From a5807e7055a62f506fe63ca4690d680ade43a715 Mon Sep 17 00:00:00 2001 From: Zhangming Yan Date: Tue, 26 Feb 2019 22:21:00 -0800 Subject: [PATCH] release v1.0 freeze --- README.md | 61 ++- docs/build/doctrees/commandline_api.doctree | Bin 33624 -> 32453 bytes docs/build/doctrees/environment.pickle | Bin 27401 -> 41768 bytes docs/build/doctrees/further_analysis.doctree | Bin 45332 -> 45385 bytes docs/build/doctrees/index.doctree | Bin 36737 -> 36844 bytes docs/build/doctrees/installation.doctree | Bin 21834 -> 27743 bytes .../doctrees/origin_imargi_methods.doctree | Bin 56996 -> 56977 bytes .../doctrees/performance profile.doctree | Bin 9616 -> 9615 bytes docs/build/doctrees/quick_example.doctree | Bin 32851 -> 36591 bytes .../step_by_step_illustration.doctree | Bin 80250 -> 81259 bytes docs/build/doctrees/technical_note.doctree | Bin 13474 -> 22932 bytes docs/build/html/.buildinfo | 2 +- .../html/_images/docker_command_example.png | Bin 18448 -> 42423 bytes .../html/_sources/commandline_api.md.txt | 70 ++-- .../html/_sources/further_analysis.md.txt | 8 +- docs/build/html/_sources/index.md.txt | 2 +- docs/build/html/_sources/installation.md.txt | 63 +++- .../html/_sources/performance profile.md.txt | 2 +- docs/build/html/_sources/quick_example.md.txt | 17 +- .../_sources/step_by_step_illustration.md.txt | 8 +- .../build/html/_sources/technical_note.md.txt | 49 ++- docs/build/html/_static/basic.css | 13 +- docs/build/html/_static/css/badge_only.css | 2 +- docs/build/html/_static/css/theme.css | 8 +- docs/build/html/_static/doctools.js | 8 +- .../html/_static/documentation_options.js | 3 +- docs/build/html/_static/js/theme.js | 6 +- docs/build/html/_static/language_data.js | 297 +++++++++++++++ docs/build/html/_static/searchtools.js | 352 ++---------------- docs/build/html/_static/websupport.js | 2 +- docs/build/html/commandline_api.html | 130 +++---- docs/build/html/further_analysis.html | 62 ++- docs/build/html/genindex.html | 52 +-- docs/build/html/index.html | 55 +-- docs/build/html/installation.html | 124 +++--- docs/build/html/origin_imargi_methods.html | 52 +-- docs/build/html/performance profile.html | 54 +-- docs/build/html/quick_example.html | 69 ++-- docs/build/html/search.html | 52 +-- docs/build/html/searchindex.js | 2 +- .../build/html/step_by_step_illustration.html | 75 ++-- docs/build/html/technical_note.html | 114 +++--- docs/source/commandline_api.md | 70 ++-- .../source/figures/docker_command_example.png | Bin 18448 -> 42423 bytes docs/source/further_analysis.md | 8 +- docs/source/index.md | 2 +- docs/source/installation.md | 3 +- docs/source/performance profile.md | 2 +- docs/source/quick_example.md | 17 +- docs/source/step_by_step_illustration.md | 8 +- docs/source/technical_note.md | 49 ++- src/Dockerfile | 2 +- src/imargi_annotate.sh | 2 +- src/imargi_convert.sh | 4 +- src/imargi_distfilter.sh | 12 +- src/imargi_stats.sh | 2 +- 56 files changed, 1058 insertions(+), 937 deletions(-) create mode 100644 docs/build/html/_static/language_data.js diff --git a/README.md b/README.md index 79a2155..dde9dee 100644 --- a/README.md +++ b/README.md @@ -15,6 +15,9 @@ iMARGI-Docker distributes the iMARGI sequencing data processing pipeline - [Build with Dockerfile](#build-with-dockerfile) - [Software Testing Demo](#software-testing-demo) - [Testing Data](#testing-data) + - [iMARGI sequencing data (paired FASTQ)](#imargi-sequencing-data-paired-fastq) + - [Reference genome data (FASTA)](#reference-genome-data-fasta) + - [bwa index data](#bwa-index-data) - [Testing Command](#testing-command) - [Testing Results](#testing-results) - [Running Time Profile](#running-time-profile) @@ -106,19 +109,37 @@ To test whether you have successfully installed iMARGI-Docker, you can follow in ### Testing Data +#### iMARGI sequencing data (paired FASTQ) + As real iMARGI sequencing data are always very big, so we randomly extracted a small chunk of real data for software testing. The data can be found in [`data`](./data/) folder. Please download them to your computer. -Besides, you need to download a human genome reference FASTA file. +- [R1 reads](https://github.com/Zhong-Lab-UCSD/iMARGI-Docker/raw/master/data/sample_R1.fastq.gz) +- [R2 reads](https://github.com/Zhong-Lab-UCSD/iMARGI-Docker/raw/master/data/sample_R2.fastq.gz) + +#### Reference genome data (FASTA) + +Besides, you need to download a human genome reference FASTA file. We use the reference genome used by [4D Nucleome](https://www.4dnucleome.org/) and -[ENCODE project](https://www.encodeproject.org/data-standards/reference-sequences/). The FASTA file of the reference +[ENCODE project](https://www.encodeproject.org/data-standards/reference-sequences/). + +The FASTA file of the reference genome is too large for us to host it in GitHub repo. You can be download it use the link: -[GRCh38_no_alt_analysis_set_GCA_000001405.15](https://www.encodeproject.org/files/GRCh38_no_alt_analysis_set_GCA_000001405.15/@@download/GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta.gz). + +- [GRCh38_no_alt_analysis_set_GCA_000001405.15](https://www.encodeproject.org/files/GRCh38_no_alt_analysis_set_GCA_000001405.15/@@download/GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta.gz) + It needs to be decompressed using `gunzip -d` command on Linux/MacOS. If your system is Windows, you can use 7Zip software to decompress the `.gz` file. Besides, you can also use the `gunzip` tool delivered in iMARGI-Docker. -We assume that you put the data and reference files in the following directory structure. +#### bwa index data + +As `bwa index` process will cost a lot of time (more than 1 hour), we suggest to download our pre-built index files for the reference +genome. Please download the following gzip compressed `bwa_index` folder and decompress it (`tar zxvf`) on your machine. + +- [bwa index files](https://sysbio.ucsd.edu/imargi_pipeline/bwa_index.tar.gz) + +*We assume that you put the data and reference files in the following directory structure.* ``` bash ~/imargi_example @@ -127,7 +148,13 @@ We assume that you put the data and reference files in the following directory s │   └── sample_R2.fastq.gz ├── output └── ref - └── GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta +    ├── GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta + └── bwa_index +    ├── bwa_index_hg38.amb +    ├── bwa_index_hg38.ann +    ├── bwa_index_hg38.bwt +     ├── sample_R1.fastq.pac +    └── sample_R2.fastq.sa ``` ### Testing Command @@ -141,6 +168,7 @@ docker run -u 1043 -v ~/imargi_example:/imargi zhonglab/imargi \ -N test_sample \ -t 4 \ -g ./ref/GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta \ + -i ./ref/bwa_index/bwa_index_hg38 \ -1 ./data/sample_R1.fastq.gz \ -2 ./data/sample_R2.fastq.gz \ -o ./output @@ -160,23 +188,30 @@ docker run -u 1043 -v ~/imargi_example:/imargi zhonglab/imargi \ - The command line is long, so `\` was used for splitting it into multiple lines in the example. It's a Linux or MacOS style. However, in Windows, you need to replace `\` with `^`. -- Building bwa index costs the most running time. If you have human genome bwa index built before, you can supply it - with `-i` argument. See more details in the +- `-i`: