Merge pull request #163 from griffithlab/singlecell

Incorporate single cell changes

Author: kcotto

CMakeLists.txt

@@ -11,8 +11,8 @@ include(TestHelper)
 
 #versioning stuff
 set (regtools_VERSION_MAJOR 0)
-set (regtools_VERSION_MINOR 5)
-set (regtools_VERSION_PATCH 2)
+set (regtools_VERSION_MINOR 0)
+set (regtools_VERSION_PATCH 1)
 
 configure_file (
     "${PROJECT_SOURCE_DIR}/src/version.h.in"

Dockerfile

@@ -2,10 +2,12 @@
 ##################### Set Inital Image to work from ############################
 
 # work from latest LTS ubuntu release
-FROM ubuntu:18.04
+FROM ubuntu:20.04
 
 # set variables
 ENV r_version 3.6.0
+ENV TZ=US/Chicago
+ENV DEBIAN_FRONTEND noninteractive
 
 # run update
 RUN apt-get update -y && apt-get install -y \
@@ -25,7 +27,8 @@ RUN apt-get update -y && apt-get install -y \
   git \
   build-essential \
   cmake \
-  python3
+  python3 \
+  python3-pip
 
 ################################################################################
 ##################### Add Container Labels #####################################
@@ -51,23 +54,38 @@ 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 SpliceAI #########################################
+
+RUN pip3 install spliceai
+RUN pip3 install --upgrade tensorflow
+RUN pip3 install keras==2.4.3
+
 ################################################################################
 ##################### Install Regtools #########################################
 
-# add repo source
+
+# removed this due to docker build pulling the correct branch already and the below command actually overwriting the desired branch to master
+# clone git repository
 ADD . /regtools
 
-# make a build directory for regtools
+# change to regtools to build it 
+
 WORKDIR /regtools
 
 # compile from source
 RUN mkdir build && cd build && cmake .. && make
 
 ################################################################################
-###################### set environment path    #################################
+################### Make scripts executable ####################################
 
-# make a build directory for regtools
-WORKDIR /scripts/
+WORKDIR /regtools/scripts
+
+RUN chmod ugo+x *
+
+################################################################################
+###################### set environment path    #################################
 
 # add regtools executable to path
-ENV PATH="/regtools/build:/usr/local/bin/R-${r_version}:${PATH}"
+ENV PATH="/regtools/build:/usr/local/bin:/usr/local/bin/R-${r_version}:${PATH}"
+

README.md

@@ -2,7 +2,7 @@
 [![Documentation Status](https://readthedocs.org/projects/regtools/badge/?version=latest)](https://readthedocs.org/projects/regtools/?badge=latest)
 [![Coverage Status](https://coveralls.io/repos/griffithlab/regtools/badge.svg?branch=master&service=github)](https://coveralls.io/github/griffithlab/regtools?branch=master)
 
-# regtools
+# RegTools
 
 Tools that integrate DNA-seq and RNA-seq data to help interpret mutations
 in a regulatory and splicing context.
@@ -14,6 +14,17 @@ in a regulatory and splicing context.
 - Annotate exon-exon junctions with information from a known transcriptome.
 - Annotate variants with splice-region(the definition of this region is configurable) annotations.
 
+## Hardware requirements
+RegTools  requires only a standard computer with enough RAM to support the in-memory operations.
+
+## Software requirements
+OS Requirements
+This package is supported for macOS and Linux. The package has been tested on the following systems:
+
+macOS: macOS 10.12 (Sierra), macOS 10.13 (High Sierra), macOS 10.14 (Mojave), macOS 10.15 (Catalina), macOS 11 (Big Sur), macOS 12 (Monterey)
+
+Linux: Ubuntu 16.04, Ubuntu 18.04, Ubuntu 20.04
+
 ## Installation
 
 Clone and install regtools by running the following:
@@ -26,6 +37,8 @@ Clone and install regtools by running the following:
     make
 ```
 
+Installation should take 1-5 minutes.
+
 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:
@@ -34,6 +47,34 @@ For convienience we also maintain a docker image available at [https://hub.docke
     regtools --help
 ```
 
