├── .dockerignore ├── .gitignore ├── Dockerfile ├── LICENSE ├── Makefile ├── README.md ├── make_IGV_snapshots.def ├── make_IGV_snapshots.py ├── regions.bed ├── regions_nf4.bed ├── report ├── Makefile ├── README.md ├── compile_Rmd_report.R ├── compile_Rnw_report.sh ├── report.Rmd └── report.Rnw └── test_data ├── test_alignments.bam ├── test_alignments.bam.bai ├── test_alignments2.bam └── test_alignments2.bam.bai /.dockerignore: -------------------------------------------------------------------------------- 1 | *.sif 2 | .dockerignore 3 | IGV_2.4.10/ 4 | *.zip 5 | igv.jar 6 | snapshots/ 7 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | # Byte-compiled / optimized / DLL files 2 | __pycache__/ 3 | *.py[cod] 4 | *$py.class 5 | 6 | # C extensions 7 | *.so 8 | 9 | # Distribution / packaging 10 | .Python 11 | env/ 12 | build/ 13 | develop-eggs/ 14 | dist/ 15 | downloads/ 16 | eggs/ 17 | .eggs/ 18 | lib/ 19 | lib64/ 20 | parts/ 21 | sdist/ 22 | var/ 23 | *.egg-info/ 24 | .installed.cfg 25 | *.egg 26 | 27 | # PyInstaller 28 | # Usually these files are written by a python script from a template 29 | # before PyInstaller builds the exe, so as to inject date/other infos into it. 30 | *.manifest 31 | *.spec 32 | 33 | # Installer logs 34 | pip-log.txt 35 | pip-delete-this-directory.txt 36 | 37 | # Unit test / coverage reports 38 | htmlcov/ 39 | .tox/ 40 | .coverage 41 | .coverage.* 42 | .cache 43 | nosetests.xml 44 | coverage.xml 45 | *,cover 46 | .hypothesis/ 47 | 48 | # Translations 49 | *.mo 50 | *.pot 51 | 52 | # Django stuff: 53 | *.log 54 | local_settings.py 55 | 56 | # Flask stuff: 57 | instance/ 58 | .webassets-cache 59 | 60 | # Scrapy stuff: 61 | .scrapy 62 | 63 | # Sphinx documentation 64 | docs/_build/ 65 | 66 | # PyBuilder 67 | target/ 68 | 69 | # IPython Notebook 70 | .ipynb_checkpoints 71 | 72 | # pyenv 73 | .python-version 74 | 75 | # celery beat schedule file 76 | celerybeat-schedule 77 | 78 | # dotenv 79 | .env 80 | 81 | # virtualenv 82 | venv/ 83 | ENV/ 84 | 85 | # Spyder project settings 86 | .spyderproject 87 | 88 | # Rope project settings 89 | .ropeproject 90 | IGV_Snapshots* 91 | bin* 92 | test.py 93 | target.bed 94 | *.sif 95 | snapshots/ 96 | -------------------------------------------------------------------------------- /Dockerfile: -------------------------------------------------------------------------------- 1 | # Docker container with the dependencies needed to run the IGV snapshot automator 2 | FROM ubuntu:16.04 3 | 4 | MAINTAINER Stephen M. Kelly 5 | 6 | RUN apt-get update && \ 7 | apt-get install -y wget \ 8 | unzip \ 9 | default-jdk \ 10 | xvfb \ 11 | xorg \ 12 | python \ 13 | make 14 | 15 | # add the source code for the repo to the container 16 | ADD . /IGV-snapshot-automator 17 | ENV PATH="/IGV-snapshot-automator/:/IGV-snapshot-automator/IGV_2.4.10/:${PATH}" 18 | 19 | # install IGV via the Makefile 20 | # then make a dummy batch script in order to load the hg19 genome into the container 21 | # https://software.broadinstitute.org/software/igv/PortCommands 22 | RUN cd /IGV-snapshot-automator && \ 23 | make install && \ 24 | printf 'new\ngenome hg19\nexit\n' > /genome.bat && \ 25 | xvfb-run --auto-servernum --server-num=1 igv.sh -b /genome.bat 26 | 27 | ENTRYPOINT ["make_IGV_snapshots.py"] 28 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | GNU GENERAL PUBLIC LICENSE 2 | Version 3, 29 June 2007 3 | 4 | Copyright (C) 2007 Free Software Foundation, Inc. 5 | Everyone is permitted to copy and distribute verbatim copies 6 | of this license document, but changing it is not allowed. 7 | 8 | Preamble 9 | 10 | The GNU General Public License is a free, copyleft license for 11 | software and other kinds of works. 12 | 13 | The licenses for most software and other practical works are designed 14 | to take away your freedom to share and change the works. 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If the Program does not specify a version number of the 576 | GNU General Public License, you may choose any version ever published 577 | by the Free Software Foundation. 578 | 579 | If the Program specifies that a proxy can decide which future 580 | versions of the GNU General Public License can be used, that proxy's 581 | public statement of acceptance of a version permanently authorizes you 582 | to choose that version for the Program. 583 | 584 | Later license versions may give you additional or different 585 | permissions. However, no additional obligations are imposed on any 586 | author or copyright holder as a result of your choosing to follow a 587 | later version. 