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sjanssen2 / spike

NGS pipeline for SNV detection in tumor context
BSD 3-Clause "New" or "Revised" License
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added the genepanel: Sujal_Gosh to project Alps #176

Closed LayalYasin closed 5 years ago

LayalYasin commented 5 years ago

Sujal always requests to know the gene coverage for a set of around 350 genes. I added those gene to a list called Sujal_Gosh.

sjanssen2 commented 5 years ago

I am not totally sure what happens if a gene from the list is NOT contained in the xxx_Covered.bed file of the capture kit. Have you checked that all those ~350 names are included?

sjanssen2 commented 5 years ago

as quick test, could you please generate the file /gpfs/project/projects/spike/Intermediate/092_genepanel_coverage/Sujal_Gosh.yaml/Alps/ALPS_60a.tsv through spike?

sjanssen2 commented 5 years ago

I tested myself and it seems to work fine :+1 ready to merge. Maybe @deyazoubi will hit the merge button such that he is aware of the changes?!0

LayalYasin commented 5 years ago

Hi Stefan,

didnt you face any errors when testing ?

because I have an error:

SyntaxError in line 1099 of /home/yasinl/spike/scripts/reports.py: invalid syntax (reports.py, line 1099) File "/home/yasinl/spike/Snakefile", line 9, in

which refers to the line: coverage_per_probe.groupby('gene')['percentcovered_0'].mean()], axis=1)

From: Stefan Janssen [notifications@github.com] Sent: Wednesday, July 10, 2019 1:37 PM To: sjanssen2/spike Cc: Yasin, Dr. Layal - UKD; Author Subject: Re: [sjanssen2/spike] added the genepanel: Sujal_Gosh to project Alps (#176)

as quick test, could you please generate the file /gpfs/project/projects/spike/Intermediate/092_genepanel_coverage/Sujal_Gosh.yaml/Alps/ALPS_60a.tsv through spike?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/sjanssen2/spike/pull/176?email_source=notifications&email_token=AHYPMLTXPHRSOCPHM3KIXDLP6XCWXA5CNFSM4H7GDFH2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODZTF26I#issuecomment-510025081, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AHYPMLTJVG2XCIMPSWKSL5LP6XCWXANCNFSM4H7GDFHQ.

sjanssen2 commented 5 years ago

is it possible that you get these issues because of your changes with the addition of two columns of the bamstat result? It went through for me without any complains. Thus I think this problem is local on your end.

sjanssen2 commented 5 years ago

p.s. you should always post the full error stack trace, not only the last line to enable better debugging.

LayalYasin commented 5 years ago

ah ok, I thought u tested the two additional columns too, thats why I asked

w.r.t the error message, unfortunatey this is the full error stack

SyntaxError in line 1099 of /home/yasinl/spike/scripts/reports.py: invalid syntax (reports.py, line 1099) File "/home/yasinl/spike/Snakefile", line 9, in

I will debug this further

From: Stefan Janssen [notifications@github.com] Sent: Wednesday, July 10, 2019 3:24 PM To: sjanssen2/spike Cc: Yasin, Dr. Layal - UKD; Author Subject: Re: [sjanssen2/spike] added the genepanel: Sujal_Gosh to project Alps (#176)

p.s. you should always post the full error stack trace, not only the last line to enable better debugging.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/sjanssen2/spike/pull/176?email_source=notifications&email_token=AHYPMLS2DW2R6ULMV64UP6DP6XPIXA5CNFSM4H7GDFH2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODZTOHVI#issuecomment-510059477, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AHYPMLUNJBY2J5NU5T26573P6XPIXANCNFSM4H7GDFHQ.