Building bwa index will cost a lot time, so we used the pre-built index files with `-i` argument. There + are some other arguments can be used for pre-generated files, such as `-R` for restriction fragment BED file and + `-c` for chromsize file.See more details in the [documentation of command line API section](https://sysbio.ucsd.edu/imargi_pipeline/commandline_api.html#imargi-wrapper-sh) -` + +- `-i`: If you don't supply bwa index files, the `imargi_wrapper.sh` will generated it automatically. It works + perfectly on Linux system. However, it doesn't work on Windows and MacOS because `bwa index` use `fsync` when build + large genome index, which cannot handle different driver formats (`-v` mount Windows/MacOS driver to Linux container). + So it's better to build it in advance. In fact, there's a solution to the problem if you are familiar with Docker + volume. Please read the + [technical note of iMARGI pipeline documentation](https://sysbio.ucsd.edu/imargi_pipeline/technical_note.html#solve-bwa-index-failure-problem) for + detail. ### Testing Results #### Running Time Profile -It took about 85 minutes to perform the pipeline. The most of time (75 min) was consumed by building bwa index files. -So once you built the bwa index, supply it to the command with `-i` next time. +It took about 15 minutes to perform the pipeline (with `-i` bwa index argument). Step | Time | Speed up suggestion ---------|----------|---------- -Generating chromosome size file | 10 sec | It's fast, but you can supply with `-c` once you've generated it. -Generating bwa index | 75 min | Supply with `-i` once you've built it. -Generating restriction fragment file | 4 min | Supply with `-R` once you've created it. +Generating chromosome size file | 10 sec | It's fast, but you can also supply with `-c` once you've generated it before. +Generating bwa index (skipped) | 75 min | Supply with `-i` if you've pre-built index files. +Generating restriction fragment file | 4 min | Supply with `-R` when you've already created it before. cleaning | 10 sec | It's fast and not parallelization. bwa mapping | 2 min | More CPU cores with `-t`. interaction pair parsing | 1 min | More CPU cores with `-t`. diff --git a/docs/build/doctrees/commandline_api.doctree b/docs/build/doctrees/commandline_api.doctree index 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zhT@0sZHS|_%qii>f)_J~0d212a0FOM@hJ%-0to^6s)>cth0|NI1d?O3jSxb%XRanW z5F%!t8B1c+0j2P?ThrqgQ-(xj)FuVHjkUlU$JZH1Igg?z6Ox z^m;vu5@ShNVfeg9ML7?zz+zWh|N(SRFA=x zlmhlW@}1=B02-cihvdF2EJ^a{}(>rZ!yv}hRUE!mpXP&)&nbz}3*;fuJa-Az= z3cVw?>deJVqwMHUIP*)XpiKCacyhv-Y)?yYyNx_ihOYU*Nwu+LZHzNiJJ~x3�~%l#(-u8{qZ=NIQ3+)ooJ!;&VW-w<@NR98Iot_ zKY2GX&H02*U4GHI-H$#NFTQr@{u0&8@lNhjS1E5kr*>*n{j}9(zaOSvoOjZ^dZ)p( z)N_kwx`gaoT5@XkrWG8;CspJ?K>@O(!R=#x^|kL}%5kckK(P(`fx+XjSi&;>`R*rv zQ}6v%Q3fUjpo9f5!!8JPia)6OEY?(t9el*h0pKbX2H)cMho2blIaFSIURD0(*KKEv mn8E9o9yHKt(UKy+{J;3x#9OM;Zx4f#AA_f>pUXO@geCx9zTwFL diff --git a/docs/build/html/_sources/commandline_api.md.txt b/docs/build/html/_sources/commandline_api.md.txt index 4f13ee6..0c39ef9 100644 --- a/docs/build/html/_sources/commandline_api.md.txt +++ b/docs/build/html/_sources/commandline_api.md.txt @@ -28,8 +28,10 @@ We created several script tools. Here we show the usage and source code of all t -O : Max offset bases for filtering pairs based on R2 5' end positions to restriction sites. Default 3. -M : Max size of ligation fragment for sequencing. It's used for filtering unligated DNA sequence. -t : Max CPU threads for parallelized processing, at least 4. (Default 8) - -1 : R1 fastq.gz file, if there are multiple files, just separated with space, such as -1 lane1_R1.fq lane2_R1.fq - -2 : R2 fastq.gz file, if there are multiple files, just separated with space, such as -1 lane1_R2.fq lane2_R2.fq + -1 : R1 fastq.gz file, if there are multiple files, just separated with space or use wildcard, + such as '-1 lane1_R1.fq.gz lane2_R1.fq.gz', or '-1 lane*_R1.fq.gz'. + -2 : R2 fastq.gz file, if there are multiple files, just separated with space or use wildcard, + such as '-2 lane1_R2.fq.gz lane2_R2.fq.gz', or '-2 lane*_R2.fq.gz'. -o : Output directoy -h : Show usage help ``` @@ -39,30 +41,25 @@ We created several script tools. Here we show the usage and source code of all t [*Source Code*](https://github.com/Zhong-Lab-UCSD/iMARGI-Docker/blob/master/src/imargi_clean.sh) ``` bash - Usage: imargi_clean.sh [-1 ] [-2 ] [-o ] [-f ] [-d ] - [-t ] [-b ] + Usage: $PROGNAME [-1 ] [-2 ] [-N ] [-o ] [-t ] Dependencies: seqtk, gzip, zcat, awk, parallel This script will clean the paired reads (R1 and R2) of iMARGI sequencing Fastq data. According to the iMARGI design, - RNA end reads (R1) start with 2 random based, and DNA end reads (R2) of successful ligation fragments start - with "CT". We need to remove the first 2 bases of R1 for better mapping. For R2, We can strictly clean the data by - filtering out those R2 reads not starting with "CT" in this step by setting "-f CT". Alternatively, - you can skip the "CT" filtering without "-f" parameter. You can apply the "CT" filtering in interaction pairs - filtering step. - If you choose to do "CT" filtering, the script also fixes the paired reads in R1. If "-d" was set as "true", - it will drop all the non "CT" started R2 reads and paired R1 reads, which outputs two fastq files with prefix - "clean_". If "-d" was "false", the filtered read pairs would also be outputed in a pair of fastq files with prefix - "drop_". "-d" only works when "-f" is set, and the default setting of "-d" is "false". + RNA end reads (R1) start with 2 random based. We need to remove the first 2 bases of R1 for better mapping. + If you provided multiple input files (different lanes) in '-1' and '-2' with ',' separator or contains wildcard, + then the output will merge multi-lanes fastq files to one clean fastq file. + The input fastq files must be gzip files, i.e., fastq.gz or fq.gz. The output files are also gzipped files fastq.gz. - -1 : R1 fastq.gz file, if there are multiple files, just separated with space, such as -1 lane1_R1.fq lane2_R1.fq - -2 : R2 fastq.gz file, if there are multiple files, just separated with space, such as -1 lane1_R2.fq lane2_R2.fq + -1 : R1 fastq.gz file, if there are multiple files, just separated with space or use wildcard, + such as '-1 lane1_R1.fq.gz lane2_R1.fq.gz', or '-1 lane*_R1.fq.gz'. + -2 : R2 fastq.gz file, if there are multiple files, just separated with space or use wildcard, + such as '-2 lane1_R2.fq.gz lane2_R2.fq.gz', or '-2 lane*_R2.fq.gz'. + -N : Base name for ouput result. Such as -N HEK_iMARGI, then output cleaned and merged fastq.gz file will be + renamed using the base name. -o : Output directoy - -f : Filtering sequence by 5' start of R2. If not set, no filtering applied. "CT" filtering can be set as "-f CT" - -d : Flag of dropping, working with "-f". Default is false, i.e., output drop_*fastq.gz files of dropped read pairs. -t : Max CPU threads for parallelized processing, at least 4. (Default 8) - -b : Fastq data block size (number of reads) for each thread. Default 2000000. -h : Show usage help ``` @@ -71,14 +68,10 @@ We created several script tools. Here we show the usage and source code of