/usr/lib/python2.7/dist-packages/cogent/format/motif.py is in python-cogent 1.9-9.
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The actual contents of the file can be viewed below.
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"""Format classes for MotifResults objects."""
from __future__ import division
from matplotlib import use
use('Agg') #suppress graphical rendering
from cogent.motif.util import MotifFormatter
from cogent.format.pdb_color import get_matching_chains,\
align_subject_to_pdb, PYMOL_FUNCTION_STRING, MAIN_FUNCTION_STRING
from cogent.format.rna_struct import color_on_structure, draw_structure
from cogent.format.fasta import fasta_from_alignment
from cogent.core.moltype import PROTEIN, RNA, DNA
from cogent.core.alignment import Alignment,SequenceCollection
from cogent.util.dict2d import Dict2D
from numpy import zeros, nonzero
from cogent.align.weights.util import AlnToProfile
from zipfile import ZipFile
from cogent.app.util import get_tmp_filename
from gzip import GzipFile
from pylab import savefig,clf
__author__ = "Jeremy Widmann"
__copyright__ = "Copyright 2007-2016, The Cogent Project"
__credits__ = ["Jeremy Widmann", "Micah Hamady"]
__license__ = "GPL"
__version__ = "1.9"
__maintainer__ = "Jeremy Widmann"
__email__ = "jeremy.widmann@colorado.edu"
__status__ = "Prototype"
def _format_number(number):
if number is None:
return "None"
return "%.2e" % number
def avg(l):
"""Returns the average of a list of numbers."""
if not l:
return None
return sum(l)/len(l)
class MotifStatsBySequence(MotifFormatter):
"""Generates HTML table with Motifs organized by sequence.
- Each sequence is listed as follows:
Seq-ID Combined-P-Value Motif-ID Motif-P-Value Motif-Seq
"""
def __init__(self,MotifResults=None):
"""init function for MotifStatsBySequence class"""
MotifFormatter.__init__(self)
self.MotifResults = MotifResults
self.ColorMap = self.getColorMap(MotifResults)
def __call__(self,order=None, wrap_html=False, title_class="ntitle",
normal_class="normal", cons_thresh=.9):
"""Call method for MotifStatsBySequence class.
wrap_html: if True, wrap in html + body, else just return table
table_class: css class to use to format table
title_class: css class to use to format titles
normal_class: css class to use to format normal text
cons_thresh: conservation threshold
"""
self.ConservationThresh = cons_thresh
html_list = []
#if MotifResults is not None
if self.MotifResults:
#Find out if the alignment has a combined P value from results
if 'CombinedP' in self.MotifResults.Results:
combined_p_string = 'Combined P-Value'
self.combinedP = True
else:
combined_p_string = ' '
self.combinedP = False
#Start HTML string with table and table headers
html_list = ["""<table cellpadding=2 cellspacing=2 border=0>
<tr class="%s">
<td>Sequence ID</td>
<td>%s</td>
<td>Motif ID</td>
<td>Motif P-Value</td>
<td>Motif Sequence</td>
</tr>""" % ( title_class, combined_p_string)]
#For each sequence in alignment get HTML for that sequence
if not order:
order = sorted(self.MotifResults.Alignment.keys())
for seqID in order:
html_list.append(self.seqLines(seqID, title_class, normal_class))
html_list.append("</table>")
if wrap_html:
return """<html><head><title>Motif Finder Results</title></head><body>%s</table></body></html>""" % ''.join(html_list)
return ''.join(html_list)
return ""
def _get_location_dict(self):
"""Builds dict of all locations.
{module:{seqID:[indices]}}
"""
location_dict = {} #Dict with locations of every motif keyed by module
#Build dict of all the locations:
# {module:{seqID:[indices]}}
if self.MotifResults:
for motif in self.MotifResults.Motifs:
for module in motif.Modules:
location_dict[module]=module.LocationDict
return location_dict
Locations = property(_get_location_dict)
def seqLines(self, seqID, title_class="ntitle", normal_class="normal"):
"""Returns HTML string for single sequence in alignment.
- Must call for each sequence in the alignment.
normal_class: css class to use to format rows
title_class: css class to use to format title cells
"""
#Variable which signifies if given sequence in alignment contains motifs
contains_motifs=False
#Generate first row in table
html_list = ["""<tr bgcolor="eeeeee" class="%s"><td class="%s">%s</td><td colspan=4> </td></tr>"""%(normal_class, title_class, seqID)]
#If there is a combined P for the sequences, put it in first row
if self.combinedP:
try:
html_list = ["""<tr bgcolor="#eeeeee" class="%s">
<td class="%s">%s</td>
<td>%s</td>
<td> </td>
<td> </td>
<td> </td>
</tr>""" % ( normal_class, title_class, seqID,
_format_number(float(
self.MotifResults.Results['CombinedP'][seqID])))]
except KeyError:
pass
#For each module
for module in self.Locations.keys():
cons_seq, cons_con_seq = self._make_conservation_consensus(module)
#Check to see if it appeared in the sequence
if seqID in self.Locations[module]:
contains_motifs=True
for index in self.Locations[module][seqID]:
cur_seq = str(module.NamedSeqs[(seqID,index)])
html_list.append("""<tr class="%s">
<td colspan=2> </td>
<td>%s</td>
<td>%s</td>
<td><span style="%s">%s</span><br>%s</td>
</tr>""" %(normal_class, module.ID,
_format_number(module.Pvalue),
self.ColorMap[module.ID],
cur_seq,
"""<font face="Courier New, Courier, monospace">%s</font>""" % ''.join(
self._flag_conserved_consensus(cons_con_seq, cons_seq, cur_seq))
))
if not contains_motifs:
html_list=[]
return ''.join(html_list)
class MotifLocationsBySequence(MotifFormatter):
"""Generates HTML table with Motifs organized by sequence.
- Each sequence is listed as follows:
Seq-ID #_bases-module_sequence-#_bases-module_sequence-#_bases-etc
"""
def __init__(self,MotifResults=None):
"""init function for MotifLocationsBySequence class"""
MotifFormatter.__init__(self)
self.MotifResults = MotifResults
self.ColorMap = self.getColorMap(MotifResults)
def _get_location_dict(self):
"""Builds dict of all locations.
