schema import Mod454Schema as Schema
|
||||
last_chrom = table = None
|
||||
db = hdf.hdf_open( conf.HDF_DATABASE, mode='a', title='HDF database')
|
||||
gp = hdf.create_group( db=db, name=conf.DATA_LABEL, desc='data group', clobber=conf.CLOBBER )
|
||||
fit_meta = conf.fit[2]
|
||||
# iterate over the file and insert into table
|
||||
for line in open( conf.fit[1], "r" ):
|
||||
if line.startswith("chrom"): continue #Skip possible header
|
||||
if line.startswith("#"): continue
|
||||
fields = line.rstrip('\r\n').split('\t')
|
||||
chrom = fields[fit_meta.chromCol]
|
||||
if chrom != last_chrom:
|
||||
if table: table.flush()
|
||||
table = hdf.create_table( db=db, name=chrom, where=gp, schema=Schema, clobber=False )
|
||||
last_chrom = chrom
|
||||
try:
|
||||
position = int(fields[fit_meta.positionCol])
|
||||
forward = float(fields[fit_meta.forwardCol])
|
||||
reverse = fit_meta.reverseCol > -1 and float(fields[fit_meta.reverseCol]) or 0.0
|
||||
row = ( position, forward, reverse, forward+reverse, )
|
||||
table.append( [ row ] )
|
||||
except ValueError:
|
||||
# Ignore bad lines
|
||||
pass
|
||||
table.flush()
|
||||
db.close()
|
||||
|
||||
def fitter( conf ):
|
||||
from mod454.fitter import fitter as mod454_fitter
|
||||
return mod454_fitter( conf )
|
||||
|
||||
def predictor( conf ):
|
||||
from mod454.predictor import predictor as mod454_predictor
|
||||
return mod454_predictor( conf )
|
||||
|
||||
def load_feature_files( conf, feats):
|
||||
"""
|
||||
Loads features from file names
|
||||
"""
|
||||
engine = sql.get_engine( conf.SQL_URI )
|
||||
sql.drop_indices(engine)
|
||||
conn = engine.connect()
|
||||
for label, fname, col_spec in feats:
|
||||
label_id = sql.make_label(engine, name=label, clobber=False)
|
||||
reader = io.NiceReaderWrapper( open(fname,"r"),
|
||||
chrom_col=col_spec.chromCol,
|
||||
start_col=col_spec.startCol,
|
||||
end_col=col_spec.endCol,
|
||||
strand_col=col_spec.strandCol,
|
||||
fix_strand=False )
|
||||
values = list()
|
||||
for interval in reader:
|
||||
print interval
|
||||
if not type( interval ) is io.GenomicInterval: continue
|
||||
row = {'label_id':label_id,
|
||||
'name':col_spec.nameCol == -1 and "%s-%s" % (str(interval.start), str(interval.end)) or interval.fields[col_spec.nameCol],
|
||||
'altname':"",
|
||||
'chrom':interval.chrom,
|
||||
'start':interval.start,
|
||||
'end':interval.end,
|
||||
'strand':interval.strand,
|
||||
'value':0,
|
||||
'freetext':""}
|
||||
values.append(row)
|
||||
insert = sql.feature_table.insert()
|
||||
conn.execute( insert, values)
|
||||
conn.close()
|
||||
sql.create_indices(engine)
|
||||
|
||||
|
||||
class Bunch( object ):
|
||||
def __init__(self, **kwargs):
|
||||
for key,value in kwargs.items():
|
||||
setattr( self, key, value )
|
||||
|
||||
class DummyConf( Bunch ):
|
||||
"""
|
||||
Fake conf module for genetrack/atlas.