all t [*Source Code*](https://github.com/Zhong-Lab-UCSD/iMARGI-Docker/blob/master/src/imargi_rsfrags.sh) ``` bash - Usage: imargi_rsfrags.sh [-r ] [-c ] [-e ] [-C ] [-o ] - [-g ] [-O offset_restriction_site] [-d ] [-D ] - [-s ] [-t ] - - Dependency: cooler + Usage: $PROGNAME [-r ] [-c ] [-e ] [-C ] [-o ] + Dependency: cooler This script use cooler digest to generate the restriction Enzyme digested fragments bed file for iMARGI - -r : Reference genome fasta file -c : Chromosome size file. -e : Enzyme name, we use AluI in iMARGI. @@ -93,9 +86,9 @@ We created several script tools. Here we show the usage and source code of all t [*Source Code*](https://github.com/Zhong-Lab-UCSD/iMARGI-Docker/blob/master/src/imargi_parse.sh) ``` bash - Usage: imargi_parse.sh [-r ] [-c ] [-R ] [-b ] [-o ] - [-Q ] [-G ] [-O ] [-M ] - [-d ] [-D ] [-t ] + Usage: $PROGNAME [-r ] [-c ] [-R ] [-b ] [-o ] + [-Q ] [-G ] [-O ] [-M ] + [-d ] [-D ] [-t ] Dependency: pairtools pbgzip @@ -123,10 +116,9 @@ We created several script tools. Here we show the usage and source code of all t [*Source Code*](https://github.com/Zhong-Lab-UCSD/iMARGI-Docker/blob/master/src/imargi_stats.sh) ``` bash - Usage: imargi_stats.sh [-D ] [-d ] [-i ] [-o ] + Usage: $PROGNAME [-D ] [-d ] [-i ] [-o ] Dependency: gzip, awk - This script can be used to filter out short-range intra-chromosomal interactions with a threshold genomic distance. -D : Distance type. The default genomic position in .pairs file is the 5' end position, so the default distance @@ -138,7 +130,7 @@ We created several script tools. Here we show the usage and source code of all t comma ',', such as '-d 1000,2000,10000,20000,100000,1000000', then the report will include the statistics number with different thresholds (space is not allowed). -i : Input .pairs.gz file. - -o : Output .pairs.gz file. + -o : Output stats text file. -h : Show usage help ``` @@ -147,11 +139,10 @@ We created several script tools. Here we show the usage and source code of all t [*Source Code*](https://github.com/Zhong-Lab-UCSD/iMARGI-Docker/blob/master/src/imargi_distfilter.sh) ``` bash - Usage: imargi_distfilter.sh [-D ] [-d ] [-F ] - [-i ] [-o ] + Usage: $PROGNAME [-D ] [-d ] [-F ] [-i ] + [-o ] Dependency: gzip, awk - This script can be used to filter out short-range intra-chromosomal interactions with a threshold genomic distance. -D : Distance type. The default genomic position in .pairs file is the 5' end position, so the default distance @@ -161,7 +152,7 @@ We created several script tools. Here we show the usage and source code of all t -d : The distance threshold for filtering. Default is 200000 (distance <200000 will be filtered out). -F : How to deal with the interactions need to be filtered out? '-F' accepts 'drop' and 'output'. 'drop' means drop those interactions. 'output' means output an new file of all the filtered out interactions with prefix - 'filterOut_'. Default is 'drop'. + 'filterOut_'. Default is 'output'. -i : Input .pairs.gz file. -o : Output .pairs.gz file. -h : Show usage help @@ -172,20 +163,19 @@ We created several script tools. Here we show the usage and source code of all t [*Source Code*](https://github.com/Zhong-Lab-UCSD/iMARGI-Docker/blob/master/src/imargi_convert.sh) ``` bash - Usage: imargi_convert.sh [-f ] [-k ] [-b ] [-i ] [-o ] + Usage: $PROGNAME [-f ] [-k ] [-b ] [-i ] [-o ] Dependency: gzip, awk, cool - This script can convert .pairs format to BEDPE, .cool, and GIVE interaction format. - -f : The target format, only accept 'cool', 'bedpe' and 'give'. For 'cool', it will generate a ".cool" file with defined resolution of -b option and a multi-resolution ".mcool" file - based on the ".cool" file. + based on the ".cool" file. For 'bedpe', the output will be pbgzip compressed file. So + keep in mind to name the output_file '-o' with '.gz' extesion. -k : Keep extra information column in BEDPE. Columns ids in .pairs file you want to keep. For example, 'cigar1,cigar2'. Default value is "", i.e., drop all extra cols. -b : bin size for cool format. Default is 5000. -i : Input file. - -o : Output file. + -o : Output file. BEDPE output is gzip compressed file. cool output are .cool and .mcool files. -h : Show usage help ``` @@ -200,7 +190,7 @@ We created several script tools. Here we show the usage and source code of all t [-m ] [-G ] [-t ] [-i ] [-o ] - Dependency: gzip, awk, cool, BEDOPS + Dependency: gzip, pairtools, lz4 pbgzip This script can annotate both RNA and DNA ends with gene annotations in GTF/GFF format or any other genomic features in a simple BED file (each line is a named genomic feature). Multiple overlapped annotation features are diff --git a/docs/build/html/_sources/further_analysis.md.txt b/docs/build/html/_sources/further_analysis.md.txt index bdf7ff6..a8f439f 100644 --- a/docs/build/html/_sources/further_analysis.md.txt +++ b/docs/build/html/_sources/further_analysis.md.txt @@ -18,7 +18,7 @@ statistics, such as number of intra- and inter-chromosomal interactions. We prov simple text data statistics report. The example command is: ``` bash -docker run -v ~/imargi_example:/imargi imargi imargi_stats.sh \ +docker run -v ~/imargi_example:/imargi zhonglab/imargi imargi_stats.sh \ -D 5end \ -d 200000 \ -i ./output/final_HEK_iMARGI.pairs.gz \ @@ -48,7 +48,7 @@ interactions with a distance threshold, which depends on the requirements of fur `imargi_distfilter.sh` tool for filtering interaction based on interaction genomic distance. The example command is: ``` bash -docker run -v ~/imargi_example:/imargi imargi imargi_distfilter.sh \ +docker run -v ~/imargi_example:/imargi zhonglab/imargi imargi_distfilter.sh \ -D 5end \ -d 20000 \ -i ./output/final_HEK_iMARGI.pairs.gz \ @@ -68,7 +68,7 @@ GTF/GFF format or any other genomic features in a simple BED file (each line is command below will generate two new gene annotation columns named as gene1 and gene2 in the output .pairs format file. ``` bash -docker run -v ~/imargi_example:/imargi imargi imargi_annotate.sh \ +docker run -v ~/imargi_example:/imargi zhonglab/imargi imargi_annotate.sh \ -A gtf \ -a ./ref/gencode.v24.annotation.gtf \ -l gene \ @@ -111,7 +111,7 @@ For further analysis and visualization, other formats instead of .pairs format m with different `-f` argument options. The example command is below: ``` bash -docker run -v ~/imargi_example:/imargi imargi imargi_convert.sh \ +docker run -v ~/imargi_example:/imargi zhonglab/imargi imargi_convert.sh \ -f bedpe \ -i ./output/final_HEK_iMARGI.pairs.gz \ -o ./output/final_HEK_iMARGI.bedpe.gz diff --git a/docs/build/html/_sources/index.md.txt b/docs/build/html/_sources/index.md.txt index b84e5b3..f5f22f1 100644 --- a/docs/build/html/_sources/index.md.txt +++ b/docs/build/html/_sources/index.md.txt @@ -78,7 +78,7 @@ The [Technical Notes](./technical_note.md) section shows more technical informat [[1]](#a1) Sridhar, B. et al. Systematic Mapping of RNA-Chromatin Interactions In Vivo. Current Biology 27, 602–609 (2017). -[[2]](#a2) Yan, Z. et al. Genome-wide co-localization of RNA-DNA interactions and fusion RNA pairs. bioRxiv 472019 (2018). doi:10.1101/472019 +[[2]](#a2) Yan, Z. et al. Genome-wide co-localization of RNA-DNA interactions and fusion