chrX and chrY skipped in prepare_phenotype_table.py about leafcutter HOT 4 CLOSED

On Mon, Feb 5, 2018 at 12:19 PM, snaqvi1990 ***@***.***> wrote: Hi, I noticed that prepare_phenotype_table.py excludes the X and Y chromosome when writing PSI values by chromosome. I have temporarily 'hacked' the script by setting chrX as chr23 and chrY as chr24, but is there any chance chrX and chrY could be included in the by chromosome output? Thanks, Sahin — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#52>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AE1pifmVIv9nfS3yUNeSsZffssTJQR1Sks5tR0Y8gaJpZM4R54TE> .

On Mon, Feb 5, 2018 at 12:34 PM, snaqvi1990 ***@***.***> wrote: How can I install this most recent version? I just re-cloned leafcutter, and there doesn't seem to be that option in prepare_phenotype_table: git clone https://github.com/davidaknowles/leafcutter python /lab/page/snaqvi/scripts/leafcutter/scripts/prepare_phenotype_table.py -h Usage: prepare_phenotype_table.py [-p num_PCs] input_perind.counts.gz Options: -h, --help show this help message and exit -p NPCS, --pcs=NPCS number of PCs output — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#52 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AE1piTR-N166LlvDJ0--8xcd_6IZ2Xnrks5tR0magaJpZM4R54TE> .