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-rw-r--r--wqflask/wqflask/marker_regression/display_mapping_results.py82
1 files changed, 41 insertions, 41 deletions
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index 3943a401..5925c38f 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -24,13 +24,13 @@
#
# Last updated by Zach 12/14/2010
-import datetime
import string
from math import *
-from PIL import (Image,ImageDraw,ImageFont,ImageColor)
-import sys,os
-import cPickle
-import httplib
+from PIL import Image
+from PIL import ImageDraw
+from PIL import ImageFont
+from PIL import ImageColor
+import os
import json
from flask import Flask, g
@@ -40,15 +40,14 @@ from htmlgen import HTMLgen2 as HT
from base import webqtlConfig
from base.GeneralObject import GeneralObject
from utility import webqtlUtil
-from utility import helper_functions
from utility import Plot
from utility.benchmark import Bench
from wqflask.interval_analyst import GeneUtil
-from base.webqtlConfig import GENERATED_TEXT_DIR, GENERATED_IMAGE_DIR
+from base.webqtlConfig import GENERATED_IMAGE_DIR
from utility.pillow_utils import draw_rotated_text, draw_open_polygon
import utility.logger
-logger = utility.logger.getLogger(__name__ )
+logger = utility.logger.getLogger(__name__)
RED = ImageColor.getrgb("red")
BLUE = ImageColor.getrgb("blue")
@@ -80,22 +79,18 @@ ARIAL_FILE = "./wqflask/static/fonts/arial.ttf"
assert(os.path.isfile(VERDANA_FILE))
-# ---- END: FONT FILES ---- #
-#########################################
-# Inteval Mapping Plot Page
-#########################################
class DisplayMappingResults(object):
+ """Inteval Mapping Plot Page"""
cMGraphInterval = 5
GRAPH_MIN_WIDTH = 900
- GRAPH_MAX_WIDTH = 10000 # Don't set this too high
+ GRAPH_MAX_WIDTH = 10000 # Don't set this too high
GRAPH_DEFAULT_WIDTH = 1280
MULT_GRAPH_DEFAULT_WIDTH = 2000
MULT_GRAPH_MIN_WIDTH = 1400
MULT_GRAPH_DEFAULT_WIDTH = 1600
GRAPH_DEFAULT_HEIGHT = 600
-
# Display order:
# UCSC BAND =========
# ENSEMBL BAND -=-=-=
@@ -106,22 +101,24 @@ class DisplayMappingResults(object):
BAND_HEIGHT = 10
BAND_HEIGHT = 10
- NUM_GENE_ROWS = 10
- EACH_GENE_HEIGHT = 6 # number of pixels tall, for each gene to display
+ NUM_GENE_ROWS = 10
+ EACH_GENE_HEIGHT = 6 # number of pixels tall, for each gene to display
EACH_GENE_ARROW_WIDTH = 5
EACH_GENE_ARROW_SPACING = 14
DRAW_DETAIL_MB = 4
DRAW_UTR_LABELS_MB = 4
qmarkImg = HT.Image('/images/qmarkBoxBlue.gif', width=10, height=13, border=0, alt='Glossary')
- # Note that "qmark.gif" is a similar, smaller, rounded-edges question mark. It doesn't look
- # like the ones on the image, though, which is why we don't use it here.
+
+ # Note that "qmark.gif" is a similar, smaller, rounded-edges
+ # question mark. It doesn't look like the ones on the image,
+ # though, which is why we don't use it here.
HELP_WINDOW_NAME = 'helpWind'
- ## BEGIN HaplotypeAnalyst
+ # BEGIN HaplotypeAnalyst
NR_INDIVIDUALS = 0
- ## END HaplotypeAnalyst
+ # END HaplotypeAnalyst
ALEX_DEBUG_BOOL_PRINT_GENE_LIST = 1
@@ -129,13 +126,13 @@ class DisplayMappingResults(object):
LODFACTOR = 4.61
- SNP_COLOR = ORANGE # Color for the SNP "seismograph"
+ SNP_COLOR = ORANGE # Color for the SNP "seismograph"
TRANSCRIPT_LOCATION_COLOR = MEDIUMPURPLE
BOOTSTRAP_BOX_COLOR = YELLOW
- LRS_COLOR = ImageColor.getrgb("#0000FF")
- SIGNIFICANT_COLOR = ImageColor.getrgb("#EBC7C7")
- SUGGESTIVE_COLOR = GAINSBORO
+ LRS_COLOR = ImageColor.getrgb("#0000FF")
+ SIGNIFICANT_COLOR = ImageColor.getrgb("#EBC7C7")
+ SUGGESTIVE_COLOR = GAINSBORO
SIGNIFICANT_WIDTH = 5
SUGGESTIVE_WIDTH = 5
ADDITIVE_COLOR_POSITIVE = GREEN
@@ -143,33 +140,33 @@ class DisplayMappingResults(object):
DOMINANCE_COLOR_POSITIVE = DARKVIOLET
DOMINANCE_COLOR_NEGATIVE = RED
- ## BEGIN HaplotypeAnalyst
+ # BEGIN HaplotypeAnalyst
HAPLOTYPE_POSITIVE = GREEN
HAPLOTYPE_NEGATIVE = RED
HAPLOTYPE_HETEROZYGOUS = BLUE
HAPLOTYPE_RECOMBINATION = DARKGRAY