RNA pairs. PNAS February 19, 2019, 116 (8) 3328-3337. https://doi.org/10.1073/pnas.1819788116 [[3]](#a3) Wu, W., Yan, Z., Wen X. & Zhong, S. iMARGI: Mapping RNA-DNA interactome by sequencing. diff --git a/docs/build/html/_sources/installation.md.txt b/docs/build/html/_sources/installation.md.txt index a404f95..95f040e 100644 --- a/docs/build/html/_sources/installation.md.txt +++ b/docs/build/html/_sources/installation.md.txt @@ -10,11 +10,11 @@ configured tools. ## Docker Container Usage Instructions -An iMARGI Docker image is available in [Docker-Hub](https://hub.docker.com/r/zhonglab/imargi). It's -much easier to apply the iMARGI pipeline using the docker container than installing and configuring all the required -tools. +An iMARGI Docker image is available in [Docker-Hub](https://hub.docker.com/r/zhonglab/imargi), and its source files are +hosted in [iMARGI-Docker GitHub repo](https://github.com/Zhong-Lab-UCSD/iMARGI-Docker). It's much easier to apply the +iMARGI pipeline using the docker container than installing and configuring all the required tools. -Docker Community Edition or Enterprise Edition is required to be installed and configured on the Linux server (root +Docker Community Edition or Enterprise Edition is required to be installed and configured on the machine (root authority is required for installing Docker CE). [Here is the guides of installing Docker CE on Ubuntu](https://docs.docker.com/install/linux/docker-ce/ubuntu/). @@ -28,7 +28,7 @@ To use the tools in the iMARGI Docker image, you need to run a Docker container. new directory with `mkdir` command through a Docker container. ``` bash -docker run -v ~/test:/imargi imargi mkdir new_dir +docker run -v ~/test:/imargi zhonglab/imargi mkdir new_dir ``` ![](./figures/docker_command_example.png) @@ -40,10 +40,47 @@ any tool in the iMARGI Docker container. ## Dependencies Instruction -All the dependencies are listed here. However, we strongly recommend using iMARGI-Docker instead of configuring these -dependencies on your Linux server. The following table shows all those required tools with simple descriptions. Some -of these tools, such as `bash`, `sort` and `zcat` are usually default installed in most of Linux distributions. Besides, -you might need root access or compiling tools on Linux system to install some of these tools. +We strongly recommend using iMARGI-Docker instead of configuring all the dependencies of iMARGI pipeline on your Linux +server. However, if you really cannot run Docker on your machine, you might want to try to configure these tools. It +requires root access to your machine and some administration experiences of Linux server. + +We cannot guarantee success of local configuration. If you encounter some problems or have suggestions, please create +issues in the [iMARGI-Docker GitHub repo](https://github.com/Zhong-Lab-UCSD/iMARGI-Docker). If you are using Ubuntu +18.04, the following command lines we used to configure iMARGI-Docker might help you. + +``` bash +# run with root account +apt-get update +apt-get install git build-essential libz-dev libbz2-dev liblzma-dev libssl-dev libcurl4-gnutls-dev \ + autoconf automake libncurses5-dev wget gawk parallel +cd /tmp && git clone https://github.com/lh3/seqtk.git && \ + cd seqtk && make && make install +cd /tmp && git clone https://github.com/samtools/htslib && \ + cd htslib && autoheader && autoconf && \ + ./configure --prefix=/usr/local && make && make install +cd /tmp && git clone https://github.com/samtools/samtools && \ + cd samtools && autoheader && autoconf && \ + ./configure --prefix=/usr/local && make && make install +cd /tmp && git clone https://github.com/lh3/bwa.git && \ + cd bwa && make && cp bwa /usr/local/bin +cd /tmp && git clone https://github.com/nh13/pbgzip && \ + cd pbgzip && sh autogen.sh && ./configure && make && make install +cd /tmp && git clone https://github.com/lz4/lz4 && \ + cd lz4 && make && make install +cd /tmp && wget http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.9.4/sratoolkit.2.9.4-ubuntu64.tar.gz && \ + tar zxvf sratoolkit.2.9.4-ubuntu64.tar.gz && cp -R sratoolkit.2.9.4-ubuntu64/bin/* /usr/local/bin + +apt-get install -y python3-dev libopenblas-dev python3-pip +pip3 install numpy cython scipy pandas click +pip3 install pairtools cooler + +cp ./src/imargi_* /usr/local/bin/ +chmod +x /usr/local/bin/imargi_* +``` + +The following table shows all the required tools with simple descriptions. Some of these tools, such as `bash`, `sort` +and `zcat` are usually default installed in most of Linux distributions. Besides, you might need root access or +compiling tools on Linux system to install some of these tools. Tool | Version | Installation | Brief description ---------|----------|---------|----------- @@ -55,10 +92,11 @@ htslib | 1.9 | [Following instruction](http://www.htslib.org/download/)| Manipul pairtools | 0.2.2 | [Following instruction](https://pairtools.readthedocs.io/en/latest/installation.html)| Utilities for processing interaction pairs lz4 | 1.8.3 | [Following instruction](https://github.com/lz4/lz4) | Extremely fast compression pbgzip | - | [Following instruction](https://github.com/nh13/pbgzip)| Compression for Genomics Data -cooler | 0.8.2 | [Following instruction](https://github.com/mirnylab/cooler)| Utilities for genomic interaction data +cooler | 0.8.3 | [Following instruction](https://github.com/mirnylab/cooler)| Utilities for genomic interaction data +HTSeq | 0.11.2 | [Following instruction](https://htseq.readthedocs.io/en/master/install.html)| Utilities for annotating interactions SRA Toolkit | 2.9.4 | [Following instruction](https://github.com/ncbi/sra-tools) | NCBI SRA tools GNU parallel | - | Linux package "parallel" | Executing jobs in parallel -[GNU awk](https://www.gnu.org/software/gawk/manual/html_node/Quick-Installation.html)| - | Linux package "gawk" | Text file processing tool +[GNU awk](https://www.gnu.org/software/gawk/manual/html_node/Quick-Installation.html)| - | Linux package "gawk", set alias awk | Text file processing tool bash | - | Linux package "bash" | Shell environment sort | - | Linux package "sort" | Sort text gunzip | - | Linux package "gunzip" | Compression tool @@ -71,4 +109,5 @@ imargi_convert.sh | 0.1| Download and `chmod +x` | Convert .pairs format to othe imargi_distfilter.sh | 0.1 | Download and `chmod +x` | Filter .pairs or BEDPE file with genomic distance threshold imargi_rsfrags.sh | 0.1 | Download and `chmod +x` | Generate restriction fragment BED file imargi_restrict.py | 0.1 | Download and `chmod +x` | Restriction site analysis of .pairs file -imargi_annotate.sh | 0.1| Download and `chmod +x` | Annotate RNA/DNA-ends with gene annotations \ No newline at end of file +imargi_annotate.sh | 0.1| Download and `chmod +x` | Annotate RNA/DNA-ends with genomic annotations +imargi_ant.py | 0.1 | Download and `chmod +x` | Annotate RNA/DNA-ends with genomic annotations, used by imargi_annotate.sh \ No newline at end of file diff --git a/docs/build/html/_sources/performance profile.md.txt b/docs/build/html/_sources/performance profile.md.txt index c9f79c5..ed25ba4 100644 --- a/docs/build/html/_sources/performance profile.md.txt +++ b/docs/build/html/_sources/performance profile.md.txt @@ -1,7 +1,7 @@ ## bwa index ``` -docker run -v ~/research/MARGI_4DN/imargi_example:/imargi imargi bwa index \ +docker run -v ~/research/MARGI_4DN/imargi_example:/imargi zhonglab/imargi bwa index \ -p ./ref/bwa_index/bwa_index_GRCh38 ./ref/GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta ``` diff --git a/docs/build/html/_sources/quick_example.md.txt b/docs/build/html/_sources/quick_example.md.txt index 83df0ef..90f1085 100644 --- a/docs/build/html/_sources/quick_example.md.txt +++ b/docs/build/html/_sources/quick_example.md.txt @@ -56,7 +56,7 @@ downloaded and prepared by fastq-dump tool. Then we can get the iMARGI sequencin format files, `SRR8206679_1.fastq.gz` and `SRR8206679_2.fastq.gz`. ``` bash -docker run -v ~/imargi_example:/imargi imargi fastq-dump --gzip --split-3 SRR8206679 +docker run -v ~/imargi_example:/imargi zhonglab/imargi fastq-dump --gzip --split-3 SRR8206679 cd ~/imargi_example mv ./SRR8206679_*.fastq.gz ./data @@ -106,7 +106,7 @@ We used ‘-N HEK_iMARGI’ argument to set base name for all the result files. ``` bash cd ~/imargi_example mkdir ./output -docker run -v ~/imargi_example:/imargi imargi imargi_wrapper.sh \ +docker run -v ~/imargi_example:/imargi zhonglab/imargi imargi_wrapper.sh \ -r hg38 \ -N HEK_iMARGI \ -t 16 \ @@ -118,6 +118,17 @@ docker run -v ~/imargi_example:/imargi imargi imargi_wrapper.sh \ As the size of sequencing data is very large (more than 350 million read pairs), it will cost about 12 hours to process. +*Tips*: + +- The command will automatically generate bwa index files based on the ref genome supplied by `-g` argument, which needs + more than 1 hour. If you have pre-built bwa index files, you can supply it with `-i` argument. + +- If you are using Windows or MacOS, you need to use pre-built bwa index files with `-i` argument. otherwise, it will + fail in the `bwa index` process. We provide Human hg38 bwa index files on our server + ([link to download](https://sysbio.ucsd.edu/imargi_pipeline/bwa_index.tar.gz)). In fact, if you are familiar with + Docker volume usage, you can find a solution in the [technical note document](./technical_note.md) + + ## Output of iMARGI Pipeline Once the iMARGI Pipeline has completed, all the result files are in the output directory. The tree structure of the @@ -167,4 +178,4 @@ detail, please check the [Step-by-step Illustration](./step_by_step_illustration **Reference:** -[[1]](#a1) Yan, Z. et al. Genome-wide co-localization of RNA-DNA interactions and fusion RNA pairs. bioRxiv 472019 (2018). doi:10.1101/472019 \ No newline at end of file +[[1]](#a1) Yan, Z. et al. Genome-wide co-localization of RNA-DNA interactions and fusion RNA pairs. PNAS February 19, 2019, 116 (8) 3328-3337. https://doi.org/10.1073/pnas.1819788116 \ No newline at end of file diff --git a/docs/build/html/_sources/step_by_step_illustration.md.txt b/docs/build/html/_sources/step_by_step_illustration.md.txt index bde8287..92116fb 100644 --- a/docs/build/html/_sources/step_by_step_illustration.md.txt +++ b/docs/build/html/_sources/step_by_step_illustration.md.txt @@ -27,7 +27,7 @@ In the [quick example](./quick_example.md) section, we use the following command are only sequencing read pairs FASTQ files and reference genome sequence FASTA file. ``` bash -docker run -v ~/imargi_example:/imargi imargi imargi_wrapper.sh \ +docker run -v ~/imargi_example:/imargi zhonglab/imargi imargi_wrapper.sh \ -r hg38 \ -N HEK_iMARGI \ -t 16 \ @@ -273,9 +273,10 @@ The output files are all in the output directory `~/imargi_example/output`. │   ├── duplication_HEK_iMARGI.pairs.gz │   ├── sorted_all_HEK_iMARGI.pairs.gz │   ├── stats_dedup_HEK_iMARGI.txt + │   ├── stats_final_HEK_iMARGI.txt │   └── unmapped_HEK_iMARGI.pairs.gz ├── final_HEK_iMARGI.pairs.gz - └── stats_final_HEK_iMARGI.txt + └── pipelineStats_HEK_iMARGI.log ``` The table below briefly described all the output files. @@ -289,7 +290,10 @@ The table below briefly described all the output files. |Intermediate parsing results| `duplication_HEK_iMARGI.pairs.gz` | `./parse_temp` | .pairs | Duplicated pairs | 506 MB | |Intermediate parsing results| `unmapped_HEK_iMARGI.pairs.gz` | `./parse_temp` | .pairs | Unmapped pairs | 3.0 GB | |Intermediate parsing results| `drop_HEK_iMARGI.pairs.gz` | `./parse_temp` | .pairs | Filtered out in-valid RNA-DNA interactions | 891 MB | +|Intermediate parsing results| `stats_dedup_HEK_iMARGI.txt`
`stats_final_HEK_iMARGI.txt` | `./parse_temp` | text | Stats report generated by pairtools | 1 KB | |Final output| `final_HEK_iMARGI.pairs.gz` | `./` | .pairs | Final output of valid RNA-DNA interactions | 1.3 GB | +|Pipeline stats log| `pipelineStats_HEK_iMARGI.log` | `./` | Simple number report of processed number of reads| 1 KB | + ### The iMARGI Pipeline Output .pairs Format diff --git a/docs/build/html/_sources/technical_note.md.txt b/docs/build/html/_sources/technical_note.md.txt index 79731c7..45ab1e1 100644 --- a/docs/build/html/_sources/technical_note.md.txt +++ b/docs/build/html/_sources/technical_note.md.txt @@ -67,8 +67,8 @@ with `-u 1043`, then all the output files and directories are all belong to my u ``` bash id -uid=1043(frankyan) gid=1048(frankyan) -docker run -u 1043 -v ~/imargi_example:/imargi imargi imargi_wrapper.sh \ +# uid=1043(frankyan) gid=1048(frankyan) +docker run -u 1043 -v ~/imargi_example:/imargi zhonglab/imargi imargi_wrapper.sh \ -r hg38 \ -N HEK_iMARGI \ -t 16 \ @@ -77,3 +77,48 @@ docker run -u 1043 -v ~/imargi_example:/imargi imargi imargi_wrapper.sh \ -2 ./data/SRR8206679_1.fastq.gz \ -o ./output ``` + +## Solve `bwa index` Failure Problem + +As we created iMARGI-Docker on Linux system, so it works perfectly on Linux system. Generally, it should also work +perfectly on Windows and MacOS. However, in our test, we found one critical problem which will cause `baw index` +failure. Here we explain the problem and give a solution to this problem. + +- **Description**: When you use `imargi_wrapper.sh` without `-i` option, the script will generate bwa index files + automatically. But it will fail when you run it on Windows or MacOS. + +- **Cause**: Different operating systems have different file system formats, such as NTFS in Windows, APFS in MacOS and + ext4 in Linux. When we use `-v` option to mount host directory to Docker container, it's a kind of map between + different file system. Most of time, there isn't any problem. However, some tools cannot handle this kind of hybrid + situation, such as `fsync`, which is utilized by `bwa index` when building large genome index. So `bwa index` fails on + Windows and MacOS. + +- **Solution**: Only Windows and MacOS users need the solution. The simplest way is use pre-built bwa index files or + build without Docker. We provide human hg38 bwa index files on our server + ([link to download](https://sysbio.ucsd.edu/imargi_pipeline/bwa_index.tar.gz)). + A technical solution to the problem is to build bwa index files in a Docker volume instead of + a mounted host directory. This solution requires some knowledge of Docker volume. Here we only show demo command + lines. You need to read Docker documentation if you want to learn more. + + ``` bash + # create