Merge branch 'master' into gene_id

Author: gatoravi

.DS_Store

@@ -11,8 +11,9 @@ include(TestHelper)
 
 #versioning stuff
 set (regtools_VERSION_MAJOR 0)
-set (regtools_VERSION_MINOR 4)
-set (regtools_VERSION_PATCH 0)
+set (regtools_VERSION_MINOR 5)
+set (regtools_VERSION_PATCH 2)
+
 configure_file (
     "${PROJECT_SOURCE_DIR}/src/version.h.in"
     "${PROJECT_BINARY_DIR}/version.h"

CMakeLists.txt

@@ -0,0 +1,75 @@
+################################################################################
+##################### Set Inital Image to work from ############################
+
+# work from latest LTS ubuntu release
+FROM ubuntu:18.04
+
+# set variables
+ENV r_version 3.6.0
+
+# run update
+RUN apt-get update -y && apt-get install -y \
+  gfortran \
+  libreadline-dev \
+  libpcre3-dev \
+  libcurl4-openssl-dev \
+  build-essential \
+  zlib1g-dev \
+  libbz2-dev \
+  liblzma-dev \
+  openjdk-8-jdk \
+  wget \
+  libssl-dev \
+  libxml2-dev \
+  libnss-sss \
+  git \
+  build-essential \
+  cmake \
+  python3
+  
+################################################################################
+##################### Add Container Labels #####################################
+LABEL "Regtools_License"="MIT"
+LABEL "Description"="Software package which integrate DNA-seq and RNA-seq data\
+                     to help interpret mutations in a regulatory and splicing\
+                     context."
+
+################################################################################
+####################### Install R ##############################################
+
+# change working dir
+WORKDIR /usr/local/bin
+
+# install R
+RUN wget https://cran.r-project.org/src/base/R-3/R-${r_version}.tar.gz
+RUN tar -zxvf R-${r_version}.tar.gz
+WORKDIR /usr/local/bin/R-${r_version}
+RUN ./configure --prefix=/usr/local/ --with-x=no
+RUN make
+RUN make install
+
+# install R packages
+RUN R --vanilla -e 'install.packages(c("data.table", "plyr", "tidyverse"), repos = "http://cran.us.r-project.org")'
+
+################################################################################
+##################### Install Regtools #########################################
+
+# clone git repository
+RUN cd / && git clone https://github.com/griffithlab/regtools.git
+
+# make a build directory for regtools
+WORKDIR /regtools/
+
+
+# compile from source
+RUN mkdir build && cd build && cmake .. && make
+
+################################################################################
+###################### set environment path    #################################
+
+# make a build directory for regtools
+WORKDIR /regtools/scripts/
+
+# add regtools executable to path
+ENV PATH="/regtools/build:/usr/local/bin/R-${r_version}:${PATH}"
+

Dockerfile

@@ -16,7 +16,7 @@ in a regulatory and splicing context.
 
 ## Installation
 
-Clone and install regtools by running:
+Clone and install regtools by running the following:
 ```
     git clone https://github.com/griffithlab/regtools
     cd regtools/
@@ -26,6 +26,8 @@ Clone and install regtools by running:
     make
 ```
 