588 | 589 | 15. Disclaimer of Warranty. 590 | 591 | THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY 592 | APPLICABLE LAW. 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Interpretation of Sections 15 and 16. 613 | 614 | If the disclaimer of warranty and limitation of liability provided 615 | above cannot be given local legal effect according to their terms, 616 | reviewing courts shall apply local law that most closely approximates 617 | an absolute waiver of all civil liability in connection with the 618 | Program, unless a warranty or assumption of liability accompanies a 619 | copy of the Program in return for a fee. 620 | 621 | END OF TERMS AND CONDITIONS 622 | 623 | How to Apply These Terms to Your New Programs 624 | 625 | If you develop a new program, and you want it to be of the greatest 626 | possible use to the public, the best way to achieve this is to make it 627 | free software which everyone can redistribute and change under these terms. 628 | 629 | To do so, attach the following notices to the program. It is safest 630 | to attach them to the start of each source file to most effectively 631 | state the exclusion of warranty; and each file should have at least 632 | the "copyright" line and a pointer to where the full notice is found. 633 | 634 | 635 | Copyright (C) 636 | 637 | This program is free software: you can redistribute it and/or modify 638 | it under the terms of the GNU General Public License as published by 639 | the Free Software Foundation, either version 3 of the License, or 640 | (at your option) any later version. 641 | 642 | This program is distributed in the hope that it will be useful, 643 | but WITHOUT ANY WARRANTY; without even the implied warranty of 644 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 645 | GNU General Public License for more details. 646 | 647 | You should have received a copy of the GNU General Public License 648 | along with this program. If not, see . 649 | 650 | Also add information on how to contact you by electronic and paper mail. 651 | 652 | If the program does terminal interaction, make it output a short 653 | notice like this when it starts in an interactive mode: 654 | 655 | Copyright (C) 656 | This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. 657 | This is free software, and you are welcome to redistribute it 658 | under certain conditions; type `show c' for details. 659 | 660 | The hypothetical commands `show w' and `show c' should show the appropriate 661 | parts of the General Public License. Of course, your program's commands 662 | might be different; for a GUI interface, you would use an "about box". 663 | 664 | You should also get your employer (if you work as a programmer) or school, 665 | if any, to sign a "copyright disclaimer" for the program, if necessary. 666 | For more information on this, and how to apply and follow the GNU GPL, see 667 | . 668 | 669 | The GNU General Public License does not permit incorporating your program 670 | into proprietary programs. If your program is a subroutine library, you 671 | may consider it more useful to permit linking proprietary applications with 672 | the library. If this is what you want to do, use the GNU Lesser General 673 | Public License instead of this License. But first, please read 674 | . 675 | -------------------------------------------------------------------------------- /Makefile: -------------------------------------------------------------------------------- 1 | # download and install IGV 2 | install: igv.jar 3 | 4 | igv.jar: IGV_2.4.10.zip 5 | unzip IGV_2.4.10.zip && \ 6 | rm -f IGV_2.4.10.zip && \ 7 | ln -s IGV_2.4.10/igv.jar 8 | 9 | IGV_2.4.10.zip: 10 | wget http://data.broadinstitute.org/igv/projects/downloads/2.4/IGV_2.4.10.zip -O tmp && mv tmp IGV_2.4.10.zip 11 | 12 | .INTERMEDIATE: tmp 13 | 14 | 15 | # build the Docker container from the current repo dir 16 | DOCKER_TAG:=stevekm/igv-snapshot-automator 17 | docker-build: 18 | docker build -t "$(DOCKER_TAG)" . 