Docker volume ref_vol + docker volume create --name ref_vol + # start a temporary container to cp ref genome FASTA to Docker volume ref_vol + docker run -v ref_vol:/data --name helper busybox true + docker cp ./ref/GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta helper:/data + docker rm helper + # run imargi pipeline with two '-v' arguments + docker run \ + -v /d/imargi_example:/imargi \ + -v ref_vol:/imargi/ref_data \ + zhonglab/imargi \ + imargi_wrapper.sh \ + -r hg38 \ + -N test_sample \ + -t 4 \ + -g ./ref_data/GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta \ + -1 ./data/sample_R1.fastq.gz \ + -2 ./data/sample_R2.fastq.gz \ + -o ./output + ``` + \ No newline at end of file diff --git a/docs/build/html/_static/basic.css b/docs/build/html/_static/basic.css index 19ced10..0807176 100644 --- a/docs/build/html/_static/basic.css +++ b/docs/build/html/_static/basic.css @@ -4,7 +4,7 @@ * * Sphinx stylesheet -- basic theme. * - * :copyright: Copyright 2007-2018 by the Sphinx team, see AUTHORS. + * :copyright: Copyright 2007-2019 by the Sphinx team, see AUTHORS. * :license: BSD, see LICENSE for details. * */ @@ -81,6 +81,10 @@ div.sphinxsidebar input { font-size: 1em; } +div.sphinxsidebar #searchbox form.search { + overflow: hidden; +} + div.sphinxsidebar #searchbox input[type="text"] { float: left; width: 80%; @@ -427,6 +431,13 @@ table.field-list td, table.field-list th { hyphens: manual; } +/* -- hlist styles ---------------------------------------------------------- */ + +table.hlist td { + vertical-align: top; +} + + /* -- other body styles ----------------------------------------------------- */ ol.arabic { diff --git a/docs/build/html/_static/css/badge_only.css b/docs/build/html/_static/css/badge_only.css index 323730a..3c33cef 100644 --- a/docs/build/html/_static/css/badge_only.css +++ b/docs/build/html/_static/css/badge_only.css @@ -1 +1 @@ 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+ if (re2.test(w)) + w = w + "e"; + else if (re3.test(w)) { + re = /.$/; + w = w.replace(re,""); + } + else if (re4.test(w)) + w = w + "e"; + } + } + + // Step 1c + re = /^(.+?)y$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(s_v); + if (re.test(stem)) + w = stem + "i"; + } + + // Step 2 + re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + suffix = fp[2]; + re = new RegExp(mgr0); + if (re.test(stem)) + w = stem + step2list[suffix]; + } + + // Step 3 + re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + suffix = fp[2]; + re = new RegExp(mgr0); + if (re.test(stem)) + w = stem + step3list[suffix]; + } + + // Step 4 + re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/; + re2 = /^(.+?)(s|t)(ion)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(mgr1); + if (re.test(stem)) + w = stem; + } + else if (re2.test(w)) { + var fp = re2.exec(w); + stem = fp[1] + fp[2]; + re2 = new RegExp(mgr1); + if (re2.test(stem)) + w = stem; + } + + // Step 5 + re = /^(.+?)e$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(mgr1); + re2 = new RegExp(meq1); + re3 = new RegExp("^" + C + v + "[^aeiouwxy]$"); + if (re.test(stem) || (re2.test(stem) && !(re3.test(stem)))) + w = stem; + } + re = /ll$/; + re2 = new RegExp(mgr1); + if (re.test(w) && re2.test(w)) { + re = /.$/; + w = w.replace(re,""); + } + + // and turn initial Y back to y + if (firstch == "y") + w = firstch.toLowerCase() + w.substr(1); + return w; + } +} + + + + + +var splitChars = (function() { + var result = {}; + var singles = [96, 180, 187, 191, 215, 247, 749, 885, 903, 907, 909, 930, 1014, 1648, + 1748, 1809, 2416, 2473, 2481, 2526, 2601, 2609, 2612, 2615, 2653, 2702, + 2706, 2729, 2737, 2740, 2857, 2865, 2868, 2910, 2928, 2948, 2961, 2971, + 2973, 3085, 3089, 3113, 3124, 3213, 3217, 3241, 3252, 3295, 3341, 3345, + 3369, 3506, 3516, 3633, 3715, 3721, 3736, 3744, 3748, 3750, 3756, 3761, + 3781, 3912, 4239, 4347, 4681, 4695, 4697, 4745, 4785, 4799, 4801, 4823, + 4881, 5760, 5901, 5997, 6313, 7405, 8024, 8026, 8028, 8030, 8117, 8125, + 8133, 8181, 8468, 8485, 8487, 8489, 8494, 8527, 11311, 11359, 11687, 11695, + 11703, 11711, 11719, 11727, 11735, 12448, 12539, 43010, 43014, 43019, 43587, + 43696, 43713, 64286, 64297, 64311, 64317, 64319, 64322, 64325, 65141]; + var i, j, start, end; + for (i = 0; i < singles.length; i++) { + result[singles[i]] = true; + } + var ranges = [[0, 47], [58, 64], [91, 94], [123, 169], [171, 177], [182, 184], [706, 709], + [722, 735], [741, 747], [751, 879], [888, 889], [894, 901], [1154, 1161], + [1318, 1328], [1367, 1368], [1370, 1376], [1416, 1487], [1515, 1519], [1523, 1568], + [1611, 1631], [1642, 1645], [1750, 1764], [1767, 1773], [1789, 1790], [1792, 1807], + [1840, 1868], [1958, 1968], [1970, 1983], [2027, 2035], [2038, 2041], [2043, 2047], + [2070, 2073], [2075, 2083], [2085, 2087], [2089, 2307], [2362, 2364], [2366, 2383], + [2385, 2391], [2402, 2405], [2419, 2424], [2432, 2436], [2445, 2446], [2449, 2450], + [2483, 2485], [2490, 2492], [2494, 2509], [2511, 2523], [2530, 2533], [2546, 2547], + [2554, 2564], [2571, 2574], [2577, 2578], [2618, 2648], [2655, 2661], [2672, 2673], + [2677, 2692], [2746, 2748], [2750, 2767], [2769, 2783], [2786, 2789], [2800, 2820], + [2829, 2830], [2833, 2834], [2874, 2876], [2878, 2907], [2914, 2917], [2930, 2946], + [2955, 2957], [2966, 2968], [2976, 2978], [2981, 2983], [2987, 2989], [3002, 3023], + [3025, 3045], [3059, 3076], [3130, 3132], [3134, 3159], [3162, 3167], [3170, 3173], + [3184, 3191], [3199, 3204], [3258, 3260], [3262, 3293], [3298, 3301], [3312, 3332], + [3386, 3388], [3390, 3423], [3426, 3429], [3446, 3449], [3456, 3460], [3479, 3481], + [3518, 3519], [3527, 3584], [3636, 3647], [3655, 3663], [3674, 3712], [3717, 3718], + [3723, 3724], [3726, 3731], [3752, 3753], [3764, 3772], [3774, 3775], [3783, 3791], + [3802, 3803], [3806, 3839], [3841, 3871], [3892, 3903], [3949, 3975], [3980, 4095], + [4139, 4158], [4170, 4175], [4182, 4185], [4190, 4192], [4194, 4196], [4199, 4205], + [4209, 4212], [4226, 4237], [4250, 4255], [4294, 4303], [4349, 4351], [4686, 4687], + [4702, 4703], [4750, 4751], [4790, 4791], [4806, 4807], [4886, 4887], [4955, 4968], + [4989, 4991], [5008, 5023], [5109, 5120], [5741, 5742], [5787, 5791], [5867, 5869], + [5873, 5887], [5906, 5919], [5938, 5951], [5970, 5983], [6001, 6015], [6068, 6102], + [6104, 6107], [6109, 6111], [6122, 6127], [6138, 6159], [6170, 6175], [6264, 6271], + [6315, 6319], [6390, 6399], [6429, 6469], [6510, 6511], [6517, 6527], [6572, 6592], + [6600, 6607], [6619, 6655], [6679, 6687], [6741, 6783], [6794, 6799], [6810, 6822], + [6824, 6916], [6964, 6980], [6988, 6991], [7002, 7042], [7073, 7085], [7098, 7167], + [7204, 7231], [7242, 7244], [7294, 7400], [7410, 7423], [7616, 7679], [7958, 7959], + [7966, 7967], [8006, 8007], [8014, 8015], [8062, 8063], [8127, 8129], [8141, 8143], + [8148, 8149], [8156, 8159], [8173, 8177], [8189, 8303], [8306, 8307], [8314, 8318], + [8330, 8335], [8341, 8449], [8451, 8454], [8456, 8457], [8470, 8472], [8478, 8483], + [8506, 8507], [8512, 8516], [8522, 8525], [8586, 9311], [9372, 9449], [9472, 10101], + [10132, 11263], [11493, 11498], [11503, 11516], [11518, 11519], [11558, 11567], + [11622, 11630], [11632, 11647], [11671, 11679], [11743, 