Closed tetedange13 closed 3 years ago
Looks good, thanks. I think I left this feature as hidden because I hadn't tested its results with Gistic myself. Are you in a position to check whether the output of this command works with Gistic without further modification?
Hi @etal ,
Sorry, I have never used GISTIC and I am completely unfamiliar with it
=> However I installed it and as far as I understood it takes 2 input files that can be both produced by cnvkit.py export
cnvkit.py export seg <SEVERAL_CNS>
(I mean GISTIC is taking it without error)cnvkit.py export gisitic <SEVERAL_CNR>
Feeding GISTIC only with mandatory "seg" file works fine, but I got an issue feeding it with both "seg" and "markers" files:
GISTIC 2.0 input error detected:
74 segment start or end positions in 'cns.gistic.seg' do not match any markers in 'cnr.gistic.markers'.
First bad position is X:150501 at line 114.
=> I guess it is because cnvkit.py export gistic
works only on autosomes (contrary to cnvkit.py export seg
)
=> Fortunately, filtering out sexual chromosomes from "seg" file produced by CNVkit is enough for GISTIC to finish without error !
To conclude: this seems OK to me, but as I said I do not know enough about GISTIC to assert results generated from "GISTIC + CNVkit's exports" are accurate
=> Maybe you should rather wait for BioComSoftware
feedback ?
Hope this helps. Have a nice day. Felix !
@tetedange13 Thank you for the PR Felix! I agree we should ideally wait for @BioComSoftware's feedback prior to merging this.
I also think there are two additional things to be done here:
Hi @tskir,
Since GISTIC presumably can only work with autosomes
Just to be clear, GISTIC itself can deal with sex-chrom (even if they are removed by default according to doc and that I could not manage to make it keep them with -rx=0
param...)
=> The issue I was getting comes from inconsistency between cnvkit.py export seg
that includes sex-chrom and current cnvkit.py export gistic
that removes them internally (based on here)
=> I do not know if there was a specific reason for that, at the time export_gistic_markers()
was written?
To sum up:
=> If you want I can commit a sex-chrom switch for cnvkit.py export seg
=> But would not it be better to simply remove the .autosome()
filter from export_gistic_markers()
?
(I tested, GISTIC is taking both files just fine)
Kind regards. Felix.
Based on the feedback we received, I think this would be the most reasonable set of changes:
.autosome()
filter@tetedange13 Do you think you could add those changes to this PR?
Hi @tskir ,
Done ! To document GISTIC export I did my best based on code docstrings + GISTIC documentation
Have a nice day. Felix.
Should fix issue #622 => Simply copy-pasted (+ adapted) code for 'jtv' export (same case with multiple ".cnr" as input) to enable 'gistic' export through command-line => This supposes "core" function for "gistic" export (within
cnvlib/export.py
) is correct, which I have not test => Maybe further tests are required ?Closes #622