19 | 20 | # run the script on the test data inside the docker container 21 | docker-test: 22 | docker run \ 23 | --rm -ti \ 24 | -v $$PWD:$$PWD \ 25 | "$(DOCKER_TAG):latest" \ 26 | $$PWD/test_data/test_alignments.bam \ 27 | -r $$PWD/regions.bed \ 28 | -o $$PWD/snapshots 29 | 30 | # build the Singularity container using Docker 31 | # bind the current directory (project root dir) into the container as /host 32 | # outputs the container file `make_IGV_snapshots.sif` in the current directory 33 | # NOTE: singularityware/singularity:v3.3.0 has `singularity` as the entrypoint 34 | singularity-build: 35 | docker run --privileged --rm -ti \ 36 | -v $$PWD:/host \ 37 | singularityware/singularity:v3.3.0 \ 38 | build \ 39 | /host/make_IGV_snapshots.sif \ 40 | /host/make_IGV_snapshots.def 41 | 42 | # recipe to shell into the singularity container with Docker 43 | singularity-shell: 44 | docker run --privileged --rm -ti \ 45 | -v $$PWD:/host \ 46 | singularityware/singularity:v3.3.0 \ 47 | shell \ 48 | /host/make_IGV_snapshots.sif 49 | 50 | # run the script on the test data inside the Singularity container using Docker 51 | # uses default paths for regions.bed and igv.jar 52 | singularity-test: 53 | docker run \ 54 | --privileged \ 55 | --rm -ti \ 56 | -v $$PWD:/host \ 57 | singularityware/singularity:v3.3.0 \ 58 | run \ 59 | -B /host:/host \ 60 | /host/make_IGV_snapshots.sif \ 61 | bash -c 'make_IGV_snapshots.py /IGV-snapshot-automator/test_data/test_alignments.bam -o /host/snapshots' 62 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | #### NOTE 2 | 3 | I recommed checking out [`igv-reports`](https://github.com/igvteam/igv-reports) which has more features and active development before attempting to use this IGV-snapshot-automator. 4 | 5 | Also check out [BamSnap](https://bamsnap.readthedocs.io/en/latest/) for IGV-like bam file visualization; https://github.com/parklab/bamsnap 6 | 7 | The features of this `IGV-snapshot-automator` are entirely limited to commands that can be used in IGV batch script; 8 | 9 | - https://github.com/igvteam/igv/wiki/Batch-commands 10 | 11 | - https://software.broadinstitute.org/software/igv/batch 12 | 13 | - https://software.broadinstitute.org/software/igv/PortCommands 14 | 15 | 16 | ----- 17 | 18 | # IGV Snapshot Automator 19 | A script to automatically create and run [IGV snapshot batchscripts](http://software.broadinstitute.org/software/igv/batch). This script will first write an IGV batch script for the supplied input files, then load all supplied files for visualization (.bam, etc) in a headless IGV session and take snapshots at the locations defined in the `regions.bed` file. 20 | 21 | Designed for use on Linux systems, and intended to be used as a component of sequencing analysis pipelines. 22 | 23 | # Usage 24 | 25 | ## Download IGV 26 | 27 | Use the included Makefile recipe to download a copy of IGV 28 | 29 | ``` 30 | make install 31 | ``` 32 | 33 | ## Run Snapshotter 34 | 35 | - Put your chromosome regions to visualize in the `regions.bed` file (provided), or another BED format file 36 | 37 | - Locate your files to visualize (e.g. .bam & .bam.bai files) 38 | 39 | - Create and run batchscript. Example command: 40 | ```bash 41 | $ python make_IGV_snapshots.py /path/to/alignments1.bam /path/to/alignments2.bam 42 | ``` 43 | 44 | ## Demo 45 | 46 | To run the script on the included demo files: 47 | 48 | ```bash 49 | $ python make_IGV_snapshots.py test_data/test_alignments.bam test_data/test_alignments2.bam 50 | ``` 51 | 52 | # Options 53 | 54 | See `python make_IGV_snapshots.py --help` for available options. Here are a few: 55 | 56 | - `-r`: Path to the BED formatted regions file to use (defaults to the included demo `regions.bed`) 57 | - `-nosnap`: Make batchscript without taking snapshots 58 | - `-g`: Genome to use, e.g. `hg19` 59 | - `-ht`: Height of the snapshot, default is 500 60 | - `-o`: Name of the output directory to save the snapshots in (defaults to `IGV_Snapshots`) 61 | - `-bin`: Path to the IGV jar binary to run (defaults to `igv.jar`) 62 | - `-mem`: Memory to allocate to IGV (MB) 63 | - `-suffix`: Filename suffix to place before '.png' in the snapshots 64 | - `-onlysnap`: Skip batchscript creation and only run IGV using the supplied batchscript file 65 | - `-nf4`: "Name field 4" mode, uses values saved in 4th field of the `regions.bed` file as the output filename of the PNG snapshot. Use this when you have pre-made filenames you wish to use for each snapshot. 66 | - `-s` or `-group_by_strand`: Group alignment(s) by read strand with forward on top and reverse on the bottom. 67 | 68 | 69 | 70 | # Example Output 71 | 72 | ![chr1_713500_714900_h500](https://cloud.githubusercontent.com/assets/10505524/23584731/4cf127b4-0138-11e7-838c-a947980c8520.png) 73 | 74 | # Notes 75 | 76 | Default memory allotment is set at 4GB; this can be changed with the `-mem` argument (e.g. `-mem 1000` sets memory to 1GB). 77 | 78 | IGV may take several minutes to run, depending on the number of input files and regions to snapshot. Stdout messages from the program may not appear immediately in the console. 