11822], [11824, 12292], + [12296, 12320], [12330, 12336], [12342, 12343], [12349, 12352], [12439, 12444], + [12544, 12548], [12590, 12592], [12687, 12689], [12694, 12703], [12728, 12783], + [12800, 12831], [12842, 12880], [12896, 12927], [12938, 12976], [12992, 13311], + [19894, 19967], [40908, 40959], [42125, 42191], [42238, 42239], [42509, 42511], + [42540, 42559], [42592, 42593], [42607, 42622], [42648, 42655], [42736, 42774], + [42784, 42785], [42889, 42890], [42893, 43002], [43043, 43055], [43062, 43071], + [43124, 43137], [43188, 43215], [43226, 43249], [43256, 43258], [43260, 43263], + [43302, 43311], [43335, 43359], [43389, 43395], [43443, 43470], [43482, 43519], + [43561, 43583], [43596, 43599], [43610, 43615], [43639, 43641], [43643, 43647], + [43698, 43700], [43703, 43704], [43710, 43711], [43715, 43738], [43742, 43967], + [44003, 44015], [44026, 44031], [55204, 55215], [55239, 55242], [55292, 55295], + [57344, 63743], [64046, 64047], [64110, 64111], [64218, 64255], [64263, 64274], + [64280, 64284], [64434, 64466], [64830, 64847], [64912, 64913], [64968, 65007], + [65020, 65135], [65277, 65295], [65306, 65312], [65339, 65344], [65371, 65381], + [65471, 65473], [65480, 65481], [65488, 65489], [65496, 65497]]; + for (i = 0; i < ranges.length; i++) { + start = ranges[i][0]; + end = ranges[i][1]; + for (j = start; j <= end; j++) { + result[j] = true; + } + } + return result; +})(); + +function splitQuery(query) { + var result = []; + var start = -1; + for (var i = 0; i < query.length; i++) { + if (splitChars[query.charCodeAt(i)]) { + if (start !== -1) { + result.push(query.slice(start, i)); + start = -1; + } + } else if (start === -1) { + start = i; + } + } + if (start !== -1) { + result.push(query.slice(start)); + } + return result; +} + + diff --git a/docs/build/html/_static/searchtools.js b/docs/build/html/_static/searchtools.js index 41b8336..5ff3180 100644 --- a/docs/build/html/_static/searchtools.js +++ b/docs/build/html/_static/searchtools.js @@ -1,331 +1,52 @@ /* - * searchtools.js_t + * searchtools.js * ~~~~~~~~~~~~~~~~ * * Sphinx JavaScript utilities for the full-text search. * - * :copyright: Copyright 2007-2018 by the Sphinx team, see AUTHORS. + * :copyright: Copyright 2007-2019 by the Sphinx team, see AUTHORS. * :license: BSD, see LICENSE for details. * */ - -/* Non-minified version JS is _stemmer.js if file is provided */ -/** - * Porter Stemmer - */ -var Stemmer = function() { - - var step2list = { - ational: 'ate', - tional: 'tion', - enci: 'ence', - anci: 'ance', - izer: 'ize', - bli: 'ble', - alli: 'al', - entli: 'ent', - eli: 'e', - ousli: 'ous', - ization: 'ize', - ation: 'ate', - ator: 'ate', - alism: 'al', - iveness: 'ive', - fulness: 'ful', - ousness: 'ous', - aliti: 'al', - iviti: 'ive', - biliti: 'ble', - logi: 'log' - }; - - var step3list = { - icate: 'ic', - ative: '', - alize: 'al', - iciti: 'ic', - ical: 'ic', - ful: '', - ness: '' +if (!Scorer) { + /** + * Simple result scoring code. + */ + var Scorer = { + // Implement the following function to further tweak the score for each result + // The function takes a result array [filename, title, anchor, descr, score] + // and returns the new score. + /* + score: function(result) { + return result[4]; + }, + */ + + // query matches the full name of an object + objNameMatch: 11, + // or matches in the last dotted part of the object name + objPartialMatch: 6, + // Additive scores depending on the priority of the object + objPrio: {0: 15, // used to be importantResults + 1: 5, // used to be objectResults + 2: -5}, // used to be unimportantResults + // Used when the priority is not in the mapping. + objPrioDefault: 0, + + // query found in title + title: 15, + // query found in terms + term: 5 }; - - var c = "[^aeiou]"; // consonant - var v = "[aeiouy]"; // vowel - var C = c + "[^aeiouy]*"; // consonant sequence - var V = v + "[aeiou]*"; // vowel sequence - - var mgr0 = "^(" + C + ")?" + V + C; // [C]VC... is m>0 - var meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$"; // [C]VC[V] is m=1 - var mgr1 = "^(" + C + ")?" + V + C + V + C; // [C]VCVC... is m>1 - var s_v = "^(" + C + ")?" + v; // vowel in stem - - this.stemWord = function (w) { - var stem; - var suffix; - var firstch; - var origword = w; - - if (w.length < 3) - return w; - - var re; - var re2; - var re3; - var re4; - - firstch = w.substr(0,1); - if (firstch == "y") - w = firstch.toUpperCase() + w.substr(1); - - // Step 1a - re = /^(.+?)(ss|i)es$/; - re2 = /^(.+?)([^s])s$/; - - if (re.test(w)) - w = w.replace(re,"$1$2"); - else if (re2.test(w)) - w = w.replace(re2,"$1$2"); - - // Step 1b - re = /^(.+?)eed$/; - re2 = /^(.+?)(ed|ing)$/; - if (re.test(w)) { - var fp = re.exec(w); - re = new RegExp(mgr0); - if (re.test(fp[1])) { - re = /.$/; - w = w.replace(re,""); - } - } - else if (re2.test(w)) { - var fp = re2.exec(w); - stem = fp[1]; - re2 = new RegExp(s_v); - if (re2.test(stem)) { - w = stem; - re2 = /(at|bl|iz)$/; - re3 = new RegExp("([^aeiouylsz])\\1$"); - re4 = new RegExp("^" + C + v + "[^aeiouwxy]$"); - if (re2.test(w)) - w = w + "e"; - else if (re3.test(w)) { - re = /.$/; - w = w.replace(re,""); - } - else if (re4.test(w)) - w = w + "e"; - } - } - - // Step 1c - re = /^(.+?)y$/; - if (re.test(w)) { - var fp = re.exec(w); - stem = fp[1]; - re = new RegExp(s_v); - if (re.test(stem)) - w = stem + "i"; - } - - // Step 2 - re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/; - if (re.test(w)) { - var fp = re.exec(w); - stem = fp[1]; - suffix = fp[2]; - re = new RegExp(mgr0); - if (re.test(stem)) - w = stem + step2list[suffix]; - } - - // Step 3 - re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/; - if (re.test(w)) { - var fp = re.exec(w); - stem = fp[1]; - suffix = fp[2]; - re = new RegExp(mgr0); - if (re.test(stem)) - w = stem + step3list[suffix]; - } - - // Step 4 - re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/; - re2 = /^(.+?)(s|t)(ion)$/; - if (re.test(w)) { - var fp = re.exec(w); - stem = fp[1]; - re = new RegExp(mgr1); - if (re.test(stem)) - w = stem; - } - else if (re2.test(w)) { - var fp = re2.exec(w); - stem = fp[1] + fp[2]; - re2 = new RegExp(mgr1); - if (re2.test(stem)) - w = stem; - } - - // Step 5 - re = /^(.+?)e$/; - if (re.test(w)) { - var fp = re.exec(w); - stem = fp[1]; - re = new RegExp(mgr1); - re2 = new RegExp(meq1); - re3 = new RegExp("^" + C + v + "[^aeiouwxy]$"); - if (re.test(stem) || (re2.test(stem) && !(re3.test(stem)))) - w = stem; - } - re = /ll$/; - re2 = new RegExp(mgr1); - if (re.test(w) && re2.test(w)) { - re = /.