Mercurial > repos > dcouvin > mirureader
comparison MIRUReader/README.md @ 0:f0e3646a4e45 draft
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| author | dcouvin |
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| date | Tue, 17 Aug 2021 19:15:15 +0000 |
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| -1:000000000000 | 0:f0e3646a4e45 |
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| 1 # MIRUReader | |
| 2 | |
| 3 ## Description | |
| 4 | |
| 5 Identify 24-locus MIRU-VNTR for *Mycobacterium tuberculosis* complex (MTBC) directly from long reads generated by Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio). Also work on assembled genome. | |
| 6 | |
| 7 ## Requirements | |
| 8 | |
| 9 * Linux | |
| 10 * primersearch from [EMBOSS](http://emboss.sourceforge.net/download/) | |
| 11 * install from the official website or | |
| 12 * install via conda `conda install -c bioconda emboss` | |
| 13 * Ensure the primersearch command is in your device's environment path, where primersearch program can be executed directly by typing `primersearch` on the commandline | |
| 14 * [*pandas*](https://pandas.pydata.org/) | |
| 15 * can be installed via conda `conda install pandas` or via PyPI `pip install pandas` | |
| 16 * [*statistics*](https://pypi.org/project/statistics/) | |
| 17 * can be installed via PyPI `pip install statistics` | |
| 18 | |
| 19 ## Installation | |
| 20 | |
| 21 `git clone https://github.com/phglab/MIRUReader.git` | |
| 22 | |
| 23 ## Change log | |
| 24 #### 13/09/2019 | |
| 25 - Added a check to ensure primersearch is executable prior to MIRUReader program execution | |
| 26 - Updated documentation to the README | |
| 27 | |
| 28 #### 04/07/2019 | |
| 29 - Update output format for option '--details'. | |
| 30 | |
| 31 #### 14/06/2019 | |
| 32 - Auto convert fastq to fasta. | |
| 33 | |
| 34 ## Usage example | |
| 35 | |
| 36 For one sample analysis: | |
| 37 ``` | |
| 38 python /your/path/to/MIRUReader.py -r sample.fasta -p sampleID > miru.txt | |
| 39 ``` | |
| 40 | |
| 41 For multiple samples analysis: | |
| 42 1. Create a mapping file (mappingFile.txt) that looks like: | |
| 43 | |
| 44 sample_001.fasta sample_001 \ | |
| 45 sample_002.fasta sample_002 \ | |
| 46 ... | |
| 47 | |
| 48 2. Then run the program: | |
| 49 ``` | |
| 50 cat mappingFile.txt | while read -a line; do python /your/path/to/MIRUReader.py -r ${line[0]} -p ${line[1]}; done > miru.multiple.txt | |
| 51 ``` | |
| 52 | |
| 53 ## Output example | |
| 54 | |
| 55 ``` | |
| 56 sample_prefix 0154 0424 0577 0580 0802 0960 1644 1955 2059 2163b 2165 2347 2401 2461 2531 2687 2996 3007 3171 3192 3690 4052 4156 4348 | |
| 57 sample_001 2 4 4 2 3 3 3 2 2 5 4 4 4 2 5 1 6 3 3 5 3 7 2 3 | |
| 58 ``` | |
| 59 | |
| 60 Notes: | |
| 61 * The program is compatible to Python 2 and Python 3. | |
| 62 * Accepted reads file format includes '.fastq', '.fastq.gz', '.fasta', and '.fasta.gz'. | |
| 63 * The program output is a tab-delimited plain text which can be copied to or opened in Excel spreadsheet. | |
| 64 | |
| 65 ## Full usage | |
| 66 | |
| 67 | Main options | Description | | |
| 68 | ------------ | ----------- | | |
| 69 | -r READS | Input reads file in fastq/fasta format, can be gzipped or not gzipped | | |
| 70 | -p PREFIX | Sample ID required for naming output file. | | |
| 71 | --table TABLE | Allele calling table, default is MIRU_table. Can be user-defined in fixed format. However, providing custom allele calling table for other VNTR is not tested. | | |
| 72 | --primers PRIMERS | Primers sequences, default is MIRU_primers. Can be user-defined in fixed format. | | |
| 73 | |
| 74 | |
| 75 | Optional options | Description | | |
| 76 | ---------------- | ----------- | | |
| 77 | --amplicons | Use output from primersearch ("prefix.18.primersearch.out") and summarize MIRU profile directly. | | |
| 78 | --details | This option is for further inspection. It displays details of repeat count for each loci with total mismatch error in the primer sequences alignment. | | |
| 79 | --nofasta | Delete fasta file generated if your input read is in fastq format. | | |
| 80 | |
| 81 ## FAQ | |
| 82 1. **Why are there two MIRU allele calling tables (MIRU_table and MIRU_table_0580)?** | |
| 83 | |
| 84 MIRU loci 0580 (MIRU_table_0580) consist of a different numbering system for determination of repeat numbers as compared to the other 23 MIRU locus (MIRU_table) for MTBC isolates. | |
| 85 | |
| 86 | |
| 87 ## Troubleshooting | |
| 88 1. If an error message `OSError: primersearch is not found.` appears, please ensure your `primersearch` executable file is in your environment path (`echo $PATH`) and can be called directly. |