Skip to content
Snippets Groups Projects
Commit 25d6b9be authored by james94's avatar james94
Browse files

rules/build_hifi.smk 

update hifi build
parent ce5d6b4c
Branches
No related tags found
No related merge requests found
Hide whitespace changes
Inline Side-by-side
scripts/addFullTableForReport.py
+ 13
− 10
View file @ 25d6b9be
......@@ -2,8 +2,8 @@ import pandas as pd
from tabulate import tabulate
samples=pd.read_csv(snakemake.input.results, dtype=str, index_col=0, delim_whitespace=True, skip_blank_lines=True)
# samples=samples.reset_index
turn2FloatAndMb=['Bases_Mb','Est_Size_Mb','Longest_Scaff_Mb','Scaff_N50_Mb','Scaff_NG50_Mb','Scaff_N95_Mb','Scaff_NG95_Mb','Longest_Cont','Cont_N50_Mb','Cont_NG50_Mb','Cont_N95_Mb','Cont_NG95_Mb']
roundDecimals=['Comp_BUSCOs_%','Comp_Single_BUSCOs_%','Het_%','GC_%','QV','Completeness','Bases_Mb','Est_Size_Mb','Longest_Scaff_Mb','Scaff_N50_Mb','Scaff_NG50_Mb','Scaff_N95_Mb','Scaff_NG95_Mb','Longest_Cont','Cont_N50_Mb','Cont_NG50_Mb','Cont_N95_Mb','Cont_NG95_Mb']
turn2FloatAndMb=['Bases_Mb','Est_Size_Mb','Longest_Scaff_Mb','Scaff_N50_Mb','Scaff_NG50_Mb','Scaff_N95_Mb','Scaff_NG95_Mb','Longest_Cont_Mb','Cont_N50_Mb','Cont_NG50_Mb','Cont_N95_Mb','Cont_NG95_Mb']
roundDecimals=['Comp_BUSCOs_%','Comp_Single_BUSCOs_%','Het_%','GC_%','QV','Completeness','Bases_Mb','Est_Size_Mb','Longest_Scaff_Mb','Scaff_N50_Mb','Scaff_NG50_Mb','Scaff_N95_Mb','Scaff_NG95_Mb','Longest_Cont_Mb','Cont_N50_Mb','Cont_NG50_Mb','Cont_N95_Mb','Cont_NG95_Mb']
print('this is samples',samples)
sampleTransposed=samples.T
print('this is sampleTransposed',sampleTransposed)
......@@ -13,11 +13,14 @@ for i in range(0,4):
sampleTransposed[roundDecimals[i]]=sampleTransposed[roundDecimals[i]].str.replace('%','')
for roundHeader in roundDecimals:
sampleTransposed[roundHeader]=sampleTransposed[roundHeader].astype(float).round(2)
with open(snakemake.output[0], "w") as out:
print("", file=out)
print("\\blandscape", file=out)
print("", file=out)
print("\\tiny", file=out)
print(tabulate(sampleTransposed.rename_axis('ASM_ID'), headers='keys',tablefmt="pipe", showindex=True), file=out)
print("\\elandscape", file=out)
print("", file=out)
with open(snakemake.output[0], "w") as out_markdown:
print("", file=out_markdown)
print("\\blandscape", file=out_markdown)
print("", file=out_markdown)
print("\\tiny", file=out_markdown)
print(tabulate(sampleTransposed.rename_axis('ASM_ID'), headers='keys',tablefmt="pipe", showindex=True), file=out_markdown)
print("\\elandscape", file=out_markdown)
print("", file=out_markdown)
with open(snakemake.output[1], "w") as out_plain:
print(tabulate(sampleTransposed.rename_axis('ASM_ID'), headers='keys',tablefmt="plain", showindex=True), file=out_plain)
scripts/colouredHeatmap_legend.tsv 0 → 100644
+ 5
− 0
View file @ 25d6b9be
Gaps_per_Gb Scaff_NG50_Mb Cont_NG50_Mb QV Completeness Comp_Single_BUSCOs_%
'< 200' '> 100Mbp' '> 10Mbp' '> 50' '> 95%' '> 95%'
'200 - 1000' '10Mbp - 100Mbp' '1Mbp - 10Mbp' '40 - 50' '90% - 95%' '90% - 95%'
'1000 - 10000' '0.1Mbp - 10Mbp' '0.01Mbp - 1Mbp' '35 - 40' '80% - 90%' '80% - 90%'
'> 10000' '< 0.1Mbp' '< 0.01Mbp' '< 35' '< 80%' '< 80%'
scripts/fullTable_heatmap_external.R 0 → 100644
+ 132
− 0
View file @ 25d6b9be