{seqID:{index:module}}
"""
#Dict with locations of every module keyed by seqID
locations_list = []
module_map = {}
#If MotifResults object exists
if self.MotifResults:
#Build dict of all the locations:
# {seqID:{index:module}}
#For each motif in MotifResults object
for motif in self.MotifResults.Motifs:
#For each module in the Motif
for module in motif.Modules:
#Get the location dict for that module
location_dict = module.LocationDict
#For each sequence the module is in
for seqID in location_dict.keys():
#For each module instance in the sequence
for index in location_dict[seqID]:
#Add module to dict
locations_list.append((seqID,index,module))
module_map[(seqID,index)] = module
locations = Dict2D()
locations.fromIndices(locations_list)
self.ModuleMap = module_map
return locations
Locations = property(_get_location_dict)
def formatLine(self, seqID, max_index_len):
"""Returns motif line """
#Variable which signifies if given sequence in alignment contains motifs
contains_motifs=False
#List of strings for sequence line
seq_line_list = []
#Get all indices for the sequence
indices = []
if seqID in self.Locations:
indices = self.Locations[seqID].keys()
contains_motifs=True
indices.sort()
#Current position in sequence
pos=0
#For each index in sequence
fmt_str = "%0" + max_index_len + "d"
for index in indices:
#Add distance between motifs or ends of sequence to list if > 0
seq_line_list.append(fmt_str % (index-pos))
#Add module instance sequence to list
mod_id = self.ModuleMap[(seqID, index)].ID
seq_line_list.append( """<span style="%s" onmouseover="return overlib('Motif ID: %s');" onmouseout="return nd();">%s</span>""" % \
(self.ColorMap[mod_id], mod_id,\
self.Locations[seqID][index].NamedSeqs[(seqID,index)].Sequence))
#Find new position in sequence
pos = \
self.Locations[seqID][index].NamedSeqs[(seqID,index)].Location.End
#Add distance from end of last module to end of sequence to list if > 0
if len(self.MotifResults.Alignment.NamedSeqs[seqID])-pos > 0:
seq_line_list.append(\
str(len(self.MotifResults.Alignment.NamedSeqs[seqID])\
-pos))
return '-'.join(seq_line_list), contains_motifs
def seqLines(self, seqID, max_index_len, title_class="ntitle", normal_class="normal"):
"""Returns HTML string for single sequence in alignment.
- Must call for each sequence in the alignment.
title_class: css class to use to format title
normal_class: css class to use to format text
"""
seq_line_list, contains_motifs = self.formatLine(seqID, max_index_len)
if contains_motifs:
#Return sequence string
return """<tr class="%s">
<td class="%s">%s</td>
<td>%s</td></tr>"""%( normal_class, title_class,
seqID, seq_line_list)
else:
return ''
def __call__(self, order=None, wrap_html=False, title_class="ntitle",
normal_class="normal"):
"""Call method for MotifLocationsBySequence class.
- must pass in an alignment order
"""
html_list = []
# need to calculate this acrosss all
all_indicies = []
for locs in self.Locations.values():
all_indicies.extend(locs.keys())
max_index_len = str(len(str(max(all_indicies))))
#If MotifResults is not None
if self.MotifResults:
#For each sequence in alignment get HTML for that sequence
html_list.append("""<tr class="%s"><td>Sequence ID</td><td>Motif Locations</td></tr>""" % title_class)
if not order:
order=sorted(self.Locations.keys())
for seqID in order:
html_list.append(self.seqLines(seqID, max_index_len, title_class, normal_class))
out_str = "<table cellpadding=2 cellspacing=2 border=0>%s</table>" % ''.join(html_list)
if wrap_html:
return """<html><head><title>Motif Finder Results</title></head><body>%s</body></html>""" % out_str
return out_str
return ""
class SequenceByMotif(MotifFormatter):
"""Generates HTML table with sequences organized by Motif. """
def __init__(self,MotifResults=None):
"""init function for MotifLocationsBySequence class"""
MotifFormatter.__init__(self)
self.MotifResults = MotifResults
self.ColorMap = self.getColorMap(MotifResults)
def _get_location_dict(self):
"""Build dict of all the locations:
{module:{seqID:[indices]}}
"""
location_dict = {} #Dict with locations of every motif keyed by module
if self.MotifResults:
for motif in self.MotifResults.Motifs:
for module in motif.Modules:
location_dict[module]=module.LocationDict
return location_dict
Locations = property(_get_location_dict)
def __call__(self, wrap_html=False, title_class="ntitle",
normal_class="normal", cons_thresh=.9):
"""Call method for SequenceByMotif class. """
#Start HTML string with table and table headers
html_list = []
#Get modules
modules = self.Locations.keys()
modules.sort()
self.ConservationThresh = cons_thresh
#For each module
for module in modules:
html_list.append(self.moduleLines(module, title_class, normal_class))
out_str = """<table cellpadding=2 cellspacing=2 border=0>
<tr class="%s"><td>Motif ID</td><td>Combined P-Value</td>
<td>Sequence ID</td>
<td>Motif Sequence</td>
</tr>
%s
</table>""" % (title_class, ''.join(html_list))
if html_list:
if wrap_html:
return"""<html><head><title>Motif Finder Results</title></head><body>%s</body></html>""" % out_str
else:
return out_str
return ""
def _highlightConsensus(self, con_seq, cons_con_seq, cur_seq, cur_color):
"""
Hightlight positions identical to consensus
"""
grey_style = """background-color: #dddddd; font-family: 'Courier New', Courier"""
span_fmt = """<span style="%s">%s</span>"""
h_str = []
for ix in range(len(cur_seq)):
cur_c = cur_seq[ix]
if cur_c == cons_con_seq[ix]:
h_str.append(span_fmt % (cur_color,cur_c))
elif cur_c == con_seq[ix]:
h_str.append(span_fmt % (grey_style,cur_c))
else:
h_str.append(cur_c)
return ''.join(h_str)
def moduleLines(self, module, title_class="ntitle", normal_class="normal"):
"""Returns HTML string for single module.
- Must call for each module.
"""
cons_seq, cons_con_seq = self._make_conservation_consensus(module)
cur_color = self.ColorMap[module.ID]
#Generate first row in table
html_list = ['<tr bgcolor="#eeeeee" class="%s"><td class="%s">%s</td><td>%s</td><td> </td><td><span style="%s">%s</span></td></tr>'%\
(normal_class, title_class,
module.ID,
_format_number(module.Pvalue),
cur_color,
cons_seq,
)]
sequences = self.Locations[module].keys()
sequences.sort()
#For each sequence
for seq in sequences:
cur_seq = str(module.NamedSeqs[(seq,self.Locations[module][seq][0])] )
html_list.append("""<tr class="%s">
<td> </td>
<td> </td>
<td class="%s">%s</td>
<td style="font-family: 'Courier New', Courier, monospace">%s</td>
</tr>""" % (normal_class, title_class,
seq,
#_format_number(module.Pvalue),
self._highlightConsensus(cons_seq, cons_con_seq, cur_seq, cur_color)
))
return ''.join(html_list)
class HighlightMotifs(MotifFormatter):
"""Generates HTML table with sequences highlighted """
def makeModuleMap(self, motif_results):
"""
Need to extract this b/c can't pickle motif_results... grr.
motif_results: MotifResults object
keep_module_ids: list of module ids to keep
"""
module_map = {} #Dict with locations of every motif keyed by module
if motif_results:
for motif in motif_results.Motifs:
for module in motif.Modules:
mod_len = len(module)
mod_id = str(module.ID)
for skey, indexes in module.LocationDict.items():
if skey not in module_map:
module_map[skey] = []
for ix in indexes:
module_map[skey].append((ix, mod_id, mod_len))
return module_map
def __init__(self, MotifResults, NodeOrder=None, KeepIds=None,\
KeepAll=False, MolType=PROTEIN):
"""Set up color map and motif results
ModuleMap: flattened map (b/c of pickle problem.)
