From db275a34aee91ec8f75f7da95613fc512a13ea31 Mon Sep 17 00:00:00 2001 From: FelixKrueger Date: Fri, 1 Feb 2019 14:01:29 +0000 Subject: [PATCH] Updating files for release 0.20.1 --- NOMe_filtering | 6 +++--- bam2nuc | 10 ++++++---- bismark | 8 +++++--- bismark2bedGraph | 6 +++--- bismark2report | 10 +++++----- bismark2summary | 2 +- bismark_genome_preparation | 21 ++++++++++++++------- bismark_methylation_extractor | 4 ++-- coverage2cytosine | 4 ++-- deduplicate_bismark | 4 ++-- filter_non_conversion | 6 +++--- 11 files changed, 46 insertions(+), 35 deletions(-) diff --git a/NOMe_filtering b/NOMe_filtering index e7e14a7..3cb25df 100755 --- a/NOMe_filtering +++ b/NOMe_filtering @@ -6,7 +6,7 @@ use Getopt::Long; use Cwd; use Carp; -## This program is Copyright (C) 2010-18, Felix Krueger (felix.krueger@babraham.ac.uk) +## This program is Copyright (C) 2010-19, Felix Krueger (felix.krueger@babraham.ac.uk) ## 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 @@ -23,7 +23,7 @@ use Carp; my %chromosomes; # storing sequence information of all chromosomes/scaffolds my %processed; # keeping a record of which chromosomes have been processed -my $nome_version = 'v0.20.0'; +my $nome_version = 'v0.20.1'; my ($output_dir,$genome_folder,$zero,$CpG_only,$CX_context,$split_by_chromosome,$parent_dir,$coverage_infile,$cytosine_out,$merge_CpGs,$gc_context,$gzip,$nome) = process_commandline(); @@ -432,7 +432,7 @@ sub process_commandline{ Bismark NOMe_filtering, Version: $nome_version - Copyright 2010-18 Felix Krueger, Babraham Bioinformatics + Copyright 2010-19 Felix Krueger, Babraham Bioinformatics www.bioinformatics.babraham.ac.uk/projects/bismark/ https://github.com/FelixKrueger/Bismark diff --git a/bam2nuc b/bam2nuc index 6cabdbf..bbb15ce 100755 --- a/bam2nuc +++ b/bam2nuc @@ -6,7 +6,7 @@ use Getopt::Long; use Cwd; use Carp; -## This program is Copyright (C) 2010-18, Felix Krueger (felix.krueger@babraham.ac.uk) +## This program is Copyright (C) 2010-19, Felix Krueger (felix.krueger@babraham.ac.uk) ## 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 @@ -31,7 +31,7 @@ my %freqs; # keeping a record of which chromosomes have been processed my %genomic_freqs; my %processed; -my $bam2nuc_version = 'v0.20.0'; +my $bam2nuc_version = 'v0.20.1'; my ($output_dir,$genome_folder,$parent_dir,$samtools_path,$genome_freq_only) = process_commandline(); @@ -380,8 +380,10 @@ sub process_commandline{ bam2nuc Bismark Version: $bam2nuc_version - Copyright 2010-16 Felix Krueger, Babraham Bioinformatics + Copyright 2010-19 Felix Krueger, Babraham Bioinformatics www.bioinformatics.babraham.ac.uk/projects/bismark/ + https://github.com/FelixKrueger/Bismark + VERSION @@ -650,7 +652,7 @@ TT 5055 10.96 1314144 10.80 0.004 This file is picked up and plotted by bismark2report automatically if found in the folder. - Script last modified: 26 April 2018 + Script last modified: 07 Dec 2018 EOF ; diff --git a/bismark b/bismark index 3c41116..0b4b8fd 100755 --- a/bismark +++ b/bismark @@ -25,7 +25,7 @@ use lib "$RealBin/../lib"; my $parent_dir = getcwd(); -my $bismark_version = 'v0.20.0_dev'; +my $bismark_version = 'v0.20.1'; my $start_run = time(); # warn "Run started at: $start_run\n"; my $command_line = join (" ",@ARGV); @@ -7809,7 +7809,7 @@ sub process_command_line{ Bismark - Bisulfite Mapper and Methylation Caller. Bismark Version: $bismark_version - Copyright 2010-18 Felix Krueger, Babraham Bioinformatics + Copyright 2010-19 Felix Krueger, Babraham Bioinformatics www.bioinformatics.babraham.ac.uk/projects/ https://github.com/FelixKrueger/Bismark @@ -7825,6 +7825,7 @@ VERSION if ($bowtie1){ $bowtie2 = 0; + warn ">>> Please note that the use of Bowtie 1 is now deprecated. Bowtie 1 support will be removed from the Bismark suite in due course. <<<\n"; sleep(3); } else{ # Bowtie 2 is now the default mode (as of 27 July 2015) $bowtie2 = 1; @@ -10207,7 +10208,8 @@ BOWTIE 2 SPECIFIC OPTIONS --bowtie1 Uses Bowtie 1 instead of Bowtie 2, which might be a good choice for faster and very short alignments. Bismark assumes that raw sequence data is adapter and/or quality trimmed where - appropriate. Default: off. + appropriate. Default: off. PLEASE NOTE: that the use of Bowtie 1 is now deprecated. Bowtie 1 + support will be removed from the Bismark suite in due course. --bowtie2 Default: ON. Uses Bowtie 2 instead of Bowtie 1. Bismark limits Bowtie 2 to only perform end-to-end alignments, i.e. searches for alignments involving all read characters (also called diff --git a/bismark2bedGraph b/bismark2bedGraph index e2a01e2..98a6647 100755 --- a/bismark2bedGraph +++ b/bismark2bedGraph @@ -6,7 +6,7 @@ use Getopt::Long; use Cwd; use Carp; -## This program is Copyright (C) 2010-18, Felix Krueger (felix.krueger@babraham.ac.uk) +## This program is Copyright (C) 2010-19, Felix Krueger (felix.krueger@babraham.ac.uk) ## 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 @@ -21,7 +21,7 @@ use Carp; ## You should have received a copy of the GNU General Public License ## along with this program. If not, see . -my $bismark2bedGraph_version = 'v0.20.0'; +my $bismark2bedGraph_version = 'v0.20.1'; my @bedfiles; my @methylcalls = qw (0 0 0); # [0] = methylated, [1] = unmethylated, [2] = total @@ -626,7 +626,7 @@ sub process_commandline{ bismark2bedGraph Bismark Extractor Version: $bismark2bedGraph_version - Copyright 2010-18 Felix Krueger, Babraham Bioinformatics + Copyright 2010-19 Felix Krueger, Babraham Bioinformatics www.bioinformatics.babraham.ac.uk/projects/bismark/ https://github.com/FelixKrueger/Bismark diff --git a/bismark2report b/bismark2report index af09a2a..ac1d383 100755 --- a/bismark2report +++ b/bismark2report @@ -5,7 +5,7 @@ use Getopt::Long; use FindBin qw($RealBin); use lib "$RealBin/../lib"; -## This program is Copyright (C) 2010-18, Felix Krueger (felix.krueger@babraham.ac.uk) +## This program is Copyright (C) 2010-19, Felix Krueger (felix.krueger@babraham.ac.uk) ## This program is free software: you can redistribute it and/or modify ## it under the terms of the GNU General Public License as published by @@ -20,7 +20,7 @@ use lib "$RealBin/../lib"; ## You should have received a copy of the GNU General Public License ## along with this program. If not, see . -my $bismark2report_version = 'v0.20.0'; +my $bismark2report_version = 'v0.20.1'; my (@alignment_reports,@dedup_reports,@splitting_reports,@mbias_reports,@nuc_reports); my ($output_dir,$verbose,$manual_output_file) = process_commandline(); @@ -81,7 +81,7 @@ while (@alignment_reports){ } - # Creation timestamp + # Create timestamp $doc = getLoggingTime($doc); # BISMARK ALIGNMENT REPORT (mandatory) @@ -1017,7 +1017,7 @@ sub read_report_template{ $doc .= $_."\n"; } - close DOC or die $!; + close DOC or warn $!; return $doc; } @@ -1066,7 +1066,7 @@ sub process_commandline{ Bismark HTML Report Module bismark2report version: $bismark2report_version - Copyright 2010-18 Felix Krueger, Babraham Bioinformatics + Copyright 2010-19 Felix Krueger, Babraham Bioinformatics www.bioinformatics.babraham.ac.uk/projects/bismark/ https://github.com/FelixKrueger/Bismark diff --git a/bismark2summary b/bismark2summary index 2b2a1dd..cc37072 100755 --- a/bismark2summary +++ b/bismark2summary @@ -22,7 +22,7 @@ use lib "$RealBin/../lib"; ## You should have