⚠️ This project is effectively redundant now. The functionality can be reproduced with fast5_subset. See https://github.com/mbhall88/fast5seek/issues/7 for a further explanation. ⚠️

fast5seek

This program takes a directory (or multiple) of fast5 files along with any number of fastq, SAM, or BAM files. The output is the full paths for all fast5 files present in the fastq, BAM, or SAM files that are also in the provided fast5 directory(s).

Installation

Using python3, run

pip3 install fast5seek

Usage

It’s pretty straight-forward to use:

fast5seek -i /path/to/fast5s -r in.fastq in.bam in.sam -o out.txt

This will write all fast5 paths to a text file called out.txt - with each path on a new line.

What it does is read in the in.fastq in.bam in.sam files and extracts the read id from each record. It then goes through all the fast5 files under /path/to/fast5s and checks whether their read id is in the set of read ids from <in.fastq|in.bam|in.sam>. If it is, the path 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 a BAM 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. Program
                        will walk recursively through subdirectories.
  -r REFERENCE [REFERENCE ...], --reference REFERENCE [REFERENCE ...]
                        Fastq or BAM/SAM file(s).
  -o OUTPUT, --output OUTPUT
                        Filename to write fast5 paths to. If nothing is
                        entered, it will write the paths to STDOUT.
  -m, --mapped          Only extract read ids for mapped reads in BAM/SAM
                        files.
  --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 Inputs

It is possible to use multiple directories/files as arguments. No need to merge bam|fastq|sam files.

fast5seek -i /myfast5/dir/1/ /other/fast5/dir/2/ -r reads.sorted.bam reads2.bam

For example, if all of your fast5 directories contain the prefix myfast5_ and the reference files contain .sorted.bam, you can use wildcards to find them all if they are in the same directory.

fast5seek -i myfast5_* -r *.sorted.bam

Piping Commands

If you wanted to pipe these paths into another program, you could do something like

mkdir 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 Usage

However 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.txt
cat mapped_reads.txt | xargs cp -t subset_dir/

Contact

If there are any issues with the program please open an issue above.

Contributors

Michael Hall @mbhall88
Darrin Schultz @conchoecia