-
Notifications
You must be signed in to change notification settings - Fork 0
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #2 from ANSES-Ploufragan/dev
Dev
- Loading branch information
Showing
9 changed files
with
696 additions
and
237 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,151 @@ | ||
| #!/usr/bin/env python | ||
| # -*- coding: utf-8 -*- | ||
| # | ||
| # This file is part of the vvv2_display distribution (https://github.com/ANSES-Ploufragan/vvv2_display). | ||
| # Copyright (c) 2023 Fabrice Touzain. | ||
| # | ||
| # This program is free software: you can redistribute it and/or modify | ||
| # it under the terms of the GNU General Public License as published by | ||
| # the Free Software Foundation, version 3. | ||
| # | ||
| # This program is distributed in the hope that it will be useful, but | ||
| # WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | ||
| # General Public License for more details. | ||
| # | ||
| # You should have received a copy of the GNU General Public License | ||
| # along with this program. If not, see <http://www.gnu.org/licenses/>. | ||
| # | ||
| ### | ||
| # USE PYTHON3 | ||
| # from vcf file of vardict and bed file with contig positions, creates a vcf file with | ||
| # contigs shifted position (to create a picture of variants and annotations) | ||
| ### | ||
| import argparse, os, sys, csv, re, warnings | ||
| from os import path | ||
| import subprocess | ||
|
|
||
| # to be able to report line number in error messages | ||
| import inspect | ||
| frame = inspect.currentframe() | ||
|
|
||
| # debug | ||
| b_test_cov_depth_corr_f = False # 2023 12 19 | ||
| b_test = False | ||
|
|
||
| prog_tag = '[' + os.path.basename(__file__) + ']' | ||
|
|
||
| cov_depth_f = '' # in, cov_depth file provided by samtools depth -aa file.bam | ||
| cov_depth_corr_f = '' # out same as previous but positions on contigs are shifted according to previous contigs | ||
|
|
||
| parser = argparse.ArgumentParser() | ||
| parser.add_argument("-s", "--cov_depth_f", dest='cov_depth_f', | ||
| help="in: coverage depth file provided by samtools -aa in.bam (all contigs)", | ||
| metavar="FILE") | ||
| parser.add_argument("-c", "--cov_depth_corr_f", dest='cov_depth_corr_f', | ||
| help="out: coverage depth file corrected for position (cumulative position in case of several contigs)", | ||
| metavar="FILE") | ||
| parser.add_argument("-z", "--test_all", dest='b_test_all', | ||
| help="[Optional] run all tests", | ||
| action='store_true') | ||
| parser.add_argument("-v", "--verbose", dest='b_verbose', | ||
| help="[Optional] To have details on records when running", | ||
| action='store_true') | ||
| parser.set_defaults(b_test_all=False) | ||
| parser.set_defaults(b_verbose=False) | ||
|
|
||
| # get absolute path in case of files | ||
| args = parser.parse_args() | ||
|
|
||
| # ------------------------------------------- | ||
| # check arguments | ||
| b_test_all = args.b_test_all | ||
|
|
||
| if b_test_all: | ||
| b_test_cov_depth_corr_f = True | ||
| b_test = True | ||
| else: | ||
| b_test = b_test_cov_depth_corr_f | ||
|
|
||
| if ((not b_test)and | ||
| ((len(sys.argv) < 2) or (len(sys.argv) > 10))): | ||
| parser.print_help() | ||
| print(prog_tag + "[Error] we found "+str(len(sys.argv)) + | ||
| " arguments, exit line "+str(frame.f_lineno)) | ||
| sys.exit(0) | ||
|
|
||
| # print('args:', args) | ||
| if args.cov_depth_f is not None: | ||
| cov_depth_f = os.path.abspath(args.cov_depth_f) | ||
| elif(not b_test): | ||
| sys.exit(prog_tag + "[Error] You must provide cov_depth_f") | ||
| if args.cov_depth_corr_f is not None: | ||
| cov_depth_corr_f = os.path.abspath(args.cov_depth_corr_f) | ||
| elif(not b_test): | ||
| sys.exit(prog_tag + "[Error] You must provide cov_depth_corr_f") | ||
|
|
||
| if args.b_verbose is not None: | ||
| b_verbose = args.b_verbose | ||
|
|
||
| if b_test_cov_depth_corr_f: | ||
| test_dir = '../test_vvv2_display/' | ||
| test_name = [ | ||
| 'res' | ||
| # 'res2' | ||
| ] | ||
| for resn in test_name: | ||
| cov_depth_f = test_dir + "res2_covdepth.txt" | ||
| cov_depth_corr_f = test_dir + "res2_covdepth_corrected.txt" | ||
| cmd = ' '.join(['./correct_covdepth_f.py', | ||
| "-s", cov_depth_f, | ||
| "-c", cov_depth_corr_f | ||
| ]) | ||
| if b_verbose: | ||
| cmd = cmd + " -v" | ||
| print(prog_tag + " cmd:"+cmd) | ||
| print(prog_tag + " START") | ||
| os.system(cmd) | ||
| print(prog_tag + " END") | ||
| sys.exit() | ||
|
|
||
| # ---------------------------------------------------------------------- | ||
| # reads seqstat file to get info on genome_length and on contigs lengths | ||
| # ---------------------------------------------------------------------- | ||
| print(prog_tag + " Reads "+cov_depth_f+" file") | ||
| print(prog_tag + " Creates "+cov_depth_corr_f+" file") | ||
| o = open(cov_depth_corr_f, 'w+') | ||
|
|
||
| # init var | ||
| prev_contig_nr = 1 | ||
| contig_num = 0 | ||
|
|
||
| pos = 0 | ||
| curr_shift = 0 | ||
| with open(cov_depth_f) as cdf: | ||
| for line in cdf: | ||
| line_fields = line.split("\t") | ||
| # print("line_fields:"+','.join(line_fields)) | ||
| contig_nr = line_fields[0] | ||
| contig_pos = line_fields[1] | ||
| cov_depth = line_fields[2] | ||
| # print("line_fields:"+','.join(line_fields)) | ||
| if b_verbose: | ||
| print(prog_tag + " contig:"+contig_name+" length:"+str(contig_length)) | ||
|
|
||
| # write in output file | ||
| # if contig change, record shift to apply | ||
| if contig_nr != prev_contig_nr: | ||
| curr_shift = pos | ||
| # get position WITH SHIFT | ||
| pos = curr_shift + int(contig_pos) | ||
| pos_str = str(pos) | ||
| # write pos and related coverage depth | ||
| o.write("\t".join([pos_str, cov_depth])) | ||
| if b_verbose: | ||
| print("record pos:",pos_str,", cov_depth:", cov_depth) | ||
|
|
||
| prev_contig_nr = contig_nr | ||
| cdf.close() | ||
| o.close() | ||
|
|
||
| print(prog_tag + ' '+ cov_depth_corr_f + " file created") |
Oops, something went wrong.