suppressMessages(library(dplyr))
suppressMessages(library(formattable))
#suppressMessages(library(data.table))
fullTableOfStats<-read.table(file = snakemake@input[[1]], sep = "", header = TRUE, row.names=NULL, check.names = FALSE)
fullTableOfStats$Gaps_per_Gb <- ((fullTableOfStats$Gaps * fullTableOfStats$Est_Size_Mb)/1000)
fullTableOfStats$Gaps_per_Gb <- as.integer(fullTableOfStats$Gaps_per_Gb)
customPurple='#c699e8'
customGreen='#8fc773'
selectionOfStats_colouredHeatmap <- fullTableOfStats %>%
select(c('ASM_ID','ASM_LEVEL',
'Gaps_per_Gb', 'Scaff_NG50_Mb',
'Cont_NG50_Mb','QV',
'Completeness', 'Comp_Single_BUSCOs_%'))
sink(file = snakemake@output[[1]])
format_table(selectionOfStats_colouredHeatmap,
align =c("l","c","c","c","c", "c", "c", "c", "c"),
list(Gaps_per_Gb = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
`background-color` = ifelse(ASM_LEVEL == 'cont', "#666666",
ifelse(between(Gaps_per_Gb,1001, 10000), "#FFCC99",
ifelse(between(Gaps_per_Gb,201 , 1000), customGreen,
ifelse(Gaps_per_Gb <= 200, customPurple, "#FF9999")))))),
Scaff_NG50_Mb = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
`background-color` = ifelse(between(Scaff_NG50_Mb,0.1, 9.99999), "#FFCC99",
ifelse(between(Scaff_NG50_Mb,10, 99.99999), customGreen,
ifelse(Scaff_NG50_Mb >= 100, customPurple, "#FF9999"))))),
Cont_NG50_Mb = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
`background-color` = ifelse(between(Cont_NG50_Mb,0.01, 0.99999), "#FFCC99",
ifelse(between(Cont_NG50_Mb,1, 9.999999), customGreen,
ifelse(Cont_NG50_Mb >= 10, customPurple, "#FF9999"))))),
Completeness = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
`background-color` = ifelse(between(Completeness,80, 89.9999), "#FFCC99",
ifelse(between(Completeness,90, 94.99999), customGreen,
ifelse(Completeness >= 95, customPurple, "#FF9999"))))),
`Comp_Single_BUSCOs_%` = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
`background-color` = ifelse(between(`Comp_Single_BUSCOs_%`,80, 89.9999), "#FFCC99",
ifelse(between(`Comp_Single_BUSCOs_%`,90, 95), customGreen,
ifelse(`Comp_Single_BUSCOs_%` >= 95, customPurple, "#FF9999"))))),
QV = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
`background-color` = ifelse(between(QV,35, 39.9999999999), "#FFCC99",
ifelse(between(QV,40, 49.999999999), customGreen,
ifelse(QV >= 50, customPurple, "#FF9999")))))))
cat('<br>')
cat("\n")
cat('<br>')
legendTable<-read.table(file = snakemake@params[[1]], sep = "", header = TRUE, row.names=NULL, check.names = FALSE)
format_table(legendTable,
align =c("c","c","c", "c", "c", "c", "c"),
list(Gaps_per_Gb = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
"font.size" = "12px",
"width" = '150px',
`background-color` = ifelse(Gaps_per_Gb == '> 10000',"#FF9999",
ifelse(Gaps_per_Gb == '1000 - 10000',"#FFCC99",
ifelse(Gaps_per_Gb == '200 - 1000',customGreen, customPurple))))),
Scaff_NG50_Mb = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
"font.size" = "12px",
"width" = '150px',
`background-color` = ifelse(Scaff_NG50_Mb == '< 0.1Mbp',"#FF9999",
ifelse(Scaff_NG50_Mb == '0.1Mbp - 10Mbp',"#FFCC99",
ifelse(Scaff_NG50_Mb == '10Mbp - 100Mbp',customGreen, customPurple))))),
Cont_NG50_Mb = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