generate using make_module_map() function
Alignment: SequenceCollection or Alignment object
KeepIds: list of module ids to keep
KeepAll: When True, ignores KeepIds and highlights all motifs
"""
MotifFormatter.__init__(self)
ModuleMap = self.makeModuleMap(MotifResults)
module_ids = set([])
for skey, slist in ModuleMap.items():
for stup in slist:
module_ids.add(stup[1])
self.ColorMap = self.getColorMapS0(sorted(list(module_ids)))
self.ModuleMap = ModuleMap
self.Alignment = MotifResults.Alignment
if KeepIds is None:
KeepIds = []
self.KeepIds = set(KeepIds)
self.KeepAll = KeepAll
if not NodeOrder:
NodeOrder=self.Alignment.Names
self.NodeOrder = NodeOrder
self.MolType = MolType
self.GapMap = self.getGapMap()
self.HighlightMap = {}
def __call__(self, title_class="ntitle", normal_class="normal", row_class="highlight", table_style=''):
"""Call method for HightlightMotifs class. """
#Start HTML string with table and table headers
html_list = []
#For each module
for seq_id in self.NodeOrder:
html_list.append(self.highlightSeq(seq_id, title_class, row_class))
out_str = """<table cellpadding=2 cellspacing=2 border=0 %s>
<tr class="ntitle">
<td colspan=2><p>Selected Motifs Highlighted on Sequences:</p> </td>
</tr>
<tr class="%s"><td nowrap>Sequence ID</td>
<td>Sequence</td>
</tr>
%s
</table>""" % (table_style, title_class, ''.join(html_list))
if html_list:
return out_str
return ""
def getGapMap(self):
"""Returns dict mapping gapped_coord to ungapped_coord in self.Alignment
- {seq_id:{gapped_coord:ungapped_coord}}
"""
gap_map = {}
for k,v in self.Alignment.items():
gapped, ungapped = self.MolType.gapMaps(v)
gap_map[k] = gapped
return gap_map
def highlightSeq(self, seq_id, title_class="ntitle", row_class="highlight"):
"""Returns HTML string for single sequence.
seq_id: sequence_id to highlight
"""
#Generate first row in table
row_tmpl = """<tr class="%s">
<td class="%s">%s</td>
<td>%s</td>
</tr>"""
mo_span_tmpl = """<span style="%s" onmouseover="return overlib('%s');" onmouseout="return nd();">%s</span>"""
seq_list = list(self.Alignment.NamedSeqs[seq_id])
seq_len = len(seq_list)
seq_mask = zeros(seq_len)
mod_id_map = {}
if seq_id in self.ModuleMap:
for mod_tup in self.ModuleMap[seq_id]:
ix, mod_id, mod_len = mod_tup
# skip modules we con't care about
if not self.KeepAll and mod_id not in self.KeepIds:
continue
mod_mask = zeros(seq_len)
# mask motif region
for i in range(ix,ix+mod_len):
gapped_ix = self.GapMap[seq_id][i]
mod_mask[gapped_ix] = 1
# add to sequence map
seq_mask += mod_mask
# map module ids to indexes
for jx in range(ix,ix+mod_len):
gapped_jx = self.GapMap[seq_id][jx]
if gapped_jx not in mod_id_map:
mod_id_map[gapped_jx] = []
mod_id_map[gapped_jx].append(mod_id)
# get module regions
#need to take [0] element of nonzero() since numpy returns a tuple
# where Numeric did not
for jx in nonzero(seq_mask)[0]:
# if overlapping use red background, otherwise display color
if seq_mask[jx] > 1:
style = "background-color: red"
else:
#style = self.ColorMap[mod_id_map[jx][0]].replace("font-family: 'Courier New', Courier, monospace", "")
style = self.ColorMap[mod_id_map[jx][0]]
seq_list[jx] = mo_span_tmpl % (style,
"<br>".join(['Motif ID: %s' % \
x for x in mod_id_map[jx]]),
seq_list[jx])
# cache data
self.HighlightMap[seq_id] = ''.join(seq_list)
# return row output
return row_tmpl % (row_class, title_class, seq_id, ''.join(seq_list))
class HighlightMotifsForm(MotifFormatter):
"""Generates HTML form to submit module ids """
def __init__(self,
MotifResults,
FormAction="/cgi-bin/motifcluster/highlight.py",
FormTarget="_blank"):
"""Set up color map and motif results
MotifResults: MotifResults object
ModuleIds: List of module ids to highlight
FormAction: Form action cgi-script
FormTarget: Form target
"""
MotifFormatter.__init__(self)
self.MotifResults = MotifResults
self.ColorMap = self.getColorMap(MotifResults)
self.Modules= self._get_modules()
self.FormAction = FormAction
self.FormTarget = FormTarget
def _get_modules(self):
"""Build map of modules
{seq_id:[(ix, module_id, module_len)]
"""
modules = []
if self.MotifResults:
for motif in self.MotifResults.Motifs:
for module in motif.Modules:
modules.append(module)
return modules
def __call__(self, title_class="ntitle", normal_class="normal", highlight_class="highlight"):
"""Call method for HightlightMotifs class. """
#Start HTML string with table and table headers
cells = []
# format cells
for module in self.Modules:
cur_tup = (module.Pvalue, len(module.LocationDict),
self.moduleRow(module))
cells.append(cur_tup)
# sort by p value, then frequency
cells = [x[-1] for x in sorted(cells)]
cur_cells = []
header_tmpl = """<td bgcolor=ffffff> </td><td>ID</td> <td>Motif</td> <td>Fequency</td> <td>P-Value</td>"""
header_cells = []
num_headers = len(cells)
if num_headers > 3:
num_headers = 3
for i in range(num_headers):
header_cells.append(header_tmpl)
header_row = """<tr bgcolor=eeeeee class="%s">%s</tr>""" % (title_class, ''.join(header_cells))
html_out = []
html_out.append("""<tr class="%s">""" % highlight_class)
for ix, cell in enumerate(cells):
if ix % 3 == 0:
if cur_cells:
html_out.append("""%s</tr><tr class="%s">""" % (''.join(cur_cells), highlight_class))
cur_cells = []
cur_cells.append(cell)
else:
cur_cells.append(cell)
html_out.append("%s</tr>" % ''.join(cur_cells))
out_str = """
<form action="%s" method="POST" target="%s">
<table cellpadding=2 cellspacing=2 border=0>
%s
%s
</table>
<p>
<input type="Submit" value="Highlight Selected Motifs" />
</p>
</form>
""" % (self.FormAction, self.FormTarget,
header_row, ''.join(html_out))
if cells:
return out_str
return ""
def moduleRow(self, module):
"""Returns HTML string for single module.
module: module to generate
"""
#Generate first row in table
cells_tmpl = """<td bgcolor=dddddd><input type="checkbox" name="module_ids" value="%s" checked /></td><td>%s</td><td ><span style="%s">%s</span></td><td>%d</td><td>%s</td>"""
# return row output
return cells_tmpl % (module.ID,
module.ID,
self.ColorMap[module.ID],
str(module),
#module.ConsensusSequence,
len(module.LocationDict),
_format_number(module.Pvalue))
class HighlightOnCrystal(MotifFormatter):
"""Generates pymol script to highlight motifs on crystal structure.
