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Merge pull request #169 from microPIECE-team/pre_release_v1.5.1
Preparation v1.5.1
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‎README.md‎

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@@ -31,13 +31,13 @@ For the minimal workflow it needs a genome file, as well as its annotation file
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## Installation
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Please install the dependencies and run
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```
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git clone -b v1.5.0 git@github.com:microPIECE-team/microPIECE.git
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git clone -b v1.5.1 git@github.com:microPIECE-team/microPIECE.git
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```
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or download the latest release as `*.tar.gz` or `*.zip` file:
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```
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curl -L -o microPIECE_v1.5.0.tar.gz https://github.com/microPIECE-team/microPIECE/archive/v1.5.0.tar.gz
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curl -L -o microPIECE_v1.5.1.tar.gz https://github.com/microPIECE-team/microPIECE/archive/v1.5.1.tar.gz
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# or
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curl -L -o microPIECE_v1.5.0.zip https://github.com/microPIECE-team/microPIECE/archive/v1.5.0.zip
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curl -L -o microPIECE_v1.5.1.zip https://github.com/microPIECE-team/microPIECE/archive/v1.5.1.zip
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```
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## Docker
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### Information about the docker images:
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| Branch | Size | Layers | Comment |
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|-|-|-|-|
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|[![](https://images.microbadger.com/badges/version/micropiece/micropiece:v1.5.0.svg)](https://microbadger.com/images/micropiece/micropiece:v1.5.0) | [![](https://images.microbadger.com/badges/image/micropiece/micropiece:v1.5.0.svg)](https://microbadger.com/images/micropiece/micropiece:v1.5.0) | [![](https://images.microbadger.com/badges/commit/micropiece/micropiece:v1.5.0.svg)](https://microbadger.com/images/micropiece/micropiece:v1.5.0) | Latest release [v1.5.0](https://github.com/microPIECE-team/microPIECE/releases/tag/v1.5.0) |
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|[![](https://images.microbadger.com/badges/version/micropiece/micropiece:v1.5.1.svg)](https://microbadger.com/images/micropiece/micropiece:v1.5.1) | [![](https://images.microbadger.com/badges/image/micropiece/micropiece:v1.5.1.svg)](https://microbadger.com/images/micropiece/micropiece:v1.5.1) | [![](https://images.microbadger.com/badges/commit/micropiece/micropiece:v1.5.1.svg)](https://microbadger.com/images/micropiece/micropiece:v1.5.1) | Latest release [v1.5.1](https://github.com/microPIECE-team/microPIECE/releases/tag/v1.5.1) |
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|[![](https://images.microbadger.com/badges/version/micropiece/micropiece:master.svg)](https://microbadger.com/images/micropiece/micropiece:master) | [![](https://images.microbadger.com/badges/image/micropiece/micropiece:master.svg)](https://microbadger.com/images/micropiece/micropiece:master) | [![](https://images.microbadger.com/badges/commit/micropiece/micropiece:master.svg)](https://microbadger.com/images/micropiece/micropiece:master) | |
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|[![](https://images.microbadger.com/badges/version/micropiece/micropiece:develop.svg)](https://microbadger.com/images/micropiece/micropiece:develop) | [![](https://images.microbadger.com/badges/image/micropiece/micropiece:develop.svg)](https://microbadger.com/images/micropiece/micropiece:develop) | [![](https://images.microbadger.com/badges/commit/micropiece/micropiece:develop.svg)](https://microbadger.com/images/micropiece/micropiece:develop) | |
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```
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docker pull micropiece/micropiece:v1.5.0
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docker pull micropiece/micropiece:v1.5.1
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git clone git@github.com:microPIECE-team/microPIECE-testset.git testset
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docker run -it --rm -v $PWD:/data micropiece/micropiece:v1.5.0 microPIECE.pl \
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docker run -it --rm -v $PWD:/data micropiece/micropiece:v1.5.1 microPIECE.pl \
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--genomeA testset/NC_035109.1_reduced_AAE_genome.fa \
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--genomeB testset/NC_007416.3_reduced_TCA_genome.fa \
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--annotationA testset/NC_035109.1_reduced_AAE_genome.gff \
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No features so far
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- [v1.5.1](https://github.com/microPIECE-team/microPIECE/releases/tag/v1.5.1) (2018-04-11)
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Added optimized pre-binning step for `Piranha` (Fixes [#132](https://github.com/microPIECE-team/microPIECE/issues/132))
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<div>
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This version is archived as <a href="https://doi.org/10.5281/zenodo.1216823"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.1216823.svg" alt="DOI" /></a>.
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</div>
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- [v1.5.0](https://github.com/microPIECE-team/microPIECE/releases/tag/v1.5.0) (2018-04-10)
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Removing additional length cutoff during CLIP transfer (Fixes [#153](https://github.com/microPIECE-team/microPIECE/issues/153))

