# RNA MAP
[](https://github.com/YesselmanLab/rna_map/actions/workflows/docker_linux_build.yml)
[](https://github.com/psf/black)
[](https://github.com/PyCQA/pylint)
[](http://badge.fury.io/py/rna-map)
## How to install
```
pip install rna-map
```
### with docker
```shell
# on linux and intel mac
docker build -t rna-map -f docker/Dockerfile .
# on mac with apple silicon / or other arm64 platforms
docker build -t rna-map --platform linux/amd64 -f docker/Dockerfile .
```
## How to use
```
rna-map --help
Usage: rna-map [OPTIONS]
rapid analysis of RNA mutational profiling (MaP) experiments.
Main arguments:
These are the main arguments for the command line interface
-fa, --fasta PATH The fasta file containing the reference
sequences [required]
-fq1, --fastq1 PATH The fastq file containing the single end reads
or the first pair of paired end reads
[required]
-fq2, --fastq2 TEXT The fastq file containing the second pair of
paired end reads
--dot-bracket TEXT The directory containing the input files
-pf, --param-file TEXT A yml formatted file to specify parameters, see
rna_map/resources/default.yml for an example
-pp, --param-preset TEXT run a set of parameters for specific uses like
'barcoded-libraries'
Mapping options:
These are the options for pre processing of fastq files and alignment to
reference sequences
--skip-fastqc do not run fastqc for quality control of
sequence data
--skip-trim-galore do not run trim galore for quality control of
sequence data
--tg-q-cutoff INTEGER the quality cutoff for trim galore
--bt2-alignment-args TEXT the arguments to pass to bowtie2 for alignment
seperated by commas
--save-unaligned the path to save unaligned reads to
Bit vector options:
These are the options for the bit vector step
--skip-bit-vector do not run the bit vector step
--summary-output-only do not generate bit vector files or plots
recommended when there are thousands of
reference sequences
--plot-sequence plot sequence and structure is supplied under
the population average plots
--map-score-cutoff INTEGER reject any bit vector where the mapping score
for bowtie2 alignment is less than this value
--qscore-cutoff INTEGER quality score of read nucleotide, sets to
ambigious if under this val
--mutation-count-cutoff INTEGER
maximum number of mutations allowed in a bit
vector will be discarded if higher
--percent-length-cutoff FLOAT minium percent of the length of the reference
sequence allowed in a bit vector will be
discarded if lower
--min-mut-distance INTEGER minimum distance between mutations in a bit
vector will be discarded if lower
Docker options:
These are the options for running the command line interface in a docker
container
--docker Run the program in a docker container
--docker-image TEXT The docker image to use
--docker-platform TEXT The platform to use for the docker image
Misc options:
These are the options for the misc stage
--overwrite overwrite the output directory if it exists
--restore-org-behavior restore the original behavior of the rna_map
--stricter-bv-constraints use stricter constraints for bit vector
generation, use at your own risk!
--debug enable debug mode
Other options:
--help Show this message and exit.
```
### running paired end reads
```shell
rna-map -fa test/resources/case_1/test.fasta -fq1 test/resources/case_unit/test_mate1.fastq -fq2 test/resources/case_unit/test_mate2.fastq
```
```shell
rna_map.CLI - INFO -
88888888ba 888b 88 db 88b d88 db 88888888ba
88 "8b 8888b 88 d88b 888b d888 d88b 88 "8b
88 ,8P 88 `8b 88 d8'`8b 88`8b d8'88 d8'`8b 88 ,8P
88aaaaaa8P' 88 `8b 88 d8' `8b 88 `8b d8' 88 d8' `8b 88aaaaaa8P'
88""""88' 88 `8b 88 d8YaaaaY8b 88 `8b d8' 88 d8YaaaaY8b 88""""""'
88 `8b 88 `8b 88 d8""""""""8b 88 `8b d8' 88 d8""""""""8b 88
88 `8b 88 `8888 d8' `8b 88 `888' 88 d8' `8b 88
88 `8b 88 `888 d8' `8b 88 `8' 88 d8' `8b 88
rna_map.CLI - INFO - ran at commandline as:
rna_map.CLI - INFO - /Users/jyesselm/miniconda3/envs/py3/bin/rna-map -fa test/resources/case_1/test.fasta -fq1 test/resources/case_unit/test_mate1.fastq -fq2 test/resources/case_unit/test_mate2.fastq
rna_map.RUN - INFO - fasta file: test/resources/case_1/test.fasta exists
rna_map.RUN - INFO - found 1 valid reference sequences in test/resources/case_1/test.fasta
rna_map.RUN - INFO - fastq1 file: test/resources/case_unit/test_mate1.fastq exists
rna_map.RUN - INFO - fastq2 file: test/resources/case_unit/test_mate2.fastq exists
rna_map.RUN - INFO - two fastq files supplied, thus assuming paired reads
rna_map.MAPPING - INFO - bowtie2 2.4.5 detected!
rna_map.MAPPING - INFO - fastqc v0.11.9 detected!
rna_map.MAPPING - INFO - trim_galore 0.6.6 detected!
rna_map.MAPPING - INFO - cutapt 1.18 detected!
rna_map.MAPPING - INFO - building directory structure
rna_map.MAPPING - INFO - bowtie2 2.4.5 detected!
rna_map.MAPPING - INFO - fastqc v0.11.9 detected!
rna_map.MAPPING - INFO - trim_galore 0.6.6 detected!
rna_map.MAPPING - INFO - cutapt 1.18 detected!
