gtc_final_report.py

[smuchakiel]

Dear all,

I have many GTC files and want to convert them into finalreports. Sadly I can't get the programm running. I have the manifest and the clusterfile.

Do you have an example for running gtc_final_report.py with all the parameters?

Best,

[KelleyRyanM]

Hi, Usage for that that example script would look something like python gtc_final_report.py "location of manifest BPM file" "location of directory with GTC files" "location to write output file"

Can you provide more detail on what kind of error you get when you try to run the command?

[smuchakiel]

Dear Kelly,

thanks for the fast answer. How do I add the path of the GTC files, the manifest and the clusterfile? Or should I just start python gtc_final_report.py?

Best,

---

Sören Mucha (MSc, PhD student)

Institute of Clinical Molecular Biology Christian-Albrechts-University of Kiel

University Hospital Schleswig Holstein · Campus Kiel Rosalind-Franklin-Str. 12 · 24105 Kiel, Germany

Fon: +49 (0) 431 500 15145· s.mucha@ikmb.uni-kiel.de · www.ikmb.uni-kiel.de [3]

Am 2017-11-03 18:48, schrieb KelleyRyanM:

Hi, Usage for that that example script would look something like python gtc_final_report.py

Can you provide more detail on what kind of error you get when you try to run the command?

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[KelleyRyanM]

Sorry, looks like the markdown formatting swallowed part of my comment. Please see the updated response above with respect to the locations of the script arguments.

[smuchakiel]

If I start the python script with this:

python gtc_final_report.py /home/user/Downloads/BeadArrayFiles-develop/examples/HumanCoreExome-12-v1-1-C.bpm /home/user/Downloads/BeadArrayFiles-develop/examples/

I received this error:

File "gtc_final_report.py", line 5, in from IlluminaBeadArrayFiles import GenotypeCalls, BeadPoolManifest, code2genotype File "/usr/local/lib/python2.7/dist-packages/IlluminaBeadArrayFiles/init.py", line 1, in from IlluminaBeadArrayFiles import version, code2genotype, NC, AA, AB, BB, RefStrand, SourceStrand, GenotypeCalls, NormalizationTransform, ScannerData, BeadPoolManifest File "/usr/local/lib/python2.7/dist-packages/IlluminaBeadArrayFiles/IlluminaBeadArrayFiles.py", line 30, in from numpy import cos, sin, pi, arctan2, float32, uint16, int32, seterr, frombuffer, dtype ImportError: No module named numpy

Some manual like this would be good for running the programm:

usage: gtc_to_vcf.py [-h] [--gtc-file GTC_FILE] --manifest-file MANIFEST_FILE --genome-fasta-file GENOME_FASTA_FILE [--output-vcf-file OUTPUT_VCF_FILE] [--skip-indels] [--log-file LOG_FILE] [--expand-identifiers] [--unsquash-duplicates] [--auxiliary-loci AUXILIARY_LOCI] [--version]

Convert GTC file to VCF format

Best,

[KelleyRyanM]

Hi, It looks like you don't have the "numpy" package (http://www.numpy.org/) available in your python installation. There are some instructions here (https://www.scipy.org/install.html) for how to install numpy, but the exact method will depend on your OS and python distribution. Once you have the necessary dependency installed, you can execute the script with the "-h" option for usage information, as below

python .\examples\gtc_final_report.py -h usage: Generate a final report from a directory of GTC files [-h] manifest gtc_directory output_file

positional arguments: manifest BPM manifest file gtc_directory Directory containing GTC files output_file Location to write report

optional arguments: -h, --help show this help message and exit

[smuchakiel]

thank you, will try it.

Best,

[smuchakiel]

Thank you, it is working now.