79 | 80 | # Containers 81 | 82 | Docker and Singularity container files are included. Pre built container images can be found on Dockerhub at https://hub.docker.com/repository/docker/stevekm/igv-snapshot-automator 83 | 84 | ## Docker 85 | 86 | The Docker container can be built with the included Makefile recipe 87 | 88 | ``` 89 | make docker-build 90 | ``` 91 | 92 | The test data can be run with 93 | 94 | ``` 95 | make docker-test 96 | ``` 97 | 98 | ## Singularity 99 | 100 | The Singularity container can be built using Docker with the included Makefile recipe 101 | 102 | ``` 103 | make singularity-build 104 | ``` 105 | 106 | The test data can be run with 107 | 108 | ``` 109 | make singularity-test 110 | ``` 111 | 112 | # Software Requirements 113 | - Python 2.7 or 3+ 114 | - bash version 4.1.2+ 115 | - IGV (download script provided in `bin` directory) 116 | - Xvfb 117 | - xdpyinfo 118 | - Java runtime environment 119 | - Docker or Singularity for building and running containers 120 | 121 | # Notes 122 | 123 | Some alternative implementations of the same basic methodology used here for creating IGV snapshots can also be found implemented in Nextflow pipelines; 124 | 125 | - https://github.com/stevekm/IGV-snapshot-nf 126 | 127 | - https://github.com/NYU-Molecular-Pathology/NGS580-nf/blob/3ba2f970c3fbee56080ba60727f7bf43cb1be3b2/main.nf#L4701-L4876 128 | 129 | Running a batch script on IGV: 130 | 131 | - https://software.broadinstitute.org/software/igv/batch 132 | 133 | - https://software.broadinstitute.org/software/igv/PortCommands 134 | 135 | Details on interpretation of IGV visualizations can be found here: 136 | 137 | - https://software.broadinstitute.org/software/igv/book/export/html/37 138 | 139 | IGV available preferences which could be included in IGV batch scripts: 140 | 141 | - https://software.broadinstitute.org/software/igv/prefs.properties 142 | 143 | `igv-reports` which makes HTML report outputs with embedded Javascript IGV viewer 144 | 145 | - https://github.com/igvteam/igv-reports 146 | -------------------------------------------------------------------------------- /make_IGV_snapshots.def: -------------------------------------------------------------------------------- 1 | BootStrap: docker 2 | From: ubuntu:16.04 3 | 4 | %setup 5 | # project repo is mounted inside Docker container as /host; copy it into the container 6 | cp -r /host ${SINGULARITY_ROOTFS}/IGV-snapshot-automator 7 | 8 | %post 9 | apt-get update && \ 10 | apt-get install -y wget \ 11 | unzip \ 12 | default-jdk \ 13 | xvfb \ 14 | xorg \ 15 | python \ 16 | make 17 | 18 | cd /IGV-snapshot-automator && make install 19 | 20 | export PATH="/IGV-snapshot-automator/:/IGV-snapshot-automator/IGV_2.4.10/:${PATH}" 21 | 22 | # make a dummy batch script in order to load the hg19 genome into the container 23 | # https://software.broadinstitute.org/software/igv/PortCommands 24 | printf 'new\ngenome hg19\nexit\n' > /genome.bat 25 | xvfb-run --auto-servernum --server-num=1 igv.sh -b /genome.bat 26 | 27 | # TODO: not sure why this does not work... 28 | # %test 29 | # make_IGV_snapshots.py -h 30 | 31 | %environment 32 | export PATH="/IGV-snapshot-automator/:/IGV-snapshot-automator/IGV_2.4.10/:${PATH}" 33 | -------------------------------------------------------------------------------- /make_IGV_snapshots.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | ''' 4 | This script will load IGV in a virtual X window, load all supplied input files 5 | as tracks, and take snapshots at the coorindates listed in the BED formatted 6 | region file. 7 | 8 | If you don't have a copy of IGV, get it here: 9 | http://data.broadinstitute.org/igv/projects/downloads/IGV_2.3.81.zip 10 | 11 | example IGV batch script: 12 | 13 | new 14 | snapshotDirectory IGV_Snapshots 15 | load test_alignments.bam 16 | genome hg19 17 | maxPanelHeight 500 18 | goto chr1:713167-714758 19 | snapshot chr1_713167_714758_h500.png 20 | goto chr1:713500-714900 21 | snapshot chr1_713500_714900_h500.png 22 | exit 23 | ''' 24 | 25 | # ~~~~ LOAD PACKAGES ~~~~~~ # 26 | import sys 27 | import os 28 | import errno 29 | import subprocess as sp 30 | import argparse 31 | 32 | THIS_DIR = os.path.dirname(os.path.realpath(__file__)) 33 | default_igv_jar = os.path.join(THIS_DIR, 'igv.jar') 34 | default_output_dir = os.path.join(THIS_DIR, "IGV_Snapshots") 35 | default_regions_bed = os.path.join(THIS_DIR, 'regions.bed') 36 | # ~~~~ CUSTOM FUNCTIONS ~~~~~~ # 37 | def file_exists(myfile, kill = False): 38 | ''' 39 | Checks to make sure a file exists, optionally kills the script 40 | ''' 41 | import os 42 | import sys 43 | if not os.path.isfile(myfile): 44 | print("ERROR: File '{}' does not exist!".format(myfile)) 45 | if kill == True: 46 | print("Exiting...") 