"""
def __init__(self, MotifResults=None, cons_thresh=0.9, MolType=PROTEIN):
"""init function for HighlightOnAlignment class.
MotifResults: motif results object
"""
MotifFormatter.__init__(self)
self.ConservationThresh = float(cons_thresh)
ModuleMap, ModuleConsMap = self.makeModuleMap(MotifResults)
module_ids = set([])
for skey, slist in ModuleMap.items():
for stup in slist:
module_ids.add(stup[1])
self.ColorMapHex = self.getColorMapS0(sorted(list(module_ids)))
self.ModuleMap = ModuleMap
self.ModuleConsMap = ModuleConsMap
self.MotifResults = MotifResults
self.ColorMap = self.getColorMapRgb(MotifResults)
self.GapMap = {}
self.HighlightMap = {}
self.MolType=MolType
self.RunScriptString = \
'''
from pymol import cmd
cmd.load("%s")
cmd.do("run %s")
'''
self.ColorFunctionString = \
'''
color_map = %s
color_command_list = %s
sticks_command_list = %s
#Set color list using color_map
set_color_list(list(color_map.items()))
#Set seq colors
for color_cmd in color_command_list:
colors,indices,chain_id = color_cmd
set_seq_colors(colors,indices,chain_id)
#Set sticks
for sticks_cmd in sticks_command_list:
indices,chain_id = sticks_cmd
set_show_shapes(indices,chain_id)
'''
def __call__(self,seq_id,pdb_id,\
sequence_type='Protein',\
zipfile_dir='.',
pdb_dir='/quicksand2/hamady/data/cron_sync/pdb/'):
"""call method for HighlightOnCrystal class.
Generates pymol script for highlighting motifs on crystal structure and
creates .zip archive with pdb file and pymol script.
"""
#Get PDB file
curr_pdb = \
[x.rstrip("\n") for x in self.getPdb(pdb_id,pdb_dir).readlines()]
#Get subject sequence
subject_seq = self.MotifResults.Alignment.NamedSeqs[seq_id]
#Get PDB chains
pdb_matching, ungapped_to_pdb = \
get_matching_chains(subject_seq,curr_pdb,sequence_type)
pdb_aligned = align_subject_to_pdb(subject_seq,pdb_matching)
#get color command list
color_command_list, found_seq_motifs, missed_seq_motifs = \
self.makeColorCommandLists(seq_id,pdb_aligned,ungapped_to_pdb)
#get sticks command list
sticks_command_list = \
self.makeSticksCommandsConservedPositions(seq_id, pdb_aligned,\
ungapped_to_pdb)
#Generate pdb file
pdb_out = pdb_id+'.pdb'
#Generate pymol script
pymol_script_list = [PYMOL_FUNCTION_STRING,MAIN_FUNCTION_STRING]
pymol_script_list.append(self.ColorFunctionString % (self.ColorMap,\
color_command_list,sticks_command_list))
pymol_script_string = ''.join(pymol_script_list)
pymol_script_name = '%s_motif_coloring.pml' % (pdb_id)
pymol_execute_name = '%s_double_click_me.pml' % (pdb_id)
pymol_execute_string = \
self.RunScriptString % (pdb_out,pymol_script_name)
#Generate zip file
output_pre = get_tmp_filename(zipfile_dir, prefix="pdb_%s_" % pdb_id)
if output_pre.endswith(".txt"):
output_pre = output_pre[:-4]
zip_dir = output_pre.split("/")[-1]
output_filename = output_pre + ".zip"
web_name = output_filename.split("/")[-1]
curr_zip = ZipFile(output_filename,'w')
curr_zip.writestr(zip_dir + "/" + pymol_script_name,pymol_script_string)
curr_zip.writestr(zip_dir + "/" + pdb_out,'\n'.join(curr_pdb))
curr_zip.writestr(zip_dir + "/" + pymol_execute_name,pymol_execute_string)
curr_zip.close()
alignment_html = {}
for k,v in pdb_aligned.items():
alignment_html[k]=self.highlightSeq(seq_id,v[0],pdb_id,v[1])
#set up return dictionary
return_dir = { "output_filename":output_filename,
"web_name":web_name,
"colored_alignment":alignment_html,
#"found_seq_motifs":found_seq_motifs,
"found_seq_motifs":[(module.ID, _format_number(module.Pvalue)) for module in self.MotifResults.Modules if module.ID in found_seq_motifs],
"missed_seq_motifs":missed_seq_motifs,
"all_motifs":[(module.ID, _format_number(module.Pvalue)) for module in self.MotifResults.Modules],
"all_motif_colors":self.ColorMapHex}
return return_dir
def getConservedPositions(self,min_conservation=1.0):
"""Returns dict mapping motif id to list of conserved positions.
"""
conserved_positions = {}
for motif in self.MotifResults.Motifs:
for module in motif.Modules:
curr_id = module.ID
conserved_positions[curr_id]=[]
curr_profile = AlnToProfile(module,self.MotifResults.MolType)
for ix,pos in enumerate(curr_profile.rowMax()):
if pos >= min_conservation:
conserved_positions[curr_id].append(ix)
return conserved_positions
def makeColorCommandLists(self,seq_id, pdb_aligned, ungapped_to_pdb):
"""Returns lists of (colors, indices, and chain_id) for coloring.
- each chain is a separate tuple in the list.
- colors are named by motif id
"""
#list of motifs found in pdb sequence
found_seq_motifs = []
#list of motifs not in pdb sequence
missed_seq_motifs = []
color_command_list = []
#Get locations by sequence
locations = \
MotifLocationsBySequence(self.MotifResults).Locations[seq_id]
for chain, aligned in pdb_aligned.items():
#Get subject gap map
subject_gapped,subject_ungapped = \
self.MotifResults.MolType.gapMaps(aligned[0])
#Get pdb gap map
pdb_gapped,pdb_ungapped = \
self.MotifResults.MolType.gapMaps(aligned[1])
for curr_ix, curr_module in locations.items():
curr_module_len = len(str(curr_module))
curr_module_id = curr_module.ID
#curr_color = self.ColorMap[curr_module_id]
curr_color = "color_" + str(curr_module_id)
#get index list
ix_list = []
#for each position in motif
for i in range(curr_ix,curr_ix+curr_module_len):
#Get the gapped index of the motif in the subject seq
try:
sub_gap = subject_gapped[i]
except KeyError:
continue
#Get the ungapped index of the motif in the pdb seq
try:
pdb_ungap = pdb_ungapped[sub_gap]
#Get the index of the position in pdb coordinates
pdb_ix = ungapped_to_pdb[chain][pdb_ungap]
ix_list.append(pdb_ix)
except KeyError:
continue
if ix_list:
ix_string = '+'.join(map(str,ix_list))
color_command_list.append(([curr_color],[ix_string],chain))
found_seq_motifs.append(curr_module_id)
else:
missed_seq_motifs.append(curr_module_id)
return color_command_list, found_seq_motifs, missed_seq_motifs
def makeSticksCommandsConservedPositions(self,seq_id, pdb_aligned,\
ungapped_to_pdb, min_conservation=1.0):
"""Returns list of (indices, chain_id) to show sticks at indices.
