adpated combining_dfs.py and plotting.R for gid and attempting to make it generic
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3 changed files with 91 additions and 81 deletions
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@ -57,10 +57,10 @@ from combining_FIXME import detect_common_cols
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from reference_dict import oneletter_aa_dict # CHECK DIR STRUC THERE!
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from reference_dict import low_3letter_dict # CHECK DIR STRUC THERE!
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#=======================================================================
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#%% command line args
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#%% command line args: case sensitive
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arg_parser = argparse.ArgumentParser()
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arg_parser.add_argument('-d', '--drug', help='drug name', default = 'pyrazinamide')
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arg_parser.add_argument('-g', '--gene', help='gene name', default = 'pncA') # case sensitive
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arg_parser.add_argument('-d', '--drug', help='drug name', default = '')
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arg_parser.add_argument('-g', '--gene', help='gene name', default = '')
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arg_parser.add_argument('--datadir', help = 'Data Directory. By default, it assmumes homedir + git/Data')
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arg_parser.add_argument('-i', '--input_dir', help = 'Input dir containing pdb files. By default, it assmumes homedir + <drug> + input')
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@ -99,32 +99,37 @@ print('position regex:', pos_regex)
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# directories
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#==============
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if not datadir:
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datadir = homedir + '/' + 'git/Data'
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datadir = homedir + '/git/Data/'
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if not indir:
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indir = datadir + '/' + drug + '/input'
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indir = datadir + drug + '/input/'
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if not outdir:
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outdir = datadir + '/' + drug + '/output'
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outdir = datadir + drug + '/output/'
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#=======
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# input
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#=======
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in_filename_mcsm = gene.lower() + '_complex_mcsm_norm.csv'
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#in_filename_mcsm = gene.lower() + '_complex_mcsm_norm.csv'
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in_filename_mcsm = gene.lower() + '_complex_mcsm_norm_SAM.csv' # gidb
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in_filename_foldx = gene.lower() + '_foldx.csv'
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in_filename_dssp = gene.lower() + '_dssp.csv'
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in_filename_kd = gene.lower() + '_kd.csv'
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in_filename_rd = gene.lower() + '_rd.csv'
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in_filename_snpinfo = 'ns' + gene.lower() + '_snp_info_f.csv'
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#in_filename_deepddg = gene.lower() + '_complex_ddg_results.txt' # change to decent filename and put it in the correct dir
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in_filename_snpinfo = 'ns' + gene.lower() + '_snp_info_f.csv' # gwas f info
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in_filename_afor = gene.lower() + '_af_or.csv'
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in_filename_afor_kin = gene.lower() + '_af_or_kinship.csv'
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infile_mcsm = outdir + '/' + in_filename_mcsm
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infile_foldx = outdir + '/' + in_filename_foldx
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infile_dssp = outdir + '/' + in_filename_dssp
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infile_kd = outdir + '/' + in_filename_kd
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infile_rd = outdir + '/' + in_filename_rd
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infile_mcsm = outdir + in_filename_mcsm
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infile_foldx = outdir + in_filename_foldx
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infile_dssp = outdir + in_filename_dssp
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infile_kd = outdir + in_filename_kd
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infile_rd = outdir + in_filename_rd
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#infile_deepddg = outdir + in_filename_deepddg
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infile_snpinfo = outdir + '/' + in_filename_snpinfo
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infile_afor = outdir + '/' + in_filename_afor
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infile_afor_kin = outdir + '/' + in_filename_afor_kin
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@ -135,7 +140,9 @@ print('\nInput path:', indir
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, '\nInput filename foldx:', infile_foldx, '\n'
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, '\nInput filename dssp:', infile_dssp
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, '\nInput filename kd:', infile_kd
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, '\nInput filename rd', infile_rd , '\n'
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, '\nInput filename rd', infile_rd
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# , '\nInput filename rd', infile_deepddg , '\n'
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, '\nInput filename snp info:', infile_snpinfo, '\n'
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, '\nInput filename af or:', infile_afor
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, '\nInput filename afor kinship:', infile_afor_kin
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@ -225,10 +232,39 @@ print('\nResult of Fourth merge:', combined_df.shape
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, '\n===================================================================')
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combined_df[merging_cols_m4].apply(len)
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combined_df[merging_cols_m4].apply(len) == len(combined_df)
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#%%============================================================================
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# OR merges: TEDIOUSSSS!!!!
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#deepddg_df = pd.read_csv(infile_deepddg, sep = ' ')
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#%%============================================================================
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# Output columns
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out_filename_stab_struc = gene.lower() + '_comb_stab_struc_params.csv'
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outfile_stab_struc = outdir + '/' + out_filename_stab_struc
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print('Output filename:', outfile_stab_struc
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, '\n===================================================================')
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# write csv
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print('Writing file: combined stability and structural parameters')
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combined_df.to_csv(outfile_stab_struc, index = False)
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print('\nFinished writing file:'
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, '\nNo. of rows:', combined_df.shape[0]
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, '\nNo. of cols:', combined_df.shape[1])
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#%%============================================================================
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# OR merges: TEDIOUSSSS!!!!
