Package: fast5seek
# fast5seek[![PyPI status](https://img.shields.io/pypi/v/fast5seek.svg)](https://pypi.python.org/pypi/fast5seek)[![Build Status](https://travis-ci.org/mbhall88/fast5seek.svg?branch=master)](https://travis-ci.org/mbhall88/fast5seek)[![GitHub license](https://img.shields.io/github/license/mbhall88/fast5seek.svg)](https://github.com/mbhall88/fast5seek/blob/master/LICENSE)[![Twitter Follow](https://img.shields.io/twitter/follow/mbhall88.svg?style=social&logo=twitter&label=Follow)](https://twitter.com/mbhall88)This program takes a directory (or multiple) of fast5 files along with any numberof fastq, SAM, or BAM files. The output is the full paths for all fast5 filespresent in the fastq, BAM, or SAM files that are also in the provided fast5 directory(s).### InstallationUsing python3, run```bashpip3 install fast5seek```### UsageIt's pretty straight-forward to use:fast5seek -i /path/to/fast5s -r in.fastq in.bam in.sam -o out.txtThis will write all fast5 paths to a text file called `out.txt` - with each pathon a new line.What it does is read in the `in.fastq in.bam in.sam` files andextracts the read id from each record. It then goes through all thefast5 files under `/path/to/fast5s` and checks whether their read id is inthe set of read ids from `<in.fastq|in.bam|in.sam>`. If it is, thepath to the file is written to it's own line in `out.txt`.If no output (`-o`) is given, it will write the output to `stdout`.There is also an option to only search for read ids among mapped records in aBAM or SAM file - `-m/--mapped`.Gzipped fastq files can also be provided.#### Full Usage```usage: fast5seek [-h] -i FAST5_DIR [FAST5_DIR ...] -r REFERENCE[REFERENCE ...] [-o OUTPUT] [-m] [--log_level {0,1,2,3,4,5}][--no_progress_bar]Outputs paths of all the fast5 files from a given directory that are contained within a fastq or BAM/SAM file.Please see the github page for more detailed instructions.https://github.com/mbhall88/fast5seek/Contributors:Michael Hall (github@mbhall88)Darrin Schultz (github@conchoecia)optional arguments:-h, --help            show this help message and exit-i FAST5_DIR [FAST5_DIR ...], --fast5_dir FAST5_DIR [FAST5_DIR ...]Directory of fast5 files you want to query. Programwill walk recursively through subdirectories.-r REFERENCE [REFERENCE ...], --reference REFERENCE [REFERENCE ...]Fastq or BAM/SAM file(s).-o OUTPUT, --output OUTPUTFilename to write fast5 paths to. If nothing isentered, it will write the paths to STDOUT.-m, --mapped          Only extract read ids for mapped reads in BAM/SAMfiles.--log_level {0,1,2,3,4,5}Level of logging. 0 is none, 5 is for debugging.Default is 4 which will report info, warnings, errors,and critical information.--no_progress_bar     Do not display progress bar.```#### Multiple InputsIt is possible to use multiple directories/files asarguments. No need to merge bam|fastq|sam files.fast5seek -i /myfast5/dir/1/ /other/fast5/dir/2/ -r reads.sorted.bam reads2.bamFor example, if all of your fast5 directories contain the prefix`myfast5_` and the reference files contain `.sorted.bam`, you can usewildcards to find them all if they are in the same directory.fast5seek -i myfast5_* -r *.sorted.bam#### Piping CommandsIf you wanted to pipe these paths into another program, you could do something likemkdir subset_dir/fast5seek -i /path/to/fast5s/ -r in.fastq | xargs cp -t subset_dir/The above example would copy the `fast5` files that are found in your `fastq` to `subset_dir/`.#### Recommended UsageHowever because of the computationally intensive step required to open`fast5` files, we recommend that you first save the output of`fast5seek` to a file for safekeeping, then proceed with analysis like so:mkdir subset_dir/fast5seek -i /path/to/fast5s/ -r in.fastq -o mapped_reads.txtcat mapped_reads.txt | xargs cp -t subset_dir/### ContactIf there are any issues with the program please [open an issue above](https://github.com/mbhall88/fast5seek/issues).### ContributorsMichael Hall @mbhall88Darrin Schultz @conchoecia