Off-shelf Truseq myeloid panel

[foxchase]

Dear Matthew, I tried your ambivert with Illumina truseq myeloid panel manifest file and I found your test truseq manifest file is different from the off-shelf myeloid manifest file. Any comment on how to adapt ambivert to the myeloid panel?

Thanks a lot. TruSight-Myeloid-Manifest.txt

[genomematt]

Thanks @foxchase

This issue is to do with the file having fewer columns than the original, and no apparent versioning. I had been conservative about asserting these were the correct length, and have now relaxed these checks.

I have attached the fasta version that

ambivert_truseq_manifest --manifest TruSight-Myeloid-Manifest.txt \
                         --softmask_probes --all_plus --with_probes

now produces. Can you please try this with the --fasta flag instead of --manifest and spot check a couple to ensure what I am currently producing appears correct. I will push my current changes into the dev branch, but they need another look and some more tests before I move them across to master.

You can install the dev version with pip install git+https://github.com/genomematt/AmBiVErT@1.0.0dev1

Note this file has .txt added to the end just to keep GitHub happy. TruSight-Myeloid-Manifest.fasta.txt

[foxchase]

Thank you Matthew for your reply, After I upgrade the dev version I got an issue below; :~$ ambivert -h Traceback (most recent call last): File "/home/affymetrix2/miniconda2/bin/ambivert", line 11, in load_entry_point('ambivert==0.5.1', 'console_scripts', 'ambivert')() File "/home/affymetrix2/miniconda2/lib/python2.7/site-packages/pkg_resources/init.py", line 564, in load_entry_point return get_distribution(dist).load_entry_point(group, name) File "/home/affymetrix2/miniconda2/lib/python2.7/site-packages/pkg_resources/init.py", line 2662, in load_entry_point return ep.load() File "/home/affymetrix2/miniconda2/lib/python2.7/site-packages/pkg_resources/init.py", line 2316, in load return self.resolve() File "/home/affymetrix2/miniconda2/lib/python2.7/site-packages/pkg_resources/init.py", line 2322, in resolve module = import(self.module_name, fromlist=['name'], level=0) File "/home/affymetrix2/miniconda2/lib/python2.7/site-packages/ambivert/ambivert.py", line 518 print(',',end='',file=logfile) ^ SyntaxError: invalid syntax

[foxchase]

Hi Matthew. Please discard my previous comment.

[foxchase]

Hi Matthew, just let you know it works now.