|
||||
"""
|
||||
pass
|
||||
|
||||
if __name__ == "__main__":
|
||||
options, args = doc_optparse.parse( __doc__ )
|
||||
try:
|
||||
label = options.label
|
||||
if options.fits:
|
||||
fit_name, fit_meta = options.fits.split(':')[0], [int(x)-1 for x in options.fits.split(':')[1:]]
|
||||
fit_meta = Bunch(chromCol=fit_meta[0], positionCol=fit_meta[1], forwardCol=fit_meta[2], reverseCol=fit_meta[3])
|
||||
fit = ( label, fit_name, fit_meta, )
|
||||
else:
|
||||
fit = []
|
||||
# split apart the string into nested lists, preserves order
|
||||
if options.feats:
|
||||
feats = [ (
|
||||
feat_label,
|
||||
fname,
|
||||
Bunch(chromCol=int(chromCol)-1, startCol=int(startCol)-1, endCol=int(endCol)-1,
|
||||
strandCol=int(strandCol)-1, nameCol=int(nameCol)-1),
|
||||
)
|
||||
for feat_label, fname, chromCol, startCol, endCol, strandCol, nameCol
|
||||
in ( feat.split(':') for feat in options.feats.split(',') if len(feat) > 0 )]
|
||||
else:
|
||||
feats = []
|
||||
data_dir = options.data
|
||||
output = options.output
|
||||
except:
|
||||
doc_optparse.exception()
|
||||
|
||||
main(label, fit, feats, data_dir, output)
|
||||
|
||||
@@ -1,73 +0,0 @@
|
||||
<tool id="genetrack1" name="GeneTrack">
|
||||
|
||||
<description>Track creator/viewer</description>
|
||||
|
||||
<code file="genetrack_code.py">
|
||||
<hook exec_after_process="exec_after_process" />
|
||||
</code>
|
||||
|
||||
<command interpreter="python">
|
||||
genetrack.py -l $data_label
|
||||
#if not str($fit_data) == "None"
|
||||
-1
|
||||
${fit_data}:${fit_data.metadata.chromCol}:${fit_data.metadata.positionCol}:${fit_data.metadata.forwardCol}:${fit_data.metadata.reverseCol}
|
||||
#end if
|
||||
#if $feature_data
|
||||
-2
|
||||
#end if
|
||||
#for $data in $feature_data
|
||||
${data.name}:${data.input}:${data.input.metadata.chromCol}:${data.input.metadata.startCol}:${data.input.metadata.endCol}:${data.input.metadata.strandCol}:${data.input.metadata.nameCol},
|
||||
#end for
|
||||
-d ${genetrack.files_path}
|
||||
-o ${bed_out}
|
||||
</command>
|
||||
|
||||
<inputs>
|
||||
<param name="data_label" type="text" label="Track Label" size="50">
|
||||
<validator type="regex" message="Please name the track with only alphanumeric characters.">[a-zA-Z0-9]{1,25}</validator>
|
||||
</param>
|
||||
<param name="fit_data" type="data" format="coverage" label="Coverage Dataset (optional)" optional="true" />
|
||||
<repeat name="feature_data" title="Features">
|
||||
<param name="input" type="data" format="interval" label="Dataset" />
|
||||
<param name="name" type="text" label="Feature Type (mRNA, ESTs, ORFs, etc.)" size="25">
|
||||
<validator type="regex" message="Please name the feature with only alphanumeric characters.">[a-zA-Z0-9]{1,25}</validator>
|
||||
</param>
|
||||
</repeat>
|
||||
</inputs>
|
||||
|
||||
<outputs>
|
||||
<data format="genetrack" name="genetrack" />
|
||||
<data format="bed" name="bed_out" />
|
||||
</outputs>
|
||||
|
||||
<requirements>
|
||||
<requirement type="python-module">tables</requirement>
|
||||
<requirement type="python-module">atlas</requirement>
|
||||
<requirement type="python-module">pychartdir</requirement>
|
||||
<requirement type="python-module">numpy</requirement>
|
||||
</requirements>
|
||||
<help>
|
||||
This tool takes the input Fit Data and creates a peak and curve plot
|
||||
showing the reads and fitness on each base pair. Features can be
|
||||
plotted below as tracks. Fit data is coverage output from tools like
|
||||
the Lastz tool. Features are simply interval datasets that may be
|
||||
plotted as tracks below the optional fit data. Both the fit data and
|
||||
feature datasets are optional, but at least one of either is required
|
||||
to generate a track.
|
||||
|
||||
-----
|
||||
|
||||
**Syntax**
|
||||
|
||||
- **Track Label** is the name of the generated track.
|
||||
|
||||
- **Fit Data** is the dataset to calculate coverage/reads across
|
||||
base pairs and generate a curve. This is optional, and tracks may
|
||||
be created simply showing features.
|
||||
|
||||
- **Features** are datasets (interval format) to be plotted as tracks.
|
||||
These are also optional, but at least 1 feature track or 1 fit
|
||||
data is required to generate a track.