rna_map.EXTERNAL_CMD - INFO - running fastqc
rna_map.EXTERNAL_CMD - INFO - fastqc ran without errors
rna_map.EXTERNAL_CMD - INFO - running trim_galore
rna_map.EXTERNAL_CMD - INFO - trim_galore ran without errors
rna_map.EXTERNAL_CMD - INFO - running bowtie2-build
rna_map.EXTERNAL_CMD - INFO - bowtie2-build ran without errors
rna_map.EXTERNAL_CMD - INFO - running bowtie2 alignment
rna_map.EXTERNAL_CMD - INFO - bowtie2 alignment ran without errors
rna_map.EXTERNAL_CMD - INFO - results for bowtie alignment:
25 reads; of these:
25 (100.00%) were paired; of these:
1 (4.00%) aligned concordantly 0 times
24 (96.00%) aligned concordantly exactly 1 time
0 (0.00%) aligned concordantly >1 times
96.00% overall alignment rate
rna_map.MAPPING - INFO - finished mapping!
rna_map.BIT_VECTOR - INFO - starting bitvector generation
rna_map.BIT_VECTOR - INFO - REMOVED READS:
| name | low_mapq |
|---------------|------------|
| mttr-6-alt-h3 | 0 |
rna_map.BIT_VECTOR - INFO - MUTATION SUMMARY:
| name | reads | aligned | no_mut | 1_mut | 2_mut | 3_mut | 3plus_mut | sn |
|---------------|---------|-----------|----------|---------|---------|---------|-------------|------|
| mttr-6-alt-h3 | 24 | 100 | 50 | 33.33 | 12.5 | 4.17 | 0 | 4.91 |
```
### running with docker
`--docker` flag will run the docker image. if you have run docker build first
```shell
rna-map -fa test/resources/case_1/test.fasta -fq1 test/resources/case_unit/test_mate1.fastq -fq2 test/resources/case_unit/test_mate2.fastq --docker
```
## TODO
- [ ]
- [ ] Add mac build to github actions
Raw data
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"description": "\n\n\n# RNA MAP\n\n[](https://github.com/YesselmanLab/rna_map/actions/workflows/docker_linux_build.yml)\n[](https://github.com/psf/black)\n[](https://github.com/PyCQA/pylint)\n[](http://badge.fury.io/py/rna-map)\n\n\n## How to install\n\n```\npip install rna-map\n```\n\n### with docker \n```shell\n# on linux and intel mac\ndocker build -t rna-map -f docker/Dockerfile .\n\n# on mac with apple silicon / or other arm64 platforms\ndocker build -t rna-map --platform linux/amd64 -f docker/Dockerfile .\n```\n\n## How to use \n\n```\nrna-map --help\nUsage: rna-map [OPTIONS]\n\n rapid analysis of RNA mutational profiling (MaP) experiments.\n\nMain arguments:\n These are the main arguments for the command line interface\n -fa, --fasta PATH The fasta file containing the reference\n sequences [required]\n -fq1, --fastq1 PATH The fastq file containing the single end reads\n or the first pair of paired end reads\n [required]\n -fq2, --fastq2 TEXT The fastq file containing the second pair of\n paired end reads\n --dot-bracket TEXT The directory containing the input files\n -pf, --param-file TEXT A yml formatted file to specify parameters, see\n rna_map/resources/default.yml for an example\n -pp, --param-preset TEXT run a set of parameters for specific uses like\n 'barcoded-libraries'\n\nMapping options:\n These are the options for pre processing of fastq files and alignment to\n reference sequences\n --skip-fastqc do not run fastqc for quality control of\n sequence data\n --skip-trim-galore do not run trim galore for quality control of\n sequence data\n --tg-q-cutoff INTEGER the quality cutoff for trim galore\n --bt2-alignment-args TEXT the arguments to pass to bowtie2 for alignment\n seperated by commas\n --save-unaligned the path to save unaligned reads to\n\nBit vector options:\n These are the options for the bit vector step\n --skip-bit-vector do not run the bit vector step\n --summary-output-only do not generate bit vector files or plots\n recommended when there are thousands of\n reference sequences\n --plot-sequence plot sequence and structure is supplied under\n the population average plots\n --map-score-cutoff INTEGER reject any bit vector where the mapping score\n for bowtie2 alignment is less than this value\n --qscore-cutoff INTEGER quality score of read nucleotide, sets to\n ambigious if under this val\n --mutation-count-cutoff INTEGER\n maximum number of mutations allowed in a bit\n vector will be discarded if higher\n --percent-length-cutoff FLOAT minium percent of the length of the reference\n sequence allowed in a bit vector will be\n discarded if lower\n --min-mut-distance INTEGER minimum distance between mutations in a bit\n vector will be discarded if lower\n\nDocker options:\n These are the options for running the command line interface in a docker\n container\n --docker Run the program in a docker container\n --docker-image TEXT The docker image to use\n --docker-platform TEXT The platform to use for the docker image\n\nMisc options:\n These are the options for the misc stage\n --overwrite overwrite the output directory if it exists\n --restore-org-behavior restore the original behavior of the rna_map\n --stricter-bv-constraints use stricter constraints for bit vector\n generation, use at your own risk!\n --debug enable debug mode\n\nOther options:\n --help Show this message and exit.\n\n```\n\n### running paired end reads\n\n```shell\n rna-map -fa test/resources/case_1/test.fasta -fq1 test/resources/case_unit/test_mate1.fastq -fq2 test/resources/case_unit/test_mate2.fastq \n```\n\n```shell\nrna_map.CLI - 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