- each chain is a separate tuple in the list.
"""
conserved_positions = self.getConservedPositions()
show_command_list = []
#Get locations by sequence
locations = \
MotifLocationsBySequence(self.MotifResults).Locations[seq_id]
for chain, aligned in pdb_aligned.items():
#Get subject gap map
subject_gapped,subject_ungapped = \
self.MotifResults.MolType.gapMaps(aligned[0])
#Get pdb gap map
pdb_gapped,pdb_ungapped = \
self.MotifResults.MolType.gapMaps(aligned[1])
for curr_ix, curr_module in locations.items():
curr_module_id = curr_module.ID
curr_module_conserved = conserved_positions[curr_module_id]
#get index list
ix_list = []
#for each position in motif
for i in curr_module_conserved:
#Get the gapped index of the motif in the subject seq
try:
sub_gap = subject_ungapped[i]
except KeyError:
continue
#Get the ungapped index of the motif in the pdb seq
try:
pdb_ungap = pdb_gapped[sub_gap]
#Get the index of the position in pdb coordinates
pdb_ix = ungapped_to_pdb[pdb_ungap]
ix_list.append(pdb_ix)
except KeyError:
continue
if ix_list:
show_command_list.append((ix_list,chain))
return show_command_list
def getPdb(self,pdb_id, pdb_dir):
"""Returns open pdb file.
- currently gets pdb file from pdb website.
"""
pdb_file = pdb_dir + "pdb%s.ent" % pdb_id.lower()
of = None
try:
of = open(pdb_file)
except Exception, e:
of = GzipFile(pdb_file + ".gz")
return of
def getGapMap(self,seq_id,gapped_seq):
"""Returns dict mapping gapped_coord to ungapped_coord in self.Alignment
- {seq_id:{gapped_coord:ungapped_coord}}
"""
gap_map = {}
gapped, ungapped = self.MolType.gapMaps(gapped_seq)
gap_map[seq_id] = gapped
return gap_map
def highlightSeq(self, seq_id, seq_aligned, pdb_id, pdb_aligned,\
title_class="ntitle", row_class="highlight"):
"""Returns HTML string for single sequence.
seq_id: sequence_id to highlight
"""
#Generate first row in table
seq_row_tmpl = """<tr class="%s">
<td class="%s">%s</td>
<td>%s</td>
</tr>"""
mo_span_tmpl = """<span style="%s" onmouseover="return overlib('%s');" onmouseout="return nd();">%s</span>"""
seq_list = list(seq_aligned)
pdb_list = list(pdb_aligned)
seq_len = len(seq_list)
seq_mask = zeros(seq_len)
#pdb sequence mask
pdb_mask = zeros(seq_len)
mod_id_map = {}
self.GapMap = self.getGapMap(seq_id,seq_aligned)
cons_str = list(" " * len(seq_list))
if seq_id in self.ModuleMap:
for mod_tup in self.ModuleMap[seq_id]:
ix, mod_id, mod_len = mod_tup
cons_seq, cons_con_seq = self.ModuleConsMap[mod_id]
cur_seq = ''.join(seq_list[ix:ix+mod_len])
cc_str = self._flag_conserved_consensus(cons_con_seq, cons_seq, cur_seq)
cons_str[ix:ix+mod_len] = cc_str
mod_mask = zeros(seq_len)
#pdb module mask
pdb_mod_mask = zeros(seq_len)
# mask motif region
for i in range(ix,ix+mod_len):
gapped_ix = self.GapMap[seq_id][i]
mod_mask[gapped_ix] = 1
#only allow coloring of ungapped pdb sequence
if pdb_list[gapped_ix] != '-':
pdb_mod_mask[gapped_ix]=1
# add to sequence map
seq_mask += mod_mask
pdb_mask += pdb_mod_mask
# map module ids to indexes
for jx in range(ix,ix+mod_len):
gapped_jx = self.GapMap[seq_id][jx]
if gapped_jx not in mod_id_map:
mod_id_map[gapped_jx] = []
mod_id_map[gapped_jx].append(mod_id)
mm_str = []
for ix in range(len(seq_list)):
if seq_list[ix] == pdb_list[ix]:
mm_str.append("|")
else:
mm_str.append("*")
# get module regions
for jx in nonzero(seq_mask)[0]:
# if overlapping use red background, otherwise display color
if seq_mask[jx] > 1:
style = "background-color: red"
else:
style = self.ColorMapHex[mod_id_map[jx][0]].replace("font-family: 'Courier New', Courier, monospace", "")
seq_list[jx] = mo_span_tmpl % (style,
"<br>".join(['Motif ID: %s' % \
x for x in mod_id_map[jx]]),
seq_list[jx])
pdb_list[jx] = mo_span_tmpl % (style,
"<br>".join(['Motif ID: %s' % \
x for x in mod_id_map[jx]]),
pdb_list[jx])
clean_cons_str = []
for item in cons_str:
if item == " ":
clean_cons_str.append(" ")
else:
clean_cons_str.append(item)
cons_str = ''.join(clean_cons_str)
# cache data
self.HighlightMap[seq_id] = ''.join(seq_list)
# return row output
seq_row = seq_row_tmpl % (row_class, title_class, seq_id, ''.join(seq_list))
pdb_row = seq_row_tmpl % (row_class, title_class, pdb_id, ''.join(pdb_list))
high_row = seq_row_tmpl % (row_class, title_class, "Cons", ''.join(cons_str))
mm_row = seq_row_tmpl % (row_class, title_class, "Mismatch", ''.join(mm_str))
return ''.join(['<table>',high_row,seq_row,mm_row, pdb_row,'</table>'])
def makeModuleMap(self, motif_results):
"""
Need to extract this b/c can't pickle motif_results... grr.
motif_results: MotifResults object
keep_module_ids: list of module ids to keep
"""
module_map = {} #Dict with locations of every motif keyed by module
module_cons_map = {}
if motif_results:
for motif in motif_results.Motifs:
for module in motif.Modules:
mod_id = str(module.ID)
mod_len = len(str(module))
if mod_id not in module_cons_map:
module_cons_map[mod_id] = self._make_conservation_consensus(module)
for skey, indexes in module.LocationDict.items():
if skey not in module_map:
module_map[skey] = []
for ix in indexes:
module_map[skey].append((ix, mod_id, mod_len))
return module_map, module_cons_map
class ColorSecondaryStructurePostscript(MotifFormatter):
"""Generates postscript file with motifs highlighted on 2D structure """
def makeModuleMap(self, motif_results):
"""
Need to extract this b/c can't pickle motif_results... grr.
