Converts a fastq filename into the format needed by GeoMx NGS Pipeline
From page 42 of the GeoMx NGS Readout User Manual: The GeoMx NGS Pipeline looks for FASTQ files with a naming structure such as DSP-1001250001985-A-A02_S2_L001_R1_001.fastq.gz where DSP-1001250001985-A-A02 = Sample ID matching Configuration file, SeqCodeIndices.csv, or Sample ID Translator File. S2 = Sample sheet number. L001 = Lane number (include even if your flow cell had only 1 lane). R1 = Forward or reverse, read 1 or 2. 001 = Should always be 001. The suffix .fastq.gz indicates a compressed file.
This script takes a file with a filename formatting of A02_CKDL230023209-1A_H75KCDSX7_L2_1.fq.gz where L2 is Lane number
and 1 is R1 (forward read) and updates the filename to be DSP-1001660018726-A-A02_S32_L002_R1_001.fastq.gz where leading
zeroes are added to the Lane number, 001 is added to the end of the filename, and fastq replaces fq. Sample ID and
Sample sheet number are obtained from other necessary files (a configuration ini file and a QC or sample sheet to get the
sample location).
This has been run on Python 3.9 and 3.11. Modules are os, gzip, argparse, and csv but should be included with the distro
The script takes three arguments. The first is the base sample name taken from the configuration ini file. There should be a section that looks like:
[AOI_List] DSP-1001660018726-A-A01 = 1001660018726,A01,0.00 DSP-1001660018726-A-A02 = 1001660018726,A02,70025.09 DSP-1001660018726-A-A03 = 1001660018726,A03,159680.12 DSP-1001660018726-A-A04 = 1001660018726,A04,56077.51 DSP-1001660018726-A-A05 = 1001660018726,A05,55078.15 DSP-1001660018726-A-A06 = 1001660018726,A06,56267.45...
DSP-1001660018726-A- is what would be used for the first argument
The second argument is a comma-separated or newline-delimited text file of the sample IDs A01, A02, A03 (these correspond to
the directory names). The position in the text file should match the ordinal position on the sample sheet or QC file. These
may be in a file that looks like:
Sample (other columns deleted) A08 A12 B02 B03 B04 B05 B06 B07 B09 B10 B11 B12 C01 C02
So sample A08 would be listed first, A12 next, and so on.
The last argument is --skip-gzip. For some reason the BaseSpace Sequence Hub can't read
the as-shipped gz files. Normally decompressing and re-gzipping works but it adds a lot
of time. If you've tested a few of the original files and BaseSpace doesn't complain
(usually it's an error on a bad separator) then the re-gzipping can be skipped.
Developed in Python 3.9
We welcome external contributions, although it is a good idea to contact the maintainers before embarking on any significant development work to make sure the proposed changes are a good fit.
Contributors agree to license their code under the license in use by this
project (see LICENSE).
To contribute:
- Fork the repo
- Make changes on a branch
- Create a pull request
See LICENSE for details.
REPLACE: Who should people contact with questions?
See AUTHORS the full list of authors.