47 | sys.exit() 48 | 49 | def subprocess_cmd(command): 50 | ''' 51 | Runs a terminal command with stdout piping enabled 52 | ''' 53 | import subprocess as sp 54 | process = sp.Popen(command,stdout=sp.PIPE, shell=True) 55 | proc_stdout = process.communicate()[0].strip() 56 | print(proc_stdout) 57 | 58 | def make_chrom_region_list(region_file, nf4_mode= False): 59 | ''' 60 | Creates a list of tuples representing the regions from the BED file; 61 | [(chrom, start, stop), ...] 62 | ''' 63 | region_list = [] 64 | with open(region_file) as f: 65 | for line in f: 66 | if nf4_mode == True: 67 | if len(line.split()) >= 4: 68 | chrom, start, stop, name = line.split()[0:4] 69 | region_list.append((chrom, start, stop, name)) 70 | else: 71 | if len(line.split()) >= 3: 72 | chrom, start, stop = line.split()[0:3] 73 | region_list.append((chrom, start, stop)) 74 | elif len(line.split()) == 2: 75 | chrom, start = line.split() 76 | region_list.append((chrom, start, start)) 77 | return(region_list) 78 | 79 | def make_IGV_chrom_loc(region): 80 | ''' 81 | return a chrom location string in IGV format 82 | region is a tuple with at least 3 entries 83 | ''' 84 | chrom, start, stop = region[0:3] 85 | return('{}:{}-{}'.format(chrom, start, stop)) 86 | 87 | def make_snapshot_filename(region, height, suffix = None): 88 | ''' 89 | formats a filename for the IGV snapshot 90 | region is a tuple with at least 3 entries; if a 4th entry exists, use it as the filename 91 | ''' 92 | if len(region) >= 4: 93 | chrom, start, stop, name = region[0:4] 94 | return('{}'.format(name)) # '{}.png'.format(name) # don't include file extension! user must do this ahead of time! 95 | elif len(region) == 3: 96 | chrom, start, stop = region 97 | if suffix == None: 98 | return('{}_{}_{}_h{}.png'.format(chrom, start, stop, height)) 99 | elif suffix != None: 100 | return('{}_{}_{}_h{}{}.png'.format(chrom, start, stop, height, str(suffix))) 101 | 102 | def mkdir_p(path, return_path=False): 103 | ''' 104 | recursively create a directory and all parent dirs in its path 105 | ''' 106 | import sys 107 | import os 108 | import errno 109 | 110 | try: 111 | os.makedirs(path) 112 | except OSError as exc: # Python >2.5 113 | if exc.errno == errno.EEXIST and os.path.isdir(path): 114 | pass 115 | else: 116 | raise 117 | if return_path: 118 | return path 119 | 120 | def get_open_X_server(): 121 | ''' 122 | Search for an open Xvfb port to render into 123 | ''' 124 | x_serv_command= ''' 125 | for serv_num in $(seq 1 1000); do 126 | if ! (xdpyinfo -display :${serv_num})&>/dev/null; then 127 | echo "$serv_num" && break 128 | fi 129 | done 130 | ''' 131 | import subprocess as sp 132 | # run the command, capture the output 133 | process = sp.Popen(x_serv_command,stdout=sp.PIPE, shell=True) 134 | x_serv_port = int(process.communicate()[0].strip()) 135 | return(x_serv_port) 136 | 137 | def initialize_file(string, output_file): 138 | ''' 139 | Write a string to the file in 'write' mode, overwriting any contents 140 | ''' 141 | with open(output_file, "w") as myfile: 142 | myfile.write(string + '\n') 143 | 144 | def append_string(string, output_file): 145 | ''' 146 | Append a string to a file 147 | ''' 148 | with open(output_file, "a") as myfile: 149 | myfile.write(string + '\n') 150 | 151 | def check_for_bai(bam_file): 152 | ''' 153 | Check to make sure a 'file.bam.bai' file is present in the same dir as the 'file.bam' file 154 | ''' 155 | file_exists(bam_file + '.bai', kill = True) 156 | 157 | def verify_input_files_list(files_list): 158 | ''' 159 | Check to make sure input files meet criteria 160 | Add more criteria as issues are found 161 | ''' 162 | for file in files_list: 163 | if file.endswith(".bam"): 164 | check_for_bai(file) 165 | 166 | def start_batchscript(input_files, IGV_batchscript_file, IGV_snapshot_dir, genome_version, image_height): 167 | ''' 168 | Initialize the batchscript file and write setup information to it 169 | ''' 170 | # ~~~~ WRITE BATCHSCRIPT SETUP INFO ~~~~~~ # 171 | print("\nWriting IGV batch script to file:\n{}\n".format(IGV_batchscript_file)) 172 | # write the first line to the file; this overwrites the contents! 