motif_results: MotifResults object
keep_module_ids: list of module ids to keep
"""
module_map = {} #Dict with locations of every motif keyed by module
if motif_results:
for motif in motif_results.Motifs:
for module in motif.Modules:
mod_len = len(module)
mod_id = str(module.ID)
for skey, indexes in module.LocationDict.items():
if skey not in module_map:
module_map[skey] = []
for ix in indexes:
module_map[skey].append((ix, mod_id, mod_len))
return module_map
def __init__(self, MotifResults, KeepIds=None,\
KeepAll=True, MolType=RNA, strict=True,circle_motif_id=None,\
SkipIds=None):
"""Set up color map and motif results
ModuleMap: flattened map (b/c of pickle problem.)
generate using make_module_map() function
Alignment: SequenceCollection or Alignment object
KeepIds: list of module ids to keep
KeepAll: When True, ignores KeepIds and highlights all motifs
"""
MotifFormatter.__init__(self)
self.ModuleMap = self.makeModuleMap(MotifResults)
module_ids = set([])
for skey, slist in self.ModuleMap.items():
for stup in slist:
module_ids.add(stup[1])
self.ColorMap = self.getColorMapRgb(MotifResults)
overlap_color = {'overlap_color':(1.0,0.0,0.0)}
self.ColorMap.update(overlap_color)
self.Alignment = MotifResults.Alignment
if KeepIds is None:
KeepIds = []
self.KeepIds = set(KeepIds)
self.KeepAll = KeepAll
self.MolType = MolType
self.GapMap = self.getGapMap()
self.HighlightMap = {}
self.Strict=strict
self.CircleId = circle_motif_id
self.SkipIds=SkipIds
def __call__(self,seq_id,sequence,struct,write_dir='.'):
"""Call method for ColorSecondaryStructure class. """
indices, colors = self.getColorIndices(seq_id,sequence)
circle_indices = []
if self.CircleId:
circle_indices = \
self.getCircleIndices(seq_id,sequence,self.CircleId)
structure_postscript = color_on_structure(\
sequence=sequence,\
struct=struct,\
color_map = self.ColorMap,\
indices=indices,\
colors=colors,\
circle_indices=circle_indices)
file_id = seq_id.split()[0]
ps_out_path = \
write_dir+'/'+file_id+'_secondary_struct.ps'
ps_out = open(ps_out_path,'w')
ps_out.write(structure_postscript)
ps_out.close()
return ps_out_path
def getGapMap(self):
"""Returns dict mapping gapped_coord to ungapped_coord in self.Alignment
- {seq_id:{gapped_coord:ungapped_coord}}
"""
gap_map = {}
for k,v in self.Alignment.items():
gapped, ungapped = self.MolType.gapMaps(v)
gap_map[k] = gapped
return gap_map
def getColorIndices(self, seq_id, sequence):
"""Returns list of indices and colors for a given sequence.
seq_id: sequence ID to highlight on structure
"""
#seq_list = list(self.Alignment.NamedSeqs[seq_id])
seq_list = list(sequence)
seq_len = len(seq_list)
seq_mask = zeros(seq_len)
mod_id_map = {}
indices = []
colors = []
gapped,ungapped = self.MolType.gapMaps(sequence)
self.GapMap[seq_id]= gapped
if self.Strict:
if seq_id not in self.ModuleMap:
raise IndexError, 'seq_id %s not in ModuleMap'%(seq_id)
else:
if seq_id not in self.ModuleMap:
return [],[]
for mod_tup in self.ModuleMap[seq_id]:
ix, mod_id, mod_len = mod_tup
# skip modules we con't care about
if not self.KeepAll and mod_id not in self.KeepIds:
continue
elif mod_id in self.SkipIds:
continue
mod_mask = zeros(seq_len)
# mask motif region
for i in range(ix,ix+mod_len):
gapped_ix = self.GapMap[seq_id][i]
mod_mask[gapped_ix] = 1
# add to sequence map
seq_mask += mod_mask
# map module ids to indexes
for jx in range(ix,ix+mod_len):
gapped_jx = self.GapMap[seq_id][jx]
if gapped_jx not in mod_id_map:
mod_id_map[gapped_jx] = []
mod_id_map[gapped_jx].append(mod_id)
# get module regions
#need to take [0] element of nonzero() since numpy returns a tuple
# where Numeric did not
for kx in nonzero(seq_mask)[0]:
# if overlapping use red background, otherwise display color
if seq_mask[kx] > 1:
curr_color = 'overlap_color'
else:
mod_id = mod_id_map[kx][0]
curr_color = 'color_'+mod_id
#append indices. Must start at 1, not 0 for RNAplot to work
indices.append(kx+1)
colors.append(curr_color)
return indices, colors
def getCircleIndices(self, seq_id, sequence, motif_id):
"""Returns list of indices to be circled for a given sequence.
seq_id: sequence ID to highlight on structure
sequence: sequence string
motif_id: ID of motif to circle.
"""
seq_list = list(sequence)
seq_len = len(seq_list)
seq_mask = zeros(seq_len)
mod_id_map = {}
indices = []
gapped,ungapped = self.MolType.gapMaps(sequence)
self.GapMap[seq_id]= gapped
if self.Strict:
if seq_id not in self.ModuleMap:
raise IndexError, 'seq_id %s not in ModuleMap'%(seq_id)
else:
if seq_id not in self.ModuleMap:
return [],[]
for mod_tup in self.ModuleMap[seq_id]:
ix, mod_id, mod_len = mod_tup
if mod_id != motif_id:
continue
# skip modules we con't care about
if not self.KeepAll and mod_id not in self.KeepIds:
continue
mod_mask = zeros(seq_len)
# mask motif region
for i in range(ix,ix+mod_len):
gapped_ix = self.GapMap[seq_id][i]
mod_mask[gapped_ix] = 1
# add to sequence map
seq_mask += mod_mask
# map module ids to indexes
for jx in range(ix,ix+mod_len):
gapped_jx = self.GapMap[seq_id][jx]
if gapped_jx not in mod_id_map:
mod_id_map[gapped_jx] = []
mod_id_map[gapped_jx].append(mod_id)
# get module regions
#need to take [0] element of nonzero() since numpy returns a tuple
# where Numeric did not
for kx in nonzero(seq_mask)[0]:
#append indices. Must start at 1, not 0 for RNAplot to work
indices.append(kx+1)
return indices
class ColorSecondaryStructureMatplotlib(MotifFormatter):
"""Generates png file with motifs highlighted on 2D structure """
def makeModuleMap(self, motif_results):
"""
Need to extract this b/c can't pickle motif_results... grr.
motif_results: MotifResults object
keep_module_ids: list of module ids to keep
"""
module_map = {} #Dict with locations of every motif keyed by module
if motif_results:
for motif in motif_results.Motifs:
for module in motif.Modules:
mod_len = len(module)
mod_id = str(module.ID)
for skey, indexes in module.LocationDict.items():
if skey not in module_map:
module_map[skey] = []
for ix in indexes:
module_map[skey].append((ix, mod_id, mod_len))
return module_map
def __init__(self, MotifResults, KeepIds=None,\
KeepAll=True, MolType=RNA, strict=True,circle_motif_id=None,\
SkipIds=None,square_motif_id=None,square_label=None):
"""Set up color map and motif results
ModuleMap: flattened map (b/c of pickle problem.)