received a copy of the GNU General Public License ## along with this program. If not, see . -my $bismark_version = '0.20.0_dev'; +my $bismark_version = '0.20.1'; # Last modified 03 01 2019 diff --git a/bismark_genome_preparation b/bismark_genome_preparation index 20832c1..f139768 100755 --- a/bismark_genome_preparation +++ b/bismark_genome_preparation @@ -6,7 +6,7 @@ use Getopt::Long; $|++; -## This program is Copyright (C) 2010-18, Felix Krueger (felix.krueger@babraham.ac.uk) +## This program is Copyright (C) 2010-19, Felix Krueger (felix.krueger@babraham.ac.uk) ## 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 @@ -37,7 +37,7 @@ my $genomic_composition; my %genomic_freqs; # storing the genomic sequence composition my %freqs; -my $bismark_version = 'v0.20.0_dev'; +my $bismark_version = 'v0.20.1'; GetOptions ('verbose' => \$verbose, 'help' => \$help, @@ -62,8 +62,11 @@ if ($version){ Bismark - Bisulfite Mapper and Methylation Caller. Bismark Genome Preparation Version: $bismark_version - Copyright 2010-18 Felix Krueger, Babraham Bioinformatics + Copyright 2010-19 Felix Krueger, Babraham Bioinformatics www.bioinformatics.babraham.ac.uk/projects/ + https://github.com/FelixKrueger/Bismark + + VERSION exit; @@ -108,6 +111,8 @@ if ($bowtie1){ } $bowtie2 = 0; $verbose and print "Aligner to be used: Bowtie (1)\n"; + + warn "Please note that the use of Bowtie 1 is now deprecated. Bowtie 1 support will be removed from the Bismark suite in due course.\n"; sleep(3); } else{ # Bowtie 2 is now the default mode (as of 27 July 2015) if ($bowtie2){ @@ -492,8 +497,7 @@ sub create_bisulfite_genome_folders{ die "The specified genome folder $genome_folder does not contain any sequence files in FastA format (with .fa, .fa.gz, .fasta or .fasta.gz file extensions)\n"; } - warn "Bisulfite Genome Indexer version $bismark_version (last modified 25 September 2018)\n"; - sleep (1); + warn "Bisulfite Genome Indexer version $bismark_version (last modified 01 February 2019)\n"; # creating a directory inside the genome folder to store the bisfulfite genomes unless it already exists my $bisulfite_dir = "${genome_folder}Bisulfite_Genome/"; @@ -634,6 +638,8 @@ two simultaneous instances of the Bowtie 1 or 2 indexer (bowtie-build or bowtie2 that the indexing process can take up to several hours; this will mainly depend on genome size and system resources. +>>> PLEASE NOTE THAT USING BOWTIE 1 IS NOW DEPRECATED, AND WILL BE REMOVED FROM BISMARK IN FUTURE VERSIONS <<< + The following is a brief description of command line options and arguments to control the @@ -657,7 +663,8 @@ OPTIONS: --bowtie2 This will create bisulfite indexes for Bowtie 2. (Default: ON). ---bowtie1 This will create bisulfite indexes for Bowtie 1. (Default: OFF). +--bowtie1 This will create bisulfite indexes for Bowtie 1. (Default: OFF). PLEASE NOTE THAT USING + BOWTIE 1 IS NOW DEPRECATED, AND WILL BE REMOVED FROM BISMARK IN FUTURE VERSIONS. --parallel INT Use several threads for each indexing process to speed up the genome preparation step. Remember that the indexing is run twice in parallel already (for the top and bottom strand @@ -686,6 +693,6 @@ ARGUMENTS: (with the file extension: .fa or .fasta (also ending in .gz)). Specifying this path is mandatory. -This script was last modified on 25 September 2018. +This script was last modified on 01 February 2019. HOW_TO } diff --git a/bismark_methylation_extractor b/bismark_methylation_extractor index cb77585..b9f24f1 100755 --- a/bismark_methylation_extractor +++ b/bismark_methylation_extractor @@ -29,7 +29,7 @@ my $parent_dir = getcwd(); my %fhs; -my $version = 'v0.20.0_dev'; +my $version = 'v0.20.1'; my ($ignore,$genomic_fasta,$single,$paired,$full,$report,$no_overlap,$merge_non_CpG,$vanilla,$output_dir,$no_header,$bedGraph,$remove,$coverage_threshold,$counts,$cytosine_report,$genome_folder,$zero,$CpG_only,$CX_context,$split_by_chromosome,$sort_size,$samtools_path,$gzip,$ignore_r2,$mbias_off,$mbias_only,$gazillion,$ample_mem,$ignore_3prime,$ignore_3prime_r2,$multicore,$yacht) = process_commandline(); ### only needed for bedGraph output @@ -1003,7 +1003,7 @@ sub process_commandline{ Bismark Methylation Extractor Bismark Extractor Version: $version - Copyright 2010-18 Felix Krueger, Babraham Bioinformatics + Copyright 2010-19 Felix Krueger, Babraham Bioinformatics www.bioinformatics.babraham.ac.uk/projects/bismark/ https://github.com/FelixKrueger/Bismark diff --git a/coverage2cytosine b/coverage2cytosine index 15d4383..a46bc01 100755 --- a/coverage2cytosine +++ b/coverage2cytosine @@ -22,7 +22,7 @@ use Carp; my %chromosomes; # storing sequence information of all chromosomes/scaffolds my %processed; # keeping a record of which chromosomes have been processed -my $coverage2cytosine_version = 'v0.20.0'; +my $coverage2cytosine_version = 'v0.20.1'; my ($output_dir,$genome_folder,$zero,$CpG_only,$CX_context,$split_by_chromosome,$parent_dir,$coverage_infile,$cytosine_out,$merge_CpGs,$gc_context,$gzip,$tetra,$nome,$disco) = process_commandline(); @@ -1559,7 +1559,7 @@ sub process_commandline{ coverage2cytosine Bismark coverage2cytosine Version: $coverage2cytosine_version - Copyright 2010-18 Felix Krueger, Babraham Bioinformatics + Copyright 2010-19 Felix Krueger, Babraham Bioinformatics www.bioinformatics.babraham.ac.uk/projects/bismark/ https://github.com/FelixKrueger/Bismark diff --git a/deduplicate_bismark b/deduplicate_bismark index 08d0c0b..609a6e4 100755 --- a/deduplicate_bismark +++ b/deduplicate_bismark @@ -40,7 +40,7 @@ use Cwd; ### start and end at the exact same position ### Deduplication in --representative mode is now no longer supported. It wasn't what people should have wanted anyway -my $dedup_version = 'v0.20.0'; +my $dedup_version = 'v0.20.1'; my @filenames; my ($single,$paired,$global_single,$global_paired,$vanilla,$samtools_path,$bam,$rrbs,$multiple,$output_dir) = process_commandline(); @@ -1042,7 +1042,7 @@ sub process_commandline{ Bismark Deduplication Module Deduplicator Version: $dedup_version - Copyright 2010-18 Felix Krueger, Babraham Bioinformatics + Copyright 2010-19 Felix Krueger, Babraham Bioinformatics www.bioinformatics.babraham.ac.uk/projects/bismark/ https://github.com/FelixKrueger/Bismark diff --git a/filter_non_conversion b/filter_non_conversion index 745a0a3..045b23b 100755 --- a/filter_non_conversion +++ b/filter_non_conversion @@ -6,7 +6,7 @@ use Cwd; $|++; -## This program is Copyright (C) 2010-18, Felix Krueger (felix.krueger@babraham.ac.uk) +## This program is Copyright (C) 2010-19, Felix Krueger (felix.krueger@babraham.ac.uk) ## 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 @@ -22,7 +22,7 @@ $|++; ## along with this program. If not, see . my $parent_dir = getcwd(); -my $filter_version = 'v0.20.0'; +my $filter_version = 'v0.20.1'; my ($single,$paired); my ($global_single,$global_paired,$samtools_path,$threshold,$consecutive,$percentage_cutoff,$minimum_count) = process_commandline(); @@ -493,7 +493,7 @@ sub process_commandline{ Bismark non-conversion filtering Bismark non-conversion version: $filter_version - Copyright 2010-18 Felix Krueger, Babraham Bioinformatics + Copyright 2010-19 Felix Krueger, Babraham Bioinformatics www.bioinformatics.babraham.ac.uk/projects/bismark/ https://github.com/FelixKrueger/Bismark