173 | initialize_file("new", IGV_batchscript_file) 174 | # add the genome version 175 | append_string("genome " + genome_version, IGV_batchscript_file) 176 | # add the snapshot dir 177 | append_string("snapshotDirectory " + IGV_snapshot_dir, IGV_batchscript_file) 178 | # add all of the input files to load as tracks 179 | for file in input_files: 180 | append_string("load " + file, IGV_batchscript_file) 181 | # add the track height 182 | append_string("maxPanelHeight " + image_height, IGV_batchscript_file) 183 | 184 | 185 | def write_batchscript_regions(region_file, IGV_batchscript_file, image_height, suffix, nf4_mode, group_by_strand=False): 186 | ''' 187 | Write the batchscript regions 188 | ''' 189 | # get the snapshot regions from the BED file 190 | print("\nGetting regions from BED file...\n") 191 | region_list = make_chrom_region_list(region_file, nf4_mode) 192 | print('Read {} regions'.format(len(region_list))) 193 | # ~~~~ WRITE BATCHSCRIPT CHROM LOC INFO ~~~~~~ # 194 | # iterate over all the regions to take snapshots of 195 | for region in region_list: 196 | # chrom, start, stop = region 197 | # convert region into IGV script format 198 | IGV_loc = make_IGV_chrom_loc(region) 199 | # create filename for output snapshot image_height 200 | snapshot_filename = make_snapshot_filename(region, image_height, suffix = suffix) 201 | # write to the batchscript 202 | append_string("goto " + IGV_loc, IGV_batchscript_file) 203 | # if user specifies, group reads by read strand 204 | if group_by_strand: 205 | append_string("group strand", IGV_batchscript_file) 206 | append_string("snapshot " + snapshot_filename, IGV_batchscript_file) 207 | 208 | 209 | def write_IGV_script(input_files, region_file, IGV_batchscript_file, IGV_snapshot_dir, genome_version, image_height, suffix = None, nf4_mode = False, group_by_strand=False): 210 | ''' 211 | write out a batchscrpt for IGV 212 | ''' 213 | start_batchscript(input_files, IGV_batchscript_file, IGV_snapshot_dir, genome_version, image_height) 214 | write_batchscript_regions(region_file, IGV_batchscript_file, image_height, suffix, nf4_mode, group_by_strand=group_by_strand) 215 | append_string("exit", IGV_batchscript_file) 216 | 217 | def run_IGV_script(igv_script, igv_jar, memMB): 218 | ''' 219 | Run an IGV batch script 220 | ''' 221 | import datetime 222 | # get the X11 Xvfb port number 223 | x_serv_port = get_open_X_server() 224 | print('\nOpen Xvfb port found on:\n{}\n'.format(x_serv_port)) 225 | # build the system command to run IGV 226 | # igv_command = "(Xvfb :{} &) && DISPLAY=:{} java -Xmx{}m -jar {} -b {} && killall Xvfb".format(x_serv_port, x_serv_port, memMB, igv_jar, igv_script) 227 | igv_command = "xvfb-run --auto-servernum --server-num=1 java -Xmx{}m -jar {} -b {}".format(memMB, igv_jar, igv_script) 228 | print('\nIGV command is:\n{}\n'.format(igv_command)) 229 | # get current time; command can take a while to finish 230 | startTime = datetime.datetime.now() 231 | print("\nCurrent time is:\n{}\n".format(startTime)) 232 | # run the IGV command 233 | print("\nRunning the IGV command...") 234 | subprocess_cmd(igv_command) 235 | elapsed_time = datetime.datetime.now() - startTime 236 | print("\nIGV finished; elapsed time is:\n{}\n".format(elapsed_time)) 237 | 238 | 239 | 240 | def main(input_files, region_file = 'regions.bed', genome = 'hg19', 241 | image_height = '500', outdir = 'IGV_Snapshots', 242 | igv_jar_bin = "bin/IGV_2.3.81/igv.jar", igv_mem = "4000", 243 | no_snap = False, suffix = None, nf4_mode = False, onlysnap = False, 244 | group_by_strand=False): 245 | ''' 246 | Main control function for the script 247 | ''' 248 | if onlysnap != False: 249 | batchscript_file = str(onlysnap) 250 | file_exists(batchscript_file, kill = True) 251 | run_IGV_script(igv_script = batchscript_file, igv_jar = igv_jar_bin, memMB = igv_mem) 252 | return() 253 | 254 | # default IGV batch script output location 255 | batchscript_file = os.path.join(outdir, "IGV_snapshots.bat") 256 | 257 | # make sure the regions file exists 258 | file_exists(region_file, kill = True) 259 | 260 | # make sure the IGV jar exists 261 | file_exists(igv_jar_bin, kill = True) 262 | 263 | # check the input files to make sure they are valid 264 | verify_input_files_list(input_files) 265 | 266 | print('\n~~~ IGV SNAPSHOT AUTOMATOR ~~~\n') 267 | print('Reference genome:\n{}\n'.format(genome)) 268 | print('Track height:\n{}\n'.format(image_height)) 269 | print('IGV binary file:\n{}\n'.format(igv_jar_bin)) 270 | print('Output directory will be:\n{}\n'.format(outdir)) 271 | print('Batchscript file will be:\n{}\n'.format(batchscript_file)) 272 | print('Region file:\n{}\n'.format(region_file)) 273 | print('Input files to snapshot:\n') 274 | for file in input_files: 275 | print(file) 276 | file_exists(file, kill = True) 277 | 278 | # make the output directory 279 | print('\nMaking the output directory...') 