def display_chr_pos_ref_alt(topOfSlideTextbox, dfRow):
chromosome = xls_parsing_functions.get_xls_value(dfRow, 'Chromosome',
'****')
pos = xls_parsing_functions.get_xls_value(dfRow, 'Position', '****')
ref = xls_parsing_functions.get_xls_value(dfRow, 'Reference Allele',
'****')
alt = xls_parsing_functions.get_xls_value(dfRow, 'Sample Allele', '****')
chrPos = ':'.join([chromosome, pos])
refAlt = ">".join([ref, alt])
text = ''.join([chrPos, refAlt])
#add the text to the slide
p = topOfSlideTextbox.add_paragraph()
try:
p.text = make_string_safe_for_unicode(text)
except ValueError:
p.text = 'no value'
def display_tscriptId_tscriptVariant_proteinVariant_and_exon(
topOfSlideTextbox, dfRow):
tscriptId = xls_parsing_functions.get_xls_value(dfRow, 'Transcript ID',
'****')
tscriptVariant = xls_parsing_functions.get_xls_value(
dfRow, 'Transcript Variant', '****')
proteinVariant = xls_parsing_functions.get_xls_value(
dfRow, 'Protein Variant', '****')
exon = xls_parsing_functions.get_xls_value(dfRow, 'Gene Region', '****')
#print tscriptId, tscriptVariant, proteinVariant
text = ' | '.join([tscriptId, tscriptVariant, proteinVariant, exon])
#add the text to the slide
p = topOfSlideTextbox.add_paragraph()
#text = text.encode('utf-8').strip()
try:
p.text = make_string_safe_for_unicode(text)
except ValueError:
p.text = 'no value'
def display_gene_function_textbox(slide, dfRow):
#ALERT--add logic that resizes the text boxes based on how much text there is
if (True): geneFunctionHeight = DEFAULT_TEXTBOX_HEIGHT
shape = slide.shapes.add_shape(MSO_SHAPE.RECTANGLE, TEXT_BOX_LEFT_OFFSET,
ELEMENT_TOP_OFFSET, TEXT_BOX_WIDTH,
geneFunctionHeight)
set_shape_color(shape, 80, 172, 196)
info = xls_parsing_functions.get_xls_value(dfRow, 'SwissProtFunction')
set_shape_text(shape, "Gene function: ", info)
return ELEMENT_TOP_OFFSET + geneFunctionHeight
def display_functional_studies_textbox(slide, dfRow, currentOffsetFromTop):
#if text in the gene function box is bleeding over, make sure to resize my new text box so it is lower down
functionalStudiesOffset = currentOffsetFromTop + OFFSET_BETWEEN_STUDIES_BOX
#ALERT--add logic that resizes the text boxes based on how much text there is
if (True): functionalStudiesHeight = DEFAULT_TEXTBOX_HEIGHT
shape = slide.shapes.add_shape(MSO_SHAPE.RECTANGLE, TEXT_BOX_LEFT_OFFSET,
functionalStudiesOffset, TEXT_BOX_WIDTH,
functionalStudiesHeight)
set_shape_color(shape, 156, 186, 95)
info = xls_parsing_functions.get_xls_value(dfRow, 'mgi')
set_shape_text(shape, "Functional studies: ", info)
return currentOffsetFromTop + DEFAULT_TEXTBOX_HEIGHT + OFFSET_BETWEEN_STUDIES_BOX
def display_gene_name(topOfSlideTextbox, dfRow):
geneName = xls_parsing_functions.get_xls_value(dfRow, 'Gene Symbol')
if len(geneName) < 2:
#print geneName
geneName = 'not found' #we need to hack around some unicode errors
try:
topOfSlideTextbox.text = make_string_safe_for_unicode("GENE: " +
geneName)
except ValueError:
topOfSlideTextbox.text = 'no value'
#we get the first paragraph (which is set by deafult), and make it bold
topOfSlideTextbox.paragraphs[0].font.bold = True
def display_known_disease_association_textbox(slide, dfRow,
currentOffsetFromTop):
knownDiseaseAssocOffset = currentOffsetFromTop + OFFSET_BETWEEN_STUDIES_BOX
#ALERT--add logic that resizes the text boxes based on how much text there is
if (True): knownDiseaseAssocHeight = DEFAULT_TEXTBOX_HEIGHT
shape = slide.shapes.add_shape(MSO_SHAPE.RECTANGLE, TEXT_BOX_LEFT_OFFSET,
knownDiseaseAssocOffset, TEXT_BOX_WIDTH,
knownDiseaseAssocHeight)
set_shape_color(shape, 190, 7, 18)
#Alert we need to change this
info = xls_parsing_functions.get_xls_value(dfRow,
'SwissProtDiseaseAssociation')
set_shape_text(shape, "Known Disease Association: ", info)
def populate_slide(slide, dfRow, udnId):
####################################
display_udn_logo(slide)
display_udn_id(slide, udnId)
#CREATE THE TOP OF THE SLIDE: Gene, name, chrom, pos etc
#we use current offset from the top as an intermediate variable that helps us put stuff in the right place
display_top_of_slide_textbox(slide, dfRow)
currentOffsetFromTop = display_gene_function_textbox(slide, dfRow)
currentOffsetFromTop = display_functional_studies_textbox(
slide, dfRow, currentOffsetFromTop)
display_known_disease_association_textbox(slide, dfRow,
currentOffsetFromTop)
currentOffsetFromTop = display_in_silico_prediction_table(slide, dfRow)
currentOffsetFromTop = display_allele_frequency_table(
slide, dfRow, currentOffsetFromTop)
#Do the 1-D tables--note that in the interest of minimal copy pasting of code some code from the display allele freq tables is re
igvStatus = xls_parsing_functions.get_xls_value(dfRow, 'IGV')
currentOffsetFromTop = display_1d_table(slide, currentOffsetFromTop, 'IGV',
igvStatus)
display_1d_table(slide, currentOffsetFromTop, 'Variant Decision', 'tbd')
def set_table_body_rows(slide, table, dfRow, rowNames):
idx = 1
for displayRowName, excelKey in rowNames:
rowValue = xls_parsing_functions.get_xls_value(dfRow, excelKey)
set_text_size_and_font(table.cell(idx, 0), TABLE_TEXT_SIZE)
set_text_size_and_font(table.cell(idx, 1), TABLE_TEXT_SIZE)
displayRowName = make_string_safe_for_unicode(displayRowName)
rowValue = make_string_safe_for_unicode(rowValue)
try:
table.cell(idx, 0).text = displayRowName
except ValueError:
table.cell(idx, 0).text = 'no value'
try:
table.cell(idx, 1).text = rowValue
except ValueError:
table.cell(idx, 1).text = 'no value'
#Make the cells white
adjust_cell_color(table, idx, 0, RGBColor(255, 255, 255))
adjust_cell_color(table, idx, 1, RGBColor(255, 255, 255))
idx += 1