+If one wishes to test their installation, we include test data under `test_data`. 
+
+Here's an example command using that data along with the example output. This should run in under a minute.
+
+```sh
+regtools cis-splice-effects identify -s RF -e 10 -i 10 test_data/HCC1395_chr22.vcf.gz test_data/HCC1395_tumor.bam test_data/chr22_with_ERCC92.fa test_data/chr22_with_ERCC92.gtf
+
+Variant 22	42129188	42129189	-1
+Variant region is 22:42128784-42130813
+
+chrom	start	end	name	score	strand	splice_site	acceptors_skipped	exons_skipped	donors_skipped	anchor	known_donor	known_acceptor	known_junction	gene_names	gene_ids	transcripts	variant_info
+position = 22:42125408-42125409
+position = 22:42130565-42130566
+22	42125407	42130567	JUNC00000001	4	+	GT-AG	0	0	0	D	1	0	0	NDUFA6-AS1	ENSG00000237037	ENST00000439129	22:42129188-42129189
+position = 22:42128881-42128882
+position = 22:42129670-42129671
+22	42128880	42129672	JUNC00000002	3	+	GT-AG	0	0	0	N	0	0	0	NA	NA	NA	22:42129188-42129189
+position = 22:42128944-42128945
+position = 22:42129031-42129032
+22	42128943	42129033	JUNC00000003	4	-	GT-GG	1	0	0	D	1	0	0	CYP2D6	ENSG00000100197	ENST00000360608,ENST00000389970,ENST00000488442	22:42129188-42129189
+position = 22:42129783-42129784
+position = 22:42143453-42143454
+22	42129782	42143455	JUNC00000004	2	+	GC-AG	9	8	9	N	0	0	0	NA	NA	NA	22:42129188-42129189
+position = 22:42130224-42130225
+position = 22:42130565-42130566
+22	42130223	42130567	JUNC00000005	2	+	GT-AG	0	0	0	N	0	0	0	NA	NA	NA	22:42129188-42129189
+```
+
 ## Contribute
 
 - Issue Tracker: github.com/griffithlab/regtools/issues

build-common/python/integrationtest.py

@@ -34,7 +34,8 @@ def inputFiles(self, *names):
         return rv
 
     def execute(self, args):
-        print("args ", args)
+        print(args ), args
+
         cmdline = "%s %s" %(self.exe_path, " ".join(args))
         vglog_file = self.tempFile("valgrind.log")
         return ValgrindWrapper(shlex.split(cmdline), vglog_file).run()

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

@@ -13,9 +13,9 @@ The `cis-splice-effects identify` command is used to identify splicing misregula
 | Input                  | Description |
 | ------                 | ----------- |
 | variants.vcf | Variant call in VCF format from which to look for cis-splice-effects.|
-| alignments.bam | Aligned RNAseq BAM/CRAM produced with a splice aware aligner, that has been indexed for example with `samtools index`. We have tested this command with alignments from TopHat.|
+| alignments.bam | Aligned RNAseq BAM/CRAM produced with a splice aware aligner, that has been indexed for example with `samtools index`. We have tested this command with alignments from HISAT2, TopHat2, STAR, kallisto, and minimap2.|
 | 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/).|
+| annotations.gtf | The GTF file specifies the transcriptome that is used to annotate the junctions and variants. For examples, the Ensembl GTFs for release 106 are [here](http://ftp.ensembl.org/pub/release-106/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.
 
@@ -26,7 +26,7 @@ The `cis-splice-effects identify` command is used to identify splicing misregula
 | -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. If you are unsure, we have created this [table](https://rnabio.org/module-09-appendix/0009/12/01/StrandSettings/) to help. |
+| -s INT    |    Strand specificity of RNA library preparation, where the options XS, use XS tags provided by aligner; RF, first-strand; FR, second-strand. This option is required. If your alignments contain XS tags, these will be used in the "unstranded" mode. If you are unsure, we have created this [table](https://rnabio.org/module-09-appendix/0009/12/01/StrandSettings/) to help. |
 | -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]    |

docs/commands/junctions-annotate.md

@@ -17,7 +17,7 @@ Gene Annotation databases such as Ensembl/RefSeq/UCSC etc. The goal of the annot
 | ------          | ----------- |
 | junctions.bed   | The BED file with the junctions that have be annotated. This file has to be in the BED12 format. One recommended way of obtaining this file is by running `regtools junctions extract`. See [here](junctions-extract.md) for more details.|
 | ref.fa          | The reference FASTA file. The donor and acceptor sequences used in the "splice-site" column are extracted from the FASTA file. |
-| annotations.gtf | The GTF file specifies the transcriptome that is used to annotate the junctions. For examples, the Ensembl GTFs for release78 are [here](ftp://ftp.ensembl.org/pub/release-78/gtf/)|
+| annotations.gtf | The GTF file specifies the transcriptome that is used to annotate the junctions. For examples, the Ensembl GTFs for release 106 are [here](http://ftp.ensembl.org/pub/release-106/gtf/).||
 