generate using make_module_map() function
Alignment: SequenceCollection or Alignment object
KeepIds: list of module ids to keep
KeepAll: When True, ignores KeepIds and highlights all motifs
"""
MotifFormatter.__init__(self)
self.ModuleMap = self.makeModuleMap(MotifResults)
module_ids = set([])
for skey, slist in self.ModuleMap.items():
for stup in slist:
module_ids.add(stup[1])
self.ColorMap = self.getColorMapRgb(MotifResults)
overlap_color = {'overlap_color':(1.0,0.0,0.0)}
self.ColorMap.update(overlap_color)
self.Alignment = MotifResults.Alignment
if KeepIds is None:
KeepIds = []
self.KeepIds = set(KeepIds)
self.KeepAll = KeepAll
self.MolType = MolType
self.GapMap = self.getGapMap()
self.HighlightMap = {}
self.Strict=strict
self.CircleId = circle_motif_id
self.SquareId = square_motif_id
self.SquareLabel = square_label
self.SkipIds=SkipIds
def __call__(self,seq_id,sequence,struct,write_dir='.'):
"""Call method for ColorSecondaryStructure class. """
indices, colors = self.getColorIndices(seq_id,sequence)
circle_indices = []
if self.CircleId:
circle_indices = \
self.getMarkedIndices(seq_id,sequence,self.CircleId)
square_indices = []
if self.SquareId:
square_indices = \
self.getMarkedIndices(seq_id,sequence,self.SquareId)
if self.SquareLabel is None:
self.SquareLabel = ''
draw_structure(sequence, struct, indices=indices, colors=colors,\
circle_indices=circle_indices, square_indices=square_indices)
file_id = seq_id.split()[0]
struct_out_path = '%s/%s_%s_secondary_struct.png'%(write_dir,\
file_id,self.SquareLabel)
savefig(struct_out_path,format='png',dpi=150)
clf()
return struct_out_path
def getGapMap(self):
"""Returns dict mapping gapped_coord to ungapped_coord in self.Alignment
- {seq_id:{gapped_coord:ungapped_coord}}
"""
gap_map = {}
for k,v in self.Alignment.items():
gapped, ungapped = self.MolType.gapMaps(v)
gap_map[k] = gapped
return gap_map
def getColorIndices(self, seq_id, sequence):
"""Returns list of indices and colors for a given sequence.
seq_id: sequence ID to highlight on structure
"""
#seq_list = list(self.Alignment.NamedSeqs[seq_id])
seq_list = list(sequence)
seq_len = len(seq_list)
seq_mask = zeros(seq_len)
mod_id_map = {}
indices = []
colors = []
gapped,ungapped = self.MolType.gapMaps(sequence)
self.GapMap[seq_id]= gapped
if self.Strict:
if seq_id not in self.ModuleMap:
raise IndexError, 'seq_id %s not in ModuleMap'%(seq_id)
else:
if seq_id not in self.ModuleMap:
return [],[]
for mod_tup in self.ModuleMap[seq_id]:
ix, mod_id, mod_len = mod_tup
# skip modules we con't care about
if not self.KeepAll and mod_id not in self.KeepIds:
continue
elif mod_id in self.SkipIds:
continue
mod_mask = zeros(seq_len)
# mask motif region
for i in range(ix,ix+mod_len):
gapped_ix = self.GapMap[seq_id][i]
mod_mask[gapped_ix] = 1
# add to sequence map
seq_mask += mod_mask
# map module ids to indexes
for jx in range(ix,ix+mod_len):
gapped_jx = self.GapMap[seq_id][jx]
if gapped_jx not in mod_id_map:
mod_id_map[gapped_jx] = []
mod_id_map[gapped_jx].append(mod_id)
# get module regions
#need to take [0] element of nonzero() since numpy returns a tuple
# where Numeric did not
for kx in nonzero(seq_mask)[0]:
# if overlapping use red background, otherwise display color
if seq_mask[kx] > 1:
curr_color = 'overlap_color'
else:
mod_id = mod_id_map[kx][0]
curr_color = 'color_'+mod_id
#append indices.
indices.append(kx)
colors.append(self.ColorMap[curr_color])
return indices, colors
def getMarkedIndices(self, seq_id, sequence, motif_id):
"""Returns list of indices to be marked for a given sequence.
seq_id: sequence ID to highlight on structure
sequence: sequence string
motif_id: ID of motif to circle.
"""
seq_list = list(sequence)
seq_len = len(seq_list)
seq_mask = zeros(seq_len)
mod_id_map = {}
indices = []
gapped,ungapped = self.MolType.gapMaps(sequence)
self.GapMap[seq_id]= gapped
if self.Strict:
if seq_id not in self.ModuleMap:
raise IndexError, 'seq_id %s not in ModuleMap'%(seq_id)
else:
if seq_id not in self.ModuleMap:
return [],[]
for mod_tup in self.ModuleMap[seq_id]:
ix, mod_id, mod_len = mod_tup
if mod_id != motif_id:
continue
# skip modules we con't care about
if not self.KeepAll and mod_id not in self.KeepIds:
continue
mod_mask = zeros(seq_len)
# mask motif region
for i in range(ix,ix+mod_len):
gapped_ix = self.GapMap[seq_id][i]
mod_mask[gapped_ix] = 1
# add to sequence map
seq_mask += mod_mask
# map module ids to indexes
for jx in range(ix,ix+mod_len):
gapped_jx = self.GapMap[seq_id][jx]
if gapped_jx not in mod_id_map:
mod_id_map[gapped_jx] = []
mod_id_map[gapped_jx].append(mod_id)
# get module regions
#need to take [0] element of nonzero() since numpy returns a tuple
# where Numeric did not
for kx in nonzero(seq_mask)[0]:
#append indices.
indices.append(kx)
return indices
class MotifsUpperCase(MotifFormatter):
"""Generates postscript file with motifs highlighted on 2D structure """
def makeModuleMap(self, motif_results):
"""
Need to extract this b/c can't pickle motif_results... grr.
motif_results: MotifResults object
keep_module_ids: list of module ids to keep
"""
module_map = {} #Dict with locations of every motif keyed by module
if motif_results:
for motif in motif_results.Motifs:
for module in motif.Modules:
mod_len = len(module)
mod_id = str(module.ID)
for skey, indexes in module.LocationDict.items():
if skey not in module_map:
module_map[skey] = []
for ix in indexes:
module_map[skey].append((ix, mod_id, mod_len))
return module_map
def __init__(self, MotifResults, KeepIds=None,\
KeepAll=True, MolType=RNA):
"""Set up color map and motif results
ModuleMap: flattened map (b/c of pickle problem.)