280 | mkdir_p(outdir) 281 | 282 | # write the IGV batch script 283 | write_IGV_script(input_files = input_files, region_file = region_file, 284 | IGV_batchscript_file = batchscript_file, 285 | IGV_snapshot_dir = outdir, genome_version = genome, 286 | image_height = image_height, suffix = suffix, 287 | nf4_mode = nf4_mode, group_by_strand=group_by_strand) 288 | 289 | # make sure the batch script file exists 290 | file_exists(batchscript_file, kill = True) 291 | 292 | # run the IGV batch script 293 | if no_snap == False: 294 | run_IGV_script(igv_script = batchscript_file, igv_jar = igv_jar_bin, memMB = igv_mem) 295 | 296 | def run(): 297 | ''' 298 | Parse script args to run the script 299 | ''' 300 | # ~~~~ GET SCRIPT ARGS ~~~~~~ # 301 | parser = argparse.ArgumentParser(description='IGV snapshot automator') 302 | # required positional args 303 | parser.add_argument("input_files", nargs='+', help="paths to the files to create snapshots from e.g. .bam, .bigwig, etc.") # , nargs='?' 304 | 305 | # required flags 306 | parser.add_argument("-r", default = default_regions_bed, type = str, dest = 'region_file', metavar = 'regions', help="BED file with regions to create snapshots over") 307 | 308 | # optional flags 309 | parser.add_argument("-g", default = 'hg19', type = str, dest = 'genome', metavar = 'genome', help="Name of the reference genome, Defaults to hg19") 310 | parser.add_argument("-ht", default = '500', type = str, dest = 'image_height', metavar = 'image height', help="Height for the IGV tracks") 311 | parser.add_argument("-o", default = default_output_dir, type = str, dest = 'outdir', metavar = 'output directory', help="Output directory for snapshots") 312 | parser.add_argument("-bin", default = default_igv_jar, type = str, dest = 'igv_jar_bin', metavar = 'IGV bin path', help="Path to the IGV jar binary to run") 313 | parser.add_argument("-mem", default = "4000", type = str, dest = 'igv_mem', metavar = 'IGV memory (MB)', help="Amount of memory to allocate to IGV, in Megabytes (MB)") 314 | parser.add_argument("-nosnap", default = False, action='store_true', dest = 'no_snap', help="Don't make snapshots, only write batchscript and exit") 315 | parser.add_argument("-suffix", default = None, dest = 'suffix', help="Filename suffix to place before '.png' in the snapshots") 316 | parser.add_argument("-nf4", default = False, action='store_true', dest = 'nf4_mode', help="'Name field 4' mode; uses the value in the fourth field of the regions file as the filename for each region snapshot") 317 | parser.add_argument("-onlysnap", default = False, dest = 'onlysnap', help="Path to batchscript file to run in IGV. Performs no error checking or other input evaluation, only runs IGV on the batchscript and exits.") 318 | parser.add_argument("-s", "-group_by_strand", default=False, 319 | dest="group_by_strand", action='store_true', 320 | help="Group reads by forward/reverse strand.") 321 | 322 | args = parser.parse_args() 323 | 324 | input_files = args.input_files 325 | region_file = args.region_file 326 | genome = args.genome 327 | image_height = args.image_height 328 | outdir = args.outdir 329 | igv_jar_bin = args.igv_jar_bin 330 | igv_mem = args.igv_mem 331 | no_snap = args.no_snap 332 | suffix = args.suffix 333 | nf4_mode = args.nf4_mode 334 | onlysnap = args.onlysnap 335 | group_by_strand = args.group_by_strand 336 | 337 | main(input_files = input_files, region_file = region_file, genome = genome, 338 | image_height = image_height, outdir = outdir, igv_jar_bin = igv_jar_bin, 339 | igv_mem = igv_mem, no_snap = no_snap, suffix = suffix, 340 | nf4_mode = nf4_mode, onlysnap = onlysnap, 341 | group_by_strand=group_by_strand) 342 | 343 | 344 | 345 | if __name__ == "__main__": 346 | run() 347 | -------------------------------------------------------------------------------- /regions.bed: -------------------------------------------------------------------------------- 1 | chr1 713167 714758 2 | chr1 713500 714900 3 | chr1 714000 715000 4 | chr1 714001 5 | -------------------------------------------------------------------------------- /regions_nf4.bed: -------------------------------------------------------------------------------- 1 | chr1 713167 714758 foo 2 | chr1 713500 714900 bar 3 | chr1 714000 715000 baz 4 | -------------------------------------------------------------------------------- /report/Makefile: -------------------------------------------------------------------------------- 