+For convienience we also maintain a docker image available at [https://hub.docker.com/r/griffithlab/regtools/](https://hub.docker.com/r/griffithlab/regtools/)
+
 ## Usage:
 
 ```
@@ -55,6 +57,7 @@ If you would like to build the documentation locally, please install
 work on most machines. Then run `mkdocs serve` from within the `regtools`
 base directory.
 
+
 ## Acknowledgements
 
 Regtools uses several open-source libraries. We would like to thank the
@@ -64,3 +67,9 @@ useful comments and code.
 ## License
 
 The project is licensed under the [MIT license](https://opensource.org/licenses/MIT).
+
+## Stable release with DOI
+
+[![DOI](https://zenodo.org/badge/35841695.svg)](https://zenodo.org/badge/latestdoi/35841695)
+
+

README.md

@@ -1,5 +1,5 @@
-# Regtools
-Regtools is a project by The Griffith Lab at the McDonnell Genome Institute.
+# RegTools
+RegTools is a project by The Griffith Lab at the McDonnell Genome Institute.
 The source for the project is on [Github.](https://github.com/griffithlab/regtools)
 
 ##License

docs/about.md

@@ -10,7 +10,7 @@ The `cis-ase identify` command is used to identify allele-specific expression ev
 | somatic-variants.vcf   | Somatic variant calls in VCF format. The tool looks for allele specific expression at polymorphic loci near the somatic variants|
 | polymorphisms.vcf   | List of polymorphic loci in the VCF format. RNA expression is checked at these sites to identify evidence of allele speciific expression|
 | dna-alignments.bam | Aligned DNA reads in the BAM format that has been indexed for example with `samtools index`. We have tested this command with alignments from BWA.|
-| dna-alignments.bam | Aligned RNAseq BAM produced with a splice aware aligner, that has been indexed for example with `samtools index`. We have tested this command with alignments from TopHat.|
+| rna-alignments.bam | Aligned RNAseq BAM produced with a splice aware aligner, that has been indexed for example with `samtools index`. We have tested this command with alignments from TopHat.|
 | ref.fa          | The reference FASTA file. The donor and acceptor sequences used in the "splice-site" column of the annotated junctions are extracted from the FASTA file. |
 | annotations.gtf | The GTF file specifies the transcriptome that is used to annotate the junctions and variants. For examples, the Ensembl GTFs for release78 are [here](ftp://ftp.ensembl.org/pub/release-78/gtf/).|
 

docs/commands/cis-ase-identify.md

@@ -0,0 +1,37 @@
+[csei]: ../images/csei_examples.png
+
+###Synopsis
+The `cis-splice-effects associate` command is used to identify splicing misregulation events. This command is similar to `cis-splice-effects identify`, but takes the BED output of `junctions extract` in lieu of a BAM file with RNA alignments. The tool then proceeds to associate non-canonical splicing junctions near the variant sites.
+
+###Usage
+`regtools cis-splice-effects associate [options] variants.vcf junctions.bed ref.fa annotations.gtf`
+
+###Input
+| Input                  | Description |
+| ------                 | ----------- |
+| variants.vcf | Variant call in VCF format from which to look for cis-splice-effects.|
+| junctions.bed | BED file of junctions to look through for evidence of splice events. The file is expected to be in the [BED12 format](junctions-extract.md#output) of the `junctions extract` output. |
+| ref.fa          | The reference FASTA file. The donor and acceptor sequences used in the "splice-site" column of the annotated junctions are extracted from the FASTA file. |
+| annotations.gtf | The GTF file specifies the transcriptome that is used to annotate the junctions and variants. For examples, the Ensembl GTFs for release78 are [here](ftp://ftp.ensembl.org/pub/release-78/gtf/).|
+
+**Note** - Please make sure that the version of the annotation GTF that you use corresponds with the version of the assembly build (ref.fa) and that the co-ordinates in the VCF file are also from the same build.
+
+###Options
+| Option  | Description |
+| ------  | ----------- |
+| -o STR	|	Output file containing the aberrant splice junctions with annotations. [STDOUT]	|
+| -v STR	|	Output file containing variants annotated as splice relevant (VCF format).	|
+| -j STR	|	Output file containing the aberrant junctions in BED12 format.	|
+| -w INT	|	Window size in b.p to associate splicing events in. The tool identifies events in variant.start +/- w basepairs. Default behaviour is to look at the window between previous and next exons.	|
+| -e INT	|	Maximum distance from the start/end of an exon to annotate a variant as relevant to splicing, the variant is in exonic space, i.e a coding variant. [3]	|
+| -i INT	|	Maximum distance from the start/end of an exon to annotate a variant as relevant to splicing, the variant is in intronic space. [2]	|