 ## Options
 

docs/commands/junctions-extract.md

@@ -1,6 +1,6 @@
 # Overview of `junctions extract` command
 
-The `junctions extract` command can be used to extract exon-exon junctions from an RNAseq BAM file. The output is a BED file in the BED12 format. We have tested this command with alignments from TopHat and by comparing the exon-exon junctions with the `junctions.bed` file produced from TopHat.
+The `junctions extract` command can be used to extract exon-exon junctions from an RNAseq BAM file. The output is a BED file in the BED12 format. We have tested this command with alignments from HISAT2, TopHat2, STAR, kallisto, and minimap2 and by comparing the exon-exon junctions with the `junctions.bed` file produced from TopHat.
 
 
 ## Usage
@@ -23,7 +23,7 @@ The `junctions extract` command can be used to extract exon-exon junctions from
 | -o      | File to write output to. STDOUT by default.|
 | -r      | Region to extract junctions in. This is specified in the format "chr:start-end". If not specified, junctions are extracted from the entire BAM file.|
 | -h      | Display help message for this command.|
-| -s      | 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. If you are unsure, we have created this [table](https://rnabio.org/module-09-appendix/0009/12/01/StrandSettings/) to help.
+| -s      | Strand specificity of RNA library preparation, where the options XS, use XS tags provided by aligner; RF, first-strand; FR, second-strand. This option is required. If your alignments contain XS tags, these will be used in the "unstranded" mode. If you are unsure, we have created this [table](https://rnabio.org/module-09-appendix/0009/12/01/StrandSettings/) to help.
 
 ## Output
 

docs/index.md

@@ -27,6 +27,34 @@ make
 regtools --help
 ```
 
+If one wishes to test their installation, we include test data under `test_data`. 
+
+Here's an example command using that data along with the example output.
+
+```sh
+regtools cis-splice-effects identify -s RF -e 10 -i 10 test_data/HCC1395_chr22.vcf.gz test_data/HCC1395_tumor.bam test_data/chr22_with_ERCC92.fa test_data/chr22_with_ERCC92.gtf
+
+Variant 22	42129188	42129189	-1
+Variant region is 22:42128784-42130813
+
+chrom	start	end	name	score	strand	splice_site	acceptors_skipped	exons_skipped	donors_skipped	anchor	known_donor	known_acceptor	known_junction	gene_names	gene_ids	transcripts	variant_info
+position = 22:42125408-42125409
+position = 22:42130565-42130566
+22	42125407	42130567	JUNC00000001	4	+	GT-AG	0	0	0	D	1	0	0	NDUFA6-AS1	ENSG00000237037	ENST00000439129	22:42129188-42129189
+position = 22:42128881-42128882
+position = 22:42129670-42129671
+22	42128880	42129672	JUNC00000002	3	+	GT-AG	0	0	0	N	0	0	0	NA	NA	NA	22:42129188-42129189
+position = 22:42128944-42128945
+position = 22:42129031-42129032
+22	42128943	42129033	JUNC00000003	4	-	GT-GG	1	0	0	D	1	0	0	CYP2D6	ENSG00000100197	ENST00000360608,ENST00000389970,ENST00000488442	22:42129188-42129189
+position = 22:42129783-42129784
+position = 22:42143453-42143454
+22	42129782	42143455	JUNC00000004	2	+	GC-AG	9	8	9	N	0	0	0	NA	NA	NA	22:42129188-42129189
+position = 22:42130224-42130225
+position = 22:42130565-42130566
+22	42130223	42130567	JUNC00000005	2	+	GT-AG	0	0	0	N	0	0	0	NA	NA	NA	22:42129188-42129189
+```
+
 For information about the individual RegTools commands, please see [the Commands page](commands/commands.md)
 
 ## Contribute

scripts/README.md

@@ -0,0 +1 @@
+test