1 | # install the 'standalone' LaTeX document class 2 | 3 | install: standalone 4 | 5 | standalone: download-standalone extract-standalone 6 | 7 | download-standalone: 8 | wget http://mirrors.ctan.org/install/macros/latex/contrib/standalone.tds.zip 9 | 10 | extract-standalone: 11 | unzip standalone.tds.zip -d ~/texmf/ 12 | 13 | clean: 14 | rm -f standalone.tds.zip 15 | 16 | .INTERMEDIATE: standalone.tds.zip -------------------------------------------------------------------------------- /report/README.md: -------------------------------------------------------------------------------- 1 | # IGV Snapshot Report 2 | 3 | This directory contains report templates to use with the IGV Snapshot output. By default, the reports will look for `.png` files in the directory `../IGV_Snapshots/`, and include each file found in a report output. 4 | 5 | If your IGV snapshot directory has a different name or path, you can either adjust the path inside the report template, or make a symlink with that name at that location. 6 | 7 | ## PDF Output 8 | 9 | A PDF report can be generated using the included `report.Rnw`. Compile it with the command: 10 | 11 | ```bash 12 | ./compile_Rnw_report.sh 13 | ``` 14 | 15 | 16 | This report requires LaTeX to be installed with the `standalone` package. If you are using Linux, or a Linux-style system, and you already have LaTeX installed, you can install this package with the included `Makefile` with the command: 17 | 18 | ```bash 19 | make install 20 | ``` 21 | 22 | ## HTML Output 23 | 24 | An HTML formatted report can be generated with the included `report.Rmd` file. Compile it with the included script: 25 | 26 | ```bash 27 | # module load pandoc/1.13.1 28 | ./compile_Rmd_report.R 29 | ``` 30 | 31 | # Software 32 | 33 | Software used in report creation 34 | 35 | - R programming langauge 36 | 37 | - `Hmisc`, `knitr` packages 38 | 39 | - LaTeX 40 | 41 | - `standalone` package 42 | 43 | - pandoc 1.13.1+ -------------------------------------------------------------------------------- /report/compile_Rmd_report.R: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env Rscript 2 | 3 | ## USAGE: compile_Rmd_report.R report.Rmd 4 | # module load pandoc/1.13.1 5 | Rmdfile <- "report.Rmd" 6 | args <- commandArgs(TRUE) 7 | if(! is.na(args[1])) Rmdfile <- as.character(args[1]) 8 | rmarkdown::render(Rmdfile) 9 | -------------------------------------------------------------------------------- /report/compile_Rnw_report.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | # compiles a .Rnw file to a .pdf 4 | # USAGE: compile_Rnw_report.sh report.Rnw 5 | 6 | Rnw_file="${1:-report.Rnw}" 7 | 8 | compile_Rnw () { 9 | # compile .Rnw to .tex 10 | local Rnw_file="$1" 11 | 12 | if [ -f "$Rnw_file" ]; then 13 | Rscript --slave --no-save --no-restore - "${Rnw_file}" <>= 4 | suppressPackageStartupMessages(library("Hmisc")) # need for latexTranslate() 5 | snapshot_dir <- "../IGV_Snapshots/" 6 | snapshot_files <- dir(snapshot_dir, pattern = '*.png', full.names = TRUE) 7 | 8 | fig_str <- " 9 | 10 | \\section{%s} 11 | \\begin{figure} 12 | \\includegraphics[width=\\textwidth, height=0.8\\textheight, keepaspectratio=true]{%s} 13 | \\caption{A picture of a gull.} 14 | \\end{figure} 15 | \\pagebreak 16 | 17 | " 18 | cat(sprintf(fig_str, latexTranslate(basename(snapshot_files)), snapshot_files)) 19 | @ 20 | \end{document} -------------------------------------------------------------------------------- /test_data/test_alignments.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/stevekm/IGV-snapshot-automator/b9f8e78a34102ec2e20d3428b29567c0ad1dfc6a/test_data/test_alignments.bam -------------------------------------------------------------------------------- /test_data/test_alignments.bam.bai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/stevekm/IGV-snapshot-automator/b9f8e78a34102ec2e20d3428b29567c0ad1dfc6a/test_data/test_alignments.bam.bai -------------------------------------------------------------------------------- /test_data/test_alignments2.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/stevekm/IGV-snapshot-automator/b9f8e78a34102ec2e20d3428b29567c0ad1dfc6a/test_data/test_alignments2.bam -------------------------------------------------------------------------------- /test_data/test_alignments2.bam.bai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/stevekm/IGV-snapshot-automator/b9f8e78a34102ec2e20d3428b29567c0ad1dfc6a/test_data/test_alignments2.bam.bai --------------------------------------------------------------------------------