"font.size" = "12px",
"width" = '150px',
`background-color` = ifelse(Cont_NG50_Mb == '< 0.01Mbp',"#FF9999",
ifelse(Cont_NG50_Mb == '0.01Mbp - 1Mbp',"#FFCC99",
ifelse(Cont_NG50_Mb == '1Mbp - 10Mbp',customGreen, customPurple))))),
QV = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
"font.size" = "12px",
"width" = '100px',
`background-color` = ifelse(QV == '< 35',"#FF9999",
ifelse(QV == '35 - 40',"#FFCC99",
ifelse(QV == '40 - 50',customGreen, customPurple))))),
Completeness = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
"font.size" = "12px",
"width" = '150px',
`background-color` = ifelse(Completeness == '< 80%',"#FF9999",
ifelse(Completeness == '80% - 90%',"#FFCC99",
ifelse(Completeness == '90% - 95%',customGreen, customPurple))))),
`Comp_Single_BUSCOs_%` = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
"font.size" = "12px",
"width" = '220px',
`background-color` = ifelse(`Comp_Single_BUSCOs_%` == '< 80%',"#FF9999",
ifelse(`Comp_Single_BUSCOs_%` == '80% - 90%',"#FFCC99",
ifelse(`Comp_Single_BUSCOs_%` == '90% - 95%',customGreen, customPurple)))))))
sink(file = NULL)
scripts/fullTable_heatmap_internalComparison.R 0 → 100644
+ 140
− 0
View file @ 25d6b9be
suppressMessages(library(dplyr))
suppressMessages(library(formattable))
fullTableOfStats<-read.table(file = snakemake@input[[1]], sep = "", header = TRUE, row.names=NULL, check.names = FALSE)
fullTableOfStats$Gaps_per_Gb <- ((fullTableOfStats$Gaps * fullTableOfStats$Est_Size_Mb)/1000)
fullTableOfStats$Gaps_per_Gb <- as.integer(fullTableOfStats$Gaps_per_Gb)
selectionOfStats_internalComparisonHeatmap <- fullTableOfStats %>%
select(c('ASM_ID','ASM_LEVEL', 'Bases_Mb', 'Het_%','GC_%', 'Gaps_per_Gb', 'Scaff', 'Cont',
'Longest_Scaff_Mb','Scaff_NG50_Mb', 'Scaff_NG95_Mb',
'Longest_Cont_Mb', 'Cont_NG50_Mb','Cont_NG95_Mb',
'QV', 'Completeness',
'Comp_BUSCOs_%','Comp_Single_BUSCOs_%'))
customBlue_max = "#2e96ff"
customBlue_min = "#dcecfc"
customGray_max = "#8c8c8c"
customGray_min = "#e6e6e6"
sink(file = snakemake@output[[1]])
format_table(selectionOfStats_internalComparisonHeatmap,
align =c("l","c","c","c","c", "c", "c", "c", "c"),
list(Bases_Mb = color_tile(customGray_min, customGray_max),
`Het_%` = color_tile(customGray_min, customGray_max),
`GC_%` = color_tile(customGray_min, customGray_max),
Gaps_per_Gb = color_tile(customBlue_max, customBlue_min),
Scaff = color_tile(customBlue_max,customBlue_min),
Cont = color_tile(customBlue_max,customBlue_min),
Longest_Scaff_Mb = color_tile(customBlue_min, customBlue_max),
Scaff_NG50_Mb = color_tile(customBlue_min, customBlue_max),
Scaff_NG95_Mb = color_tile(customBlue_min, customBlue_max),
Longest_Cont_Mb = color_tile(customBlue_min, customBlue_max),
Cont_NG50_Mb = color_tile(customBlue_min, customBlue_max),
Cont_NG95_Mb = color_tile(customBlue_min, customBlue_max),
QV = color_tile(customBlue_min, customBlue_max),
Completeness = color_tile(customBlue_min, customBlue_max),
`Comp_BUSCOs_%` = color_tile(customBlue_min, customBlue_max),
`Comp_Single_BUSCOs_%` = color_tile(customBlue_min, customBlue_max)))
cat('<br>')
cat("\n")
cat('<br>')
legendTable<-read.table(file = snakemake@params[[1]], sep = "", header = TRUE, row.names=NULL, check.names = FALSE)