|
||||
|
||||
</help>
|
||||
</tool>
|
||||
@@ -1,12 +0,0 @@
|
||||
import os
|
||||
from galaxy import eggs
|
||||
from galaxy import jobs
|
||||
from galaxy.tools.parameters import DataToolParameter
|
||||
|
||||
def exec_after_process(app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None):
|
||||
"""
|
||||
Copy data_label to genetrack.metadata.label
|
||||
"""
|
||||
out_data['genetrack'].metadata.label = param_dict['data_label']
|
||||
out_data['genetrack'].info = "Use the link below to view the custom track."
|
||||
out_data['bed_out'].info = ""
|
||||
@@ -0,0 +1,39 @@
|
||||
#!/usr/bin/env python
|
||||
|
||||
"""
|
||||
Wraps genetrack.scripts.tabs2genetrack so the tool can be executed from Galaxy.
|
||||
|
||||
usage: %prog input output shift
|
||||
"""
|
||||
|
||||
import sys
|
||||
from galaxy import eggs
|
||||
import pkg_resources
|
||||
pkg_resources.require( "GeneTrack" )
|
||||
|
||||
from genetrack.scripts import tabs2genetrack
|
||||
from genetrack import logger
|
||||
|
||||
if __name__ == "__main__":
|
||||
|
||||
parser = tabs2genetrack.option_parser()
|
||||
|
||||
options, args = parser.parse_args()
|
||||
|
||||
# uppercase the format
|
||||
options.format = options.format.upper()
|
||||
|
||||
if options.format not in ('BED', 'GFF'):
|
||||
sys.stdout = sys.stderr
|
||||
parser.print_help()
|
||||
sys.exit(-1)
|
||||
|
||||
logger.disable(options.verbosity)
|
||||
|
||||
# missing file names
|
||||
if not (options.inpname and options.outname and options.format):
|
||||
parser.print_help()
|
||||
sys.exit(-1)
|
||||
else:
|
||||
tabs2genetrack.transform(inpname=options.inpname, outname=options.outname,\
|
||||
format=options.format, shift=options.shift, index=options.index)
|
||||
@@ -0,0 +1,54 @@
|
||||
<tool id="bed2genetrack" name="Visualize BED file">
|
||||
|
||||
<description> - creates a visualization from a bed file</description>
|
||||
|
||||
<command interpreter="python">
|
||||
genetrack_indexer.py -i $input -o $output -s $shift -v 0 -f BED -x
|
||||
</command>
|
||||
|
||||
<inputs>
|
||||
|
||||
<param format="bed" name="input" type="data" help="Input data">
|
||||
<label>Select input bed file</label>
|
||||
</param>
|
||||
|
||||
<param name="shift" size="4" type="integer" value="0" help="distance in basepairs">
|
||||
<label>Shift at 5' end</label>
|
||||
</param>
|
||||
|
||||
<!-- this parameter is currently not used, may not be feasible to use it
|
||||
<param name="coverage" type="select" label="Full coverage">
|
||||
<option value="no">NO</option>
|
||||
<option value="yes">YES</option>
|
||||
</param>
|
||||
-->
|
||||
|
||||
</inputs>
|
||||
|
||||
<outputs>
|
||||
<data format="genetrack" name="output" />
|
||||
</outputs>
|
||||
|
||||
<help>
|
||||
**Help**
|
||||
|
||||
This tool will create a visualization of the bed file that is selected.
|
||||
|
||||
**Parameters**
|
||||
|
||||
- **Shift at 5' end** should be used when the location of interest is at a fixed distance from
|
||||
the 5' end for **all sequenced fragments**!
|
||||
|
||||
For example if the sequenced sample consists
|
||||
mono-nucleosomal DNA (146bp) we should expect that
|
||||
each nucleosome midpoint is located at 73 bp from the 5' end of the fragment.
|
||||
Therefore we would enter 73 as the shift parameter. Once corrected the reads
|
||||
on each strand will coincide and indicate the actual midpoints
|
||||
of the nucleosomes.
|
||||
|
||||
When shifting the averaging process in GeneTrack is able correct for longer or shorter
|
||||
than expected fragment sizes as long as the errors are reasonably random.
|
||||
|
||||
</help>
|
||||
|
||||
</tool>
|
||||
@@ -0,0 +1,40 @@
|
||||
#!/usr/bin/env python
|
||||
|
||||
"""
|
||||
Wraps genetrack.scripts.peakpred so the tool can be executed from Galaxy.