+| -I	|	Annotate variants in intronic space within a transcript(not to be used with -i).	|
+| -E	|	Annotate variants in exonic space within a transcript(not to be used with -e).	|
+| -S	|	Don't skip single exon transcripts.	|
+
+###Output
+For an explanation of the annotated junctions that are identified by this command please refer to the output of the `junctions annotate` command [here](junctions-annotate.md#output)
+For an explanation of the annotated variants that are identified by this command when using the -v option, please refer to the output of the `variants annotate` command [here](variants-annotate.md#output)
+
+###Examples
+![cis-splice-effects identify example][csei]

docs/commands/cis-splice-effects-associate.md

@@ -19,15 +19,16 @@ The `cis-splice-effects identify` command is used to identify splicing misregula
 ###Options
 | Option  | Description |
 | ------  | ----------- |
-| -o      | Output file containing the aberrant splice junctions. [STDOUT] |
-| -v      | Output file containing variants annotated as splice relevant (VCF format). |
-| -w      | Window around the variant file (in basepairs) to identify splicing events in. If specified the tool looks at +/- n b.p around the variant start position. For example -w 500 will look at a 1kb window around the variant. If this option is not specified, the default option is to look at a window that ranges from the start co-ordinate of the previous exon and ends at the end co-ordinate of the next exon i.e by treating the current exon as a cassette exon. |
-| -j      | Optional file containing the aberrant junctions in BED12 format. |
-| -e      | Maximum distance from the start/end of an exon to annotate a variant as relevant to splicing, the variant is in exonic space, i.e a coding variant. [default = 3] |
-| -i      | Maximum distance from the start/end of an exon to annotate a variant as relevant to splicing, the variant is in intronic space. [default = 2] |
-| -I      | Annotate variants in intronic space within a transcript (not to be used with -i).
-| -E      | Annotate variants in exonic space within a transcript (not to be used with -e).
-| -S      | Dont skip single exon transcripts. The default is to skip the single exon transcripts. |
+| -o STR	|	Output file containing the aberrant splice junctions with annotations. [STDOUT]	|
+| -v STR	|	Output file containing variants annotated as splice relevant (VCF format).	|
+| -j STR	|	Output file containing the aberrant junctions in BED12 format.	|
+| -s INT	|	Strand specificity of RNA library preparation, where 0 = unstranded/XS, 1 = first-strand/RF, 2 = second-strand/FR. This option is required. If your alignments contain XS tags, these will be used in the "unstranded" mode. |
+| -w INT	|	Window size in b.p to identify splicing events in. The tool identifies events in variant.start +/- w basepairs. Default behaviour is to look at the window between previous and next exons.	|
+| -e INT	|	Maximum distance from the start/end of an exon to annotate a variant as relevant to splicing, the variant is in exonic space, i.e a coding variant. [3]	|
+| -i INT	|	Maximum distance from the start/end of an exon to annotate a variant as relevant to splicing, the variant is in intronic space. [2]	|
+| -I	|	Annotate variants in intronic space within a transcript(not to be used with -i).	|
+| -E	|	Annotate variants in exonic space within a transcript(not to be used with -e).	|
+| -S	|	Don't skip single exon transcripts.	|
 
 ###Output
 For an explanation of the annotated junctions that are identified by this command please refer to the output of the `junctions annotate` command [here](junctions-annotate.md#output)

docs/commands/cis-splice-effects-identify.md

@@ -13,6 +13,7 @@ This set of tools helps identify and work with aberrant splicing events near var
 Below are links to detailed explanations of the `cis-splice-effects` sub-commands:
 
 - [identify](cis-splice-effects-identify.md)
+- [associate](cis-splice-effects-associate.md)
 
 ##cis-ase
 This set of tools helps identify and work with allele-specific-expression near variants, these could be somatic variants or germline polymorphisms/mutations. These variants are hypothesized to act in cis and affect how the gene is transcribed.

docs/commands/commands.md

@@ -20,7 +20,7 @@ Gene Annotation databases such as Ensembl/RefSeq/UCSC etc. The goal of the annot
 ###Options
 | Option  | Description |
 | ------  | ----------- |
-| -E      | Do not skip single exon genes. The default is to skip the single exon genes while annotating junctions.|
+| -S      | Do not skip single exon genes. The default is to skip the single exon genes while annotating junctions.|
 | -o      | File to write output to. STDOUT by default. The output format is described [here](#output)|
 | -h      | Display help message for this command.|