format_table(legendTable,
align =c("c","c","c", "c", "c", "c", "c","c","c","c", "c", "c", "c", "c","c", "c"),
list(Bases_Mb = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
`background-color` = ifelse(Bases_Mb == 'Max',customGray_max, customGray_min))),
`Het_%` = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
`background-color` = ifelse(`Het_%` == 'Max',customGray_max, customGray_min))),
`GC_%` = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
`background-color` = ifelse(`GC_%` == 'Max',customGray_max, customGray_min))),
Gaps_per_Gb = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
`background-color` = ifelse(Gaps_per_Gb == 'Min',customBlue_max, customBlue_min))),
Scaff = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
`background-color` = ifelse(Scaff == 'Min',customBlue_max, customBlue_min))),
Cont = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
`background-color` = ifelse(Cont == 'Min',customBlue_max, customBlue_min))),
Longest_Scaff_Mb = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
`background-color` = ifelse(Longest_Scaff_Mb == 'Max',customBlue_max, customBlue_min))),
Scaff_NG50_Mb = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
`background-color` = ifelse(Scaff_NG50_Mb == 'Max',customBlue_max, customBlue_min))),
Scaff_NG95_Mb = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
`background-color` = ifelse(Scaff_NG95_Mb == 'Max',customBlue_max, customBlue_min))),
Longest_Cont_Mb = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
`background-color` = ifelse(Longest_Cont_Mb == 'Max',customBlue_max, customBlue_min))),
Cont_NG50_Mb = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
`background-color` = ifelse(Cont_NG50_Mb == 'Max',customBlue_max, customBlue_min))),
Cont_NG95_Mb = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
`background-color` = ifelse(Cont_NG95_Mb == 'Max',customBlue_max, customBlue_min))),
QV = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
`background-color` = ifelse(QV == 'Max',customBlue_max, customBlue_min))),
Completeness = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
`background-color` = ifelse(Completeness == 'Max',customBlue_max, customBlue_min))),
`Comp_BUSCOs_%` = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
`background-color` = ifelse(`Comp_BUSCOs_%` == 'Max',customBlue_max, customBlue_min))),
`Comp_Single_BUSCOs_%` = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
`background-color` = ifelse(`Comp_Single_BUSCOs_%` == 'Max',customBlue_max, customBlue_min)))))
sink(file = NULL)
scripts/internalComparison_legend.tsv 0 → 100644
+ 3
− 0
View file @ 25d6b9be
Bases_Mb Het_% GC_% Gaps_per_Gb Scaff Cont Longest_Scaff_Mb Scaff_NG50_Mb Scaff_NG95_Mb Longest_Cont_Mb Cont_NG50_Mb Cont_NG95_Mb QV Completeness Comp_BUSCOs_% Comp_Single_BUSCOs_%
'Max' 'Max' 'Max' 'Max' 'Max' 'Max' 'Max' 'Max' 'Max' 'Max' 'Max' 'Max' 'Max' 'Max' 'Max' 'Max'
'Min' 'Min' 'Min' 'Min' 'Min' 'Min' 'Min' 'Min' 'Min' 'Min' 'Min' 'Min' 'Min' 'Min' 'Min' 'Min'
scripts/tableOnSamePage.css 0 → 100644
+ 3
− 0
View file @ 25d6b9be
<style>
.main-container { width: 1200px; max-width:2800px;}
</style>
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Please register or to comment