- ## END HaplotypeAnalyst
+ # END HaplotypeAnalyst
TOP_RIGHT_INFO_COLOR = BLACK
- CLICKABLE_WEBQTL_REGION_COLOR = ImageColor.getrgb("#F5D3D3")
+ CLICKABLE_WEBQTL_REGION_COLOR = ImageColor.getrgb("#F5D3D3")
CLICKABLE_WEBQTL_REGION_OUTLINE_COLOR = ImageColor.getrgb("#FCE9E9")
- CLICKABLE_WEBQTL_TEXT_COLOR = ImageColor.getrgb("#912828")
+ CLICKABLE_WEBQTL_TEXT_COLOR = ImageColor.getrgb("#912828")
- CLICKABLE_PHENOGEN_REGION_COLOR = ImageColor.getrgb("#A2FB94")
+ CLICKABLE_PHENOGEN_REGION_COLOR = ImageColor.getrgb("#A2FB94")
CLICKABLE_PHENOGEN_REGION_OUTLINE_COLOR = ImageColor.getrgb("#CEFEC7")
- CLICKABLE_PHENOGEN_TEXT_COLOR = ImageColor.getrgb("#1FD504")
+ CLICKABLE_PHENOGEN_TEXT_COLOR = ImageColor.getrgb("#1FD504")
- CLICKABLE_UCSC_REGION_COLOR = ImageColor.getrgb("#DDDDEE")
+ CLICKABLE_UCSC_REGION_COLOR = ImageColor.getrgb("#DDDDEE")
CLICKABLE_UCSC_REGION_OUTLINE_COLOR = ImageColor.getrgb("#EDEDFF")
- CLICKABLE_UCSC_TEXT_COLOR = ImageColor.getrgb("#333366")
+ CLICKABLE_UCSC_TEXT_COLOR = ImageColor.getrgb("#333366")
- CLICKABLE_ENSEMBL_REGION_COLOR = ImageColor.getrgb("#EEEEDD")
+ CLICKABLE_ENSEMBL_REGION_COLOR = ImageColor.getrgb("#EEEEDD")
CLICKABLE_ENSEMBL_REGION_OUTLINE_COLOR = ImageColor.getrgb("#FEFEEE")
- CLICKABLE_ENSEMBL_TEXT_COLOR = ImageColor.getrgb("#555500")
+ CLICKABLE_ENSEMBL_TEXT_COLOR = ImageColor.getrgb("#555500")
GRAPH_BACK_LIGHT_COLOR = ImageColor.getrgb("#FBFBFF")
- GRAPH_BACK_DARK_COLOR = ImageColor.getrgb("#F1F1F9")
+ GRAPH_BACK_DARK_COLOR = ImageColor.getrgb("#F1F1F9")
HELP_PAGE_REF = '/glossary.html'
@@ -196,7 +193,8 @@ class DisplayMappingResults(object):
self.temp_trait = "True"
self.group = start_vars['group']
- #Needing for form submission when doing single chr mapping or remapping after changing options
+ # Needing for form submission when doing single chr
+ # mapping or remapping after changing options
self.samples = start_vars['samples']
self.vals = start_vars['vals']
self.transform = start_vars['transform']
@@ -207,9 +205,9 @@ class DisplayMappingResults(object):
self.mapmodel_rqtl_geno = start_vars['model']
self.pair_scan = start_vars['pair_scan']
- #if self.mapping_method != "gemma" and self.mapping_method != "plink":
self.js_data = start_vars['js_data']
- self.trimmed_markers = start_vars['trimmed_markers'] #Top markers to display in table
+ # Top markers to display in table
+ self.trimmed_markers = start_vars['trimmed_markers']
if self.dataset.group.species == "rat":
self._ucscDb = "rn6"
@@ -221,7 +219,7 @@ class DisplayMappingResults(object):
#####################################
# Options
#####################################
- #Mapping options
+ # Mapping options
if start_vars['mapping_scale'] != "":
self.plotScale = start_vars['mapping_scale']
else:
@@ -542,10 +540,12 @@ class DisplayMappingResults(object):
################################################################
# footnote goes here
################################################################
- btminfo = HT.Paragraph(Id="smallsize") #Small('More information about this graph is available here.')
+ # Small('More information about this graph is available here.')
+ btminfo = HtmlGenWrapper.create_p_tag(id="smallsize")
if self.traitList and self.traitList[0].dataset and self.traitList[0].dataset.type == 'Geno':
- btminfo.append(HT.BR(), 'Mapping using genotype data as a trait will result in infinity LRS at one locus. In order to display the result properly, all LRSs higher than 100 are capped at 100.')
+ btminfo.append(HtmlGenWrapper.create_br_tag())
+ btminfo.append('Mapping using genotype data as a trait will result in infinity LRS at one locus. In order to display the result properly, all LRSs higher than 100 are capped at 100.')
def plotIntMapping(self, canvas, offset= (80, 120, 20, 100), zoom = 1, startMb = None, endMb = None, showLocusForm = ""):
im_drawer = ImageDraw.Draw(canvas)
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-26 12:02:18 +0000