generate using make_module_map() function
Alignment: SequenceCollection or Alignment object
KeepIds: list of module ids to keep
KeepAll: When True, ignores KeepIds and highlights all motifs
"""
MotifFormatter.__init__(self)
self.ModuleMap = self.makeModuleMap(MotifResults)
self.Alignment = MotifResults.Alignment
if KeepIds is None:
KeepIds = []
self.KeepIds = set(KeepIds)
self.KeepAll = KeepAll
self.MolType = MolType
self.GapMap = self.getGapMap()
self.HighlightMap = {}
def __call__(self,aln,outfile_prefix='',write_dir='.'):
"""Call method for ColorSecondaryStructure class. """
aln = SequenceCollection(aln)
new_aln = {}
for k,v in aln.NamedSeqs.items():
new_aln[k]=self.getUpperCaseSequence(k,v)
out_path = \
write_dir+'/'+outfile_prefix+'_binding_site_alignment.fasta'
out_file = open(out_path,'w')
out_file.write(fasta_from_alignment(new_aln))
out_file.close()
print out_path
return new_aln
def getGapMap(self):
"""Returns dict mapping gapped_coord to ungapped_coord in self.Alignment
- {seq_id:{gapped_coord:ungapped_coord}}
"""
gap_map = {}
for k,v in self.Alignment.items():
gapped, ungapped = self.MolType.gapMaps(v)
gap_map[k] = gapped
return gap_map
def getUpperCaseSequence(self, seq_id, sequence):
"""Returns list of indices and colors for a given sequence.
seq_id: sequence ID to highlight on structure
"""
sequence=str(sequence)
seq_len = len(sequence)
seq_mask = zeros(seq_len)
mod_id_map = {}
gapped,ungapped = self.MolType.gapMaps(sequence)
self.GapMap[seq_id] = gapped
#if there are no motifs, return lower case sequence.
if seq_id not in self.ModuleMap:
return sequence.lower()
for mod_tup in self.ModuleMap[seq_id]:
ix, mod_id, mod_len = mod_tup
# skip modules we con't care about
if not self.KeepAll and mod_id not in self.KeepIds:
continue
mod_mask = zeros(seq_len)
# mask motif region
for i in range(ix,ix+mod_len):
gapped_ix = self.GapMap[seq_id][i]
mod_mask[gapped_ix] = 1
# add to sequence map
seq_mask += mod_mask
# get upper case in module regions
new_seq = []
for kx, lc, uc in zip(seq_mask,sequence.lower(), sequence.upper()):
# if not motif region, use lower
if kx < 1:
new_seq.append(lc)
else:
new_seq.append(uc)
return ''.join(new_seq)
class MotifSequenceConstraints(MotifFormatter):
"""Generates postscript file with motifs highlighted on 2D structure """
def makeModuleMap(self, motif_results):
"""
Need to extract this b/c can't pickle motif_results... grr.
motif_results: MotifResults object
keep_module_ids: list of module ids to keep
"""
module_map = {} #Dict with locations of every motif keyed by module
if motif_results:
for motif in motif_results.Motifs:
for module in motif.Modules:
mod_len = len(module)
mod_id = str(module.ID)
for skey, indexes in module.LocationDict.items():
if skey not in module_map:
module_map[skey] = []
for ix in indexes:
module_map[skey].append((ix, mod_id, mod_len))
return module_map
def __init__(self, MotifResults, KeepIds=None,\
KeepAll=True, MolType=RNA, strict=True):
"""Set up color map and motif results
ModuleMap: flattened map (b/c of pickle problem.)
generate using make_module_map() function
Alignment: SequenceCollection or Alignment object
KeepIds: list of module ids to keep
KeepAll: When True, ignores KeepIds and highlights all motifs
"""
MotifFormatter.__init__(self)
self.ModuleMap = self.makeModuleMap(MotifResults)
self.Alignment = MotifResults.Alignment
if KeepIds is None:
KeepIds = []
self.KeepIds = set(KeepIds)
self.KeepAll = KeepAll
self.MolType = MolType
self.GapMap = self.getGapMap()
self.Strict=strict
self.MotifCharacter = \
list('0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ')
def __call__(self,seq_id,sequence,struct,write_dir='.'):
"""Call method for ColorSecondaryStructure class. """
#indices, colors = self.getColorIndices(seq_id,sequence)
indices, colors = self.getColorIndices(seq_id,sequence)
circle_indices = []
if self.CircleId:
circle_indices = \
self.getCircleIndices(seq_id,sequence,self.CircleId)
structure_postscript = color_on_structure(\
sequence=sequence,\
struct=struct,\
color_map = self.ColorMap,\
indices=indices,\
colors=colors,\
circle_indices=circle_indices)
file_id = seq_id.split()[0]
ps_out_path = \
write_dir+'/'+file_id+'_secondary_struct.ps'
ps_out = open(ps_out_path,'w')
ps_out.write(structure_postscript)
ps_out.close()
return ps_out_path
def getGapMap(self):
"""Returns dict mapping gapped_coord to ungapped_coord in self.Alignment
- {seq_id:{gapped_coord:ungapped_coord}}
"""
gap_map = {}
for k,v in self.Alignment.items():
gapped, ungapped = self.MolType.gapMaps(v)
gap_map[k] = gapped
return gap_map
def getSeqMask(self, seq_id, sequence):
"""Returns vector where motifs are present in sequence.
- seq_id: sequence ID to make seq mask.
- sequence: sequence to make seq mask with.
"""
#seq_list = list(self.Alignment.NamedSeqs[seq_id])
seq_list = list(sequence)
seq_len = len(seq_list)
seq_mask = zeros(seq_len)
mod_id_map = {}
gapped,ungapped = self.MolType.gapMaps(sequence)
self.GapMap[seq_id]= gapped
if self.Strict:
if seq_id not in self.ModuleMap:
raise IndexError, 'seq_id %s not in ModuleMap'%(seq_id)
else:
if seq_id not in self.ModuleMap:
return '',''
for mod_tup in self.ModuleMap[seq_id]:
ix, mod_id, mod_len = mod_tup
# skip modules we con't care about
if not self.KeepAll and mod_id not in self.KeepIds:
continue
elif mod_id in self.SkipIds:
continue
mod_mask = zeros(seq_len)
# mask motif region
for i in range(ix,ix+mod_len):
gapped_ix = self.GapMap[seq_id][i]
mod_mask[gapped_ix] = 1
# add to sequence map
seq_mask += mod_mask
return seq_mask
def getOverlapDicts(self,alignment):
"""Returns dicts of motifs that overlap in start or end positions.
"""
#start overlap dict
start_overlap = {}
#end overlap dict
end_overlap = {}
#Get seq_mask_dict. Calling this will construct self.GapMap for given
# sequence.
for seq_id,seq in alignment.items():
curr_seq_mask = self.getSeqMask(seq_id,seq)
#for each module
for mod_tup in self.ModuleMap[seq_id]:
ix, mod_id, mod_len = mod_tup
gapped_start = self.GapMap[seq_id][ix]
gapped_end = self.GapMap[seq_id][ix+mod_len]
if curr_seq_mask[gapped_start]>1:
start_overlap[mod_id]=seq_id
if curr_seq_mask[gapped_end]>1:
end_overlap[mod_id]=seq_id
return start_overlap, end_overlap
def getConstraintStrings(self,alignment):
"""Returns dict of constraint strings for each sequence in alignment.
- {seq_id:{1:constraint_string_1,2:constraint_string_2}}
"""
start_overlap, end_overlap = self.getOverlapDicts(alignment)
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