$/; - w = w.replace(re,""); - } - - // and turn initial Y back to y - if (firstch == "y") - w = firstch.toLowerCase() + w.substr(1); - return w; - } } - - -/** - * Simple result scoring code. - */ -var Scorer = { - // Implement the following function to further tweak the score for each result - // The function takes a result array [filename, title, anchor, descr, score] - // and returns the new score. - /* - score: function(result) { - return result[4]; - }, - */ - - // query matches the full name of an object - objNameMatch: 11, - // or matches in the last dotted part of the object name - objPartialMatch: 6, - // Additive scores depending on the priority of the object - objPrio: {0: 15, // used to be importantResults - 1: 5, // used to be objectResults - 2: -5}, // used to be unimportantResults - // Used when the priority is not in the mapping. - objPrioDefault: 0, - - // query found in title - title: 15, - // query found in terms - term: 5 -}; - - - - - -var splitChars = (function() { - var result = {}; - var singles = [96, 180, 187, 191, 215, 247, 749, 885, 903, 907, 909, 930, 1014, 1648, - 1748, 1809, 2416, 2473, 2481, 2526, 2601, 2609, 2612, 2615, 2653, 2702, - 2706, 2729, 2737, 2740, 2857, 2865, 2868, 2910, 2928, 2948, 2961, 2971, - 2973, 3085, 3089, 3113, 3124, 3213, 3217, 3241, 3252, 3295, 3341, 3345, - 3369, 3506, 3516, 3633, 3715, 3721, 3736, 3744, 3748, 3750, 3756, 3761, - 3781, 3912, 4239, 4347, 4681, 4695, 4697, 4745, 4785, 4799, 4801, 4823, - 4881, 5760, 5901, 5997, 6313, 7405, 8024, 8026, 8028, 8030, 8117, 8125, - 8133, 8181, 8468, 8485, 8487, 8489, 8494, 8527, 11311, 11359, 11687, 11695, - 11703, 11711, 11719, 11727, 11735, 12448, 12539, 43010, 43014, 43019, 43587, - 43696, 43713, 64286, 64297, 64311, 64317, 64319, 64322, 64325, 65141]; - var i, j, start, end; - for (i = 0; i < singles.length; i++) { - result[singles[i]] = true; - } - var ranges = [[0, 47], [58, 64], [91, 94], [123, 169], [171, 177], [182, 184], [706, 709], - [722, 735], [741, 747], [751, 879], [888, 889], [894, 901], [1154, 1161], - [1318, 1328], [1367, 1368], [1370, 1376], [1416, 1487], [1515, 1519], [1523, 1568], - [1611, 1631], [1642, 1645], [1750, 1764], [1767, 1773], [1789, 1790], [1792, 1807], - [1840, 1868], [1958, 1968], [1970, 1983], [2027, 2035], [2038, 2041], [2043, 2047], - [2070, 2073], [2075, 2083], [2085, 2087], [2089, 2307], [2362, 2364], [2366, 2383], - [2385, 2391], [2402, 2405], [2419, 2424], [2432, 2436], [2445, 2446], [2449, 2450], - [2483, 2485], [2490, 2492], [2494, 2509], [2511, 2523], [2530, 2533], [2546, 2547], - [2554, 2564], [2571, 2574], [2577, 2578], [2618, 2648], [2655, 2661], [2672, 2673], - [2677, 2692], [2746, 2748], [2750, 2767], [2769, 2783], [2786, 2789], [2800, 2820], - [2829, 2830], [2833, 2834], [2874, 2876], [2878, 2907], [2914, 2917], [2930, 2946], - [2955, 2957], [2966, 2968], [2976, 2978], [2981, 2983], [2987, 2989], [3002, 3023], - [3025, 3045], [3059, 3076], [3130, 3132], [3134, 3159], [3162, 3167], [3170, 3173], - [3184, 3191], [3199, 3204], [3258, 3260], [3262, 3293], [3298, 3301], [3312, 3332], - [3386, 3388], [3390, 3423], [3426, 3429], [3446, 3449], [3456, 3460], [3479, 3481], - [3518, 3519], [3527, 3584], [3636, 3647], [3655, 3663], [3674, 3712], [3717, 3718], - [3723, 3724], [3726, 3731], [3752, 3753], [3764, 3772], [3774, 3775], [3783, 3791], - [3802, 3803], [3806, 3839], [3841, 3871], [3892, 3903], [3949, 3975], [3980, 4095], - [4139, 4158], [4170, 4175], [4182, 4185], [4190, 4192], [4194, 4196], [4199, 4205], - [4209, 4212], [4226, 4237], [4250, 4255], [4294, 4303], [4349, 4351], [4686, 4687], - [4702, 4703], [4750, 4751], [4790, 4791], [4806, 4807], [4886, 4887], [4955, 4968], - [4989, 4991], [5008, 5023], [5109, 5120], [5741, 5742], [5787, 5791], [5867, 5869], - [5873, 5887], [5906, 5919], [5938, 5951], [5970, 5983], [6001, 6015], [6068, 6102], - [6104, 6107], [6109, 6111], [6122, 6127], [6138, 6159], [6170, 6175], [6264, 6271], - [6315, 6319], [6390, 6399], [6429, 6469], [6510, 6511], [6517, 6527], [6572, 6592], - [6600, 6607], [6619, 6655], [6679, 6687], [6741, 6783], [6794, 6799], [6810, 6822], - [6824, 6916], [6964, 6980], [6988, 6991], [7002, 7042], [7073, 7085], [7098, 7167], - [7204, 7231], [7242, 7244], [7294, 7400], [7410, 7423], [7616, 7679], [7958, 7959], - [7966, 7967], [8006, 8007], [8014, 8015], [8062, 8063], [8127, 8129], [8141, 8143], - [8148, 8149], [8156, 8159], [8173, 8177], [8189, 8303], [8306, 8307], [8314, 8318], - [8330, 8335], [8341, 8449], [8451, 8454], [8456, 8457], [8470, 8472], [8478, 8483], - [8506, 8507], [8512, 8516], [8522, 8525], [8586, 9311], [9372, 9449], [9472, 10101], - [10132, 11263], [11493, 11498], [11503, 11516], [11518, 11519], [11558, 11567], - [11622, 11630], [11632, 11647], [11671, 11679], [11743, 11822], [11824, 12292], - [12296, 12320], [12330, 12336], [12342, 12343], [12349, 12352], [12439, 12444], - [12544, 12548], [12590, 12592], [12687, 12689], [12694, 12703], [12728, 12783], - [12800, 12831], [12842, 12880], [12896, 12927], [12938, 12976], [12992, 13311], - [19894, 19967], [40908, 40959], [42125, 42191], [42238, 42239], [42509, 42511], - [42540, 42559], [42592, 42593], [42607, 42622], [42648, 42655], [42736, 42774], - [42784, 42785], [42889, 42890], [42893, 43002], [43043, 43055], [43062, 43071], - [43124, 43137], [43188, 43215], [43226, 43249], [43256, 43258], [43260, 43263], - [43302, 43311], [43335, 43359], [43389, 43395], [43443, 43470], [43482, 43519], - [43561, 43583], [43596, 43599], [43610, 43615], [43639, 43641], [43643, 43647], - [43698, 43700], [43703, 43704], [43710, 43711], [43715, 43738], [43742, 43967], - [44003, 44015], [44026, 44031], [55204, 55215], [55239, 55242], [55292, 55295], - [57344, 63743], [64046, 64047], [64110, 64111], [64218, 64255], [64263, 64274], - [64280, 64284], [64434, 64466], [64830, 64847], [64912, 64913], [64968, 65007], - [65020, 65135], [65277, 65295], [65306, 65312], [65339, 65344], [65371, 65381], - [65471, 65473], [65480, 65481], [65488, 65489], [65496, 65497]]; - for (i = 0; i < ranges.length; i++) { - start = ranges[i][0]; - end = ranges[i][1]; - for (j = start; j <= end; j++) { - result[j] = true; - } - } - return result; -})(); - -function splitQuery(query) { - var result = []; - var start = -1; - for (var i = 0; i < query.length; i++) { - if (splitChars[query.charCodeAt(i)]) { - if (start !== -1) { - result.push(query.slice(start, i)); - start = -1; - } - } else if (start === -1) { - start = i; - } - } - if (start !== -1) { - result.push(query.slice(start)); - } - return result; +if (!splitQuery) { + function splitQuery(query) { + return query.split(/\s+/); + } } - - - /** * Search Module */ @@ -417,7 +138,6 @@ var Search = { */ query : function(query) { var i; - var stopwords = ["a","and","are","as","at","be","but","by","for","if","in","into","is","it","near","no","not","of","on","or","such","that","the","their","then","there","these","they","this","to","was","will","with"]; // stem the searchterms and add them to the correct list var stemmer = new Stemmer(); @@ -758,4 +478,4 @@ var Search = { $(document).ready(function() { Search.init(); -}); \ No newline at end of file +}); diff --git a/docs/build/html/_static/websupport.js b/docs/build/html/_static/websupport.js index 78e14bb..3b4999e 100644 --- a/docs/build/html/_static/websupport.js +++ b/docs/build/html/_static/websupport.js @@ -4,7 +4,7 @@ * * sphinx.websupport utilities for all documentation. * - * :copyright: Copyright 2007-2018 by the Sphinx team, see AUTHORS. + * :copyright: Copyright 2007-2019 by the Sphinx team, see AUTHORS. * :license: BSD, see LICENSE for details. * */ diff --git a/docs/build/html/commandline_api.html b/docs/build/html/commandline_api.html index b94ee90..eafe2b9 100644 --- a/docs/build/html/commandline_api.html +++ b/docs/build/html/commandline_api.html @@ -17,33 +17,35 @@ - - + + + + + + + + - + + - - - -
-