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Merge pull request #46 from Darcy220606/dev
Add release 0.1.5 updates
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v<version>, <date> -- Initial release. | ||
v<0.1.0>, <date> -- Initial release. | ||
v<0.1.1>, <date> -- minor changes. | ||
v<0.1.2>, <date> -- minor changes. | ||
v<0.1.3>, <10.10.2022> -- PyPi package and conda-recipe / biocontainer release. | ||
v<0.1.4>, <18.10.2022> | ||
-- Included a new optional argument "--complete_summary" to concatenate the results from multiple samples in one table | ||
-- Added a universal log file, to append to an existing log file rather than creating multiple new ones every time a sample is run. | ||
-- The "--path_list" can be called multiple times to include a list of files from individual samples in multiple lists | ||
v<0.1.5>, <27.10.2022> -- Initial release. | ||
-- adapt reading of hmmer_hmmsearch output to deal with varying header lines | ||
-- fix syntax in "if" statements in "check_input.py" | ||
-- include "check_faa_path" function, to find .faa files also in subdirectories |
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__version__ = '0.1.4' | ||
__version__ = '0.1.5' |
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setup( | ||
name='AMPcombi', | ||
version='0.1.4', | ||
version='0.1.5', | ||
author='Anan Ibrahim, Louisa Perelo', | ||
author_email='[email protected], [email protected]', | ||
packages=['ampcombi'], | ||
|
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#!/usr/bin/env Rscript | ||
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############################## | ||
# Rscript to visualise the complete summary tables generated by AMPcombi #### | ||
############################## | ||
# Date #### | ||
# October, 19 2022 | ||
############################## | ||
# Authors #### | ||
# Anan Ibrahim | ||
# [email protected] | ||
# @darcy220606 | ||
############################## | ||
# Working_directory #### | ||
############################## | ||
#setwd("/home/aibrahim/github/testing_ampcombi_on_deepevo") | ||
############################## | ||
# Libraries used + arguments #### | ||
library(dplyr) | ||
library(DT) | ||
library(shiny) | ||
library(data.table) | ||
library(ggplot2) | ||
library("optparse") | ||
library(htmlwidgets) | ||
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option_list = list( | ||
make_option(c("-f", "--file"), type="character", default=NULL, | ||
help="AMpcombi complete summary table", metavar="character"), | ||
make_option(c("-o", "--out"), type="character", default="AMPcombi_summary.html", | ||
help="Provide the name of the output file [default= %default]", metavar="character") | ||
); | ||
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opt_parser = OptionParser(option_list=option_list); | ||
opt = parse_args(opt_parser); | ||
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############################## | ||
# Generate the html file #### | ||
############################## | ||
#args[2] = "AMPcombi_summary.html" | ||
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table <- | ||
readr::read_csv(opt$file) %>% | ||
unique() | ||
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about_page <- tabPanel( | ||
title = strong('About'), | ||
br(), | ||
includeMarkdown("https://raw.githubusercontent.com/Darcy220606/AMPcombi/dev/README.md") | ||
) | ||
## page 2: Summary table | ||
summary_page <- tabPanel(title = strong('Summary table'), | ||
mainPanel(DTOutput('tbl'), | ||
width = 20)) | ||
## page 3: Plots and figures | ||
plots_page <- tabPanel(title = strong('Plots'), | ||
titlePanel("Analysis"), | ||
sidebarLayout( | ||
sidebarPanel( | ||
), | ||
mainPanel( | ||
tabsetPanel( | ||
tabPanel( | ||
title = "Plot" | ||
), | ||
tabPanel( | ||
title = "Statistics", | ||
) | ||
) | ||
) | ||
)) | ||
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## Shiny app | ||
ui <- navbarPage( | ||
title = strong("AMPcombi"), | ||
about_page, | ||
summary_page, | ||
plots_page, | ||
tags$style(type = 'text/css', '.navbar { background-color: #a2d2ff; | ||
font-family: Arial; | ||
font-size: 15px; | ||
color: #023047; }') | ||
) | ||
server <- function(input, output) | ||
{output$tbl = renderDT(table, | ||
class = 'cell-border stripe', ## add column border | ||
options = list( paging = TRUE, ## paginate the output | ||
pageLength = 100, ## number of rows to output for each page | ||
scrollX = TRUE, ## enable scrolling on X axis | ||
scrollY = TRUE, ## enable scrolling on Y axis | ||
autoWidth = TRUE, ## use smart column width handling | ||
#width = 200, | ||
server = TRUE, ## use client-side processing only load the 100 on display | ||
dom = 'Bfrtip', | ||
#bordered = TRUE, | ||
buttons = c('csv', 'excel'), ## the user can just download what on display because server=TRUE | ||
columnDefs = list(list(targets = '_all', className = 'dt-center'), | ||
list(targets = c(0, 8, 9), visible = TRUE))), | ||
extensions = 'Buttons', | ||
selection = 'multiple', ## enable selection of a single row | ||
filter = 'top', ## include column filters at the bottom | ||
rownames = FALSE ## don't show row numbers/names | ||
)} | ||
shinyApp(ui = ui, server = server) |