|
||||
|
||||
usage: %prog input output level sigma mode exclusion strand
|
||||
"""
|
||||
|
||||
import sys
|
||||
from galaxy import eggs
|
||||
import pkg_resources
|
||||
pkg_resources.require( "GeneTrack" )
|
||||
|
||||
from genetrack.scripts import peakpred
|
||||
from genetrack import logger
|
||||
|
||||
if __name__ == "__main__":
|
||||
|
||||
parser = peakpred.option_parser()
|
||||
|
||||
options, args = parser.parse_args()
|
||||
|
||||
logger.disable(options.verbosity)
|
||||
|
||||
from genetrack import conf
|
||||
|
||||
# trigger test mode
|
||||
if options.test:
|
||||
options.inpname = conf.testdata('test-hdflib-input.gtrack')
|
||||
options.outname = conf.testdata('predictions.bed')
|
||||
|
||||
# missing input file name
|
||||
if not options.inpname and not options.outname:
|
||||
parser.print_help()
|
||||
else:
|
||||
print 'Sigma = %s' % options.sigma
|
||||
print 'Minimum peak = %s' % options.level
|
||||
print 'Peak-to-peak = %s' % options.exclude
|
||||
|
||||
peakpred.predict(options.inpname, options.outname, options)
|
||||
@@ -0,0 +1,59 @@
|
||||
<tool id="predict2genetrack" name="Peak predictor">
|
||||
|
||||
<description> - generates peak predictions from an index file</description>
|
||||
|
||||
<command interpreter="python">
|
||||
genetrack_peak_prediction.py -i $input -o $output --level=$level --sigma=$sigma --mode=$mode --exclusion=$exclusion --strand=$strand -v 0
|
||||
</command>
|
||||
|
||||
<inputs>
|
||||
|
||||
<param format="genetrack" name="input" type="data" help="Input data" label="Select input data"/>
|
||||
|
||||
<param name="method" type="select" label="Smoothing method" help="The function used to average nearby read values">
|
||||
<option value="gauss">Gaussian kernel</option>
|
||||
<!-- <option value="yes">Moving averages</option> -->
|
||||
</param>
|
||||
|
||||
<param name="sigma" size="4" type="integer" value="10" label="Smoothing factor" help="The interval over which each read is averaged" />
|
||||
|
||||
|
||||
<param name="mode" type="select" label="Peak prediction" help="Peak prediction method">
|
||||
<option value="nolap">Maximal non-overlapping</option>
|
||||
<!-- <option value="above">Above a threshold</option> -->
|
||||
<option value="all">All peaks</option>
|
||||
</param>
|
||||
|
||||
<param name="exclusion" type="integer" size="4" value="0" help="The minimal distance between peaks" label="Peak-to-peak distance">
|
||||
</param>
|
||||
|
||||
<param name="level" size="4" type="float" value="1" label="Threshold" help="Return only peaks above this value" />
|
||||
|
||||
<param name="strand" type="select" label="Strands" help="Combine strand data or predict on each strand separately">
|
||||
<option value="all">Merge strands</option>
|
||||
<!-- <option value="yes1">Above a threshold</option> -->
|
||||
<option value="two">Separate strands</option>
|
||||
</param>
|
||||
|
||||
</inputs>
|
||||
|
||||
<outputs>
|
||||
<data format="bed" name="output" />
|
||||
</outputs>
|
||||
|
||||
<help>
|
||||
**Help**
|
||||
|
||||
This tool will generate genome wide peak prediction from an index file.
|
||||
|
||||
**Parameters**
|
||||
|
||||
- **Smoothing method** the function used to average nearby values
|
||||
|
||||
- **Smoothing value** the factor used in the method
|
||||
|
||||
- **Prediction method** the function used to average nearby values
|
||||
|
||||
</help>
|
||||
|
||||
</tool>
|
||||
@@ -93,7 +93,8 @@ use_new_layout = true
|
||||
# Comma separated list of UCSC / gbrowse / GeneTrack browsers to use for viewing
|
||||
ucsc_display_sites = main,test,archaea,ucla
|
||||
gbrowse_display_sites = main,test,tair
|
||||
genetrack_display_sites = main,test
|
||||
# Define your GeneTrack servers in tool-data/shared/genetrack/genetrack_sites.txt
|
||||
#genetrack_display_sites =
|
||||
|
||||
# Serving static files (needed if running standalone)
|
||||
static_enabled = True
|
||||
|
||||
Reference in New Issue
Block a user