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#[ DELETE ]
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del(mcsm_df, foldx_df, mcsm_foldx_dfs, dssp_kd_dfs, dssp_kd_rd_dfs,rd_df, kd_df, infile_mcsm, infile_foldx, infile_dssp, infile_kd)
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del(merging_cols_m1, merging_cols_m2, merging_cols_m3, merging_cols_m4)
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del(in_filename_dssp, in_filename_foldx, in_filename_kd, in_filename_mcsm, in_filename_rd)
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@ -1,56 +1,24 @@
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#!/usr/bin/env Rscript
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#########################################################
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# TASK: formatting data that will be used for various plots
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# useful links
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#https://stackoverflow.com/questions/38851592/r-append-column-in-a-dataframe-with-frequency-count-based-on-two-columns
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# TASK: importing dir str
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# create a function that takes 'drug' and 'gene' as args,
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# This script is sourced by plotting.R to import dir str
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# for various plots, etc.
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#########################################################
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# working dir and loading libraries
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getwd()
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setwd("~/git/LSHTM_analysis/scripts/plotting")
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getwd()
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#source("Header_TT.R")
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library(ggplot2)
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library(data.table)
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library(dplyr)
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require("getopt", quietly = TRUE) #cmd parse arguments
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#========================================================
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# command line args
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#spec = matrix(c(
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# "drug" , "d", 1, "character",
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# "gene" , "g", 1, "character"
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#), byrow = TRUE, ncol = 4)
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#opt = getopt(spec)
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#drug = opt$druggene = opt$gene
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#if(is.null(drug)|is.null(gene)) {
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# stop("Missing arguments: --drug and --gene must both be specified (case-sensitive)")
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#}
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#========================================================
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# FIXME: change to cmd
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#%% variable assignment: input and output paths & filenames
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drug = "pyrazinamide"
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gene = "pncA"
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import_dirs <- function(drug, gene) {
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gene_match = paste0(gene,"_p.")
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cat(gene_match)
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#=============
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# directories and variables
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#=============
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datadir = paste0("~/git/Data")
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indir = paste0(datadir, "/", drug, "/input")
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outdir = paste0("~/git/Data", "/", drug, "/output")
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plotdir = paste0("~/git/Data", "/", drug, "/output/plots")
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dr_muts_col = paste0('dr_mutations_', drug)
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other_muts_col = paste0('other_mutations_', drug)
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resistance_col = "drtype"
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#%%===============================================================
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datadir <<- paste0("~/git/Data")
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indir <<- paste0(datadir, "/", drug, "/input")
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outdir <<- paste0("~/git/Data", "/", drug, "/output")
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plotdir <<- paste0("~/git/Data", "/", drug, "/output/plots")
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dr_muts_col <<- paste0('dr_mutations_', drug)
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other_muts_col <<- paste0('other_mutations_', drug)
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resistance_col <<- "drtype"
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}
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@ -14,31 +14,37 @@ getwd()
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library(ggplot2)
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library(data.table)
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library(dplyr)
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source("dirs.R")
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require("getopt", quietly = TRUE) #cmd parse arguments
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source("dirs.R")
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#========================================================
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# command line args
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#spec = matrix(c(
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# "drug" , "d", 1, "character",
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# "gene" , "g", 1, "character"
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#), byrow = TRUE, ncol = 4)
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spec = matrix(c(
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"drug" , "d", 1, "character",
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"gene" , "g", 1, "character"
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), byrow = TRUE, ncol = 4)
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#opt = getopt(spec)
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opt = getopt(spec)
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#drug = opt$druggene = opt$gene
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#FIXME: detect if script running from cmd, then set these
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#drug = opt$drug
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#gene = opt$gene
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# hardcoding when not using cmd
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drug = "streptomycin"
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gene = "gid"
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if(is.null(drug)|is.null(gene)) {
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stop("Missing arguments: --drug and --gene must both be specified (case-sensitive)")
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}
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#if(is.null(drug)|is.null(gene)) {
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# stop("Missing arguments: --drug and --gene must both be specified (case-sensitive)")
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#}
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#========================================================
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#======
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# input
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#======
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#in_filename = "mcsm_complex1_normalised.csv"
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in_filename_params = paste0(tolower(gene), "_all_params.csv")
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#in_filename_params = paste0(tolower(gene), "_all_params.csv")
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in_filename_params = paste0(tolower(gene), "_comb_stab_struc_params.csv") # part combined
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infile_params = paste0(outdir, "/", in_filename_params)
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cat(paste0("Input file 1:", infile_params) )
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