‎lib/microPIECE.pm‎

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use strict;
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use warnings;
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use version 0.77; our $VERSION = version->declare("v1.5.0");
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use version 0.77; our $VERSION = version->declare("v1.5.1");
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use Log::Log4perl;
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use Data::Dumper;

‎microPIECE.pl‎

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No features so far
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=item L<v1.5.1|https://github.com/microPIECE-team/microPIECE/releases/tag/v1.5.1> (2018-04-11)
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Added optimized pre-binning step for C<Piranha> (Fixes L<#132|https://github.com/microPIECE-team/microPIECE/issues/132>)
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=begin html
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This version is archived as <a href="https://doi.org/10.5281/zenodo.1216823"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.1216823.svg" alt="DOI" /></a>.
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=end html
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=begin text
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This version is archived as L<https://doi.org/10.5281/zenodo.1216823>.
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=end text
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=item L<v1.5.0|https://github.com/microPIECE-team/microPIECE/releases/tag/v1.5.0> (2018-04-10)
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Removing additional length cutoff during CLIP transfer (Fixes L<#153|https://github.com/microPIECE-team/microPIECE/issues/153>)

‎paper/paper.md‎

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orcid: 0000-0002-0512-9802
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affiliation: 1
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- name: André Billion
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orcid:
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orcid: 0000-0002-5073-3347
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affiliation: 1
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- name: Andreas Vilcinskas
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orcid: 0000-0001-8276-4968
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index: 1
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- name: Institute for Insect Biotechnology, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
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index: 2
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date: 21 February 2018
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date: 11 April 2018
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bibliography: paper.bib
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---
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‎scripts/CLIP_binned_bed_from_bam_and_transcripts_for_piranha.pl‎

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my $binsize = 20;
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my $reqfeature = "exon";
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my $pseudocounts = 0;
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my $silent = 0;
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GetOptions(
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'b|bam=s@' => \@bamfiles,
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'r|reqfeature=s' => \$reqfeature,
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'V|version' => \$version,
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'h|help|?' => \$help,
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'q|quiet' => \$silent,
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) || pod2usage(2);
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pod2usage(1) if $help;
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}
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use Term::ProgressBar;
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# check if a terminal width can be estimated
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my %global_term_settings = (
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ETA => 'linear',
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remove => 0,
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silent => $silent,
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);
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my $progress = Term::ProgressBar->new({ %global_term_settings, name => "Test", count => 100});
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my $width = $progress->term_width();
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if (! defined $width || $width > 150)
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{
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$global_term_settings{term_width} = 150;
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}
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# import the transcripts
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my %imported_transcripts = ();
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foreach my $transcript (@transcripts)
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{
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my $progress = Term::ProgressBar->new({name => "Transcript import from '$transcript'", count => -s $transcript, remove => 0, ETA => 'linear'});
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my $progress = Term::ProgressBar->new({%global_term_settings, name => "Transcript import from '$transcript'", count => -s $transcript});
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$progress->minor(0);
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my $next_val = 0;
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foreach my $seq (@{$seq})
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{
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my $progress = Term::ProgressBar->new({name => $seq->{name}, count => $seq->{len}, remove => 0, ETA => 'linear'});
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my $progress = Term::ProgressBar->new({%global_term_settings, name => $seq->{name}, count => $seq->{len} });
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$progress->minor(0);
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my $next_val = 0;
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$bins2change += @{$list_of_feature_bins->[$strand]}
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my $progress = Term::ProgressBar->new({name => $seq->{name}." Pseudocounts", count => $bins2change, remove => 0, ETA => 'linear'});
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my $progress = Term::ProgressBar->new({%global_term_settings, name => $seq->{name}." Pseudocounts", count => $bins2change});
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$progress->minor(0);
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$progress = Term::ProgressBar->new({name => $seq->{name}." BEDoutput", count => int(@counts), remove => 0, ETA => 'linear'});
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$progress = Term::ProgressBar->new({%global_term_settings, name => $seq->{name}." BEDoutput", count => int(@counts)});
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for(my $i=0; $i<@counts; $i++)

‎t/testset_gff_bed_mapping/genome.bed‎

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# case1 minus strand, exon spanning
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NC_007416.3 7770 7783 . . -
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NC_007416.3 9209 9220 . . -
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# case2 minus strand, two exon spannings
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NC_007416.3 9209 9427 . . -
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NC_007416.3 10248 10260 . . -
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NC_007416.3 7770 7783 . . -
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# case3 plus strand, one exon spanning
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NC_007416.3 13840 13852 . . +
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NC_007416.3 13946 13960 . . +
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# case4 minus strand, whole exon
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NC_007416.3 10248 10432 . . -
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# case5 minus strand, part of exon
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NC_007416.3 10248 10332 . . -

‎t/testset_gff_bed_mapping/readme‎

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test.fa : genome part
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test.gff : gff part
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tr.bed : bed file with transcriptome coordinates
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genome.bed : bed file with genome coordinates

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