KeyError: 'chrom' about leafcutter HOT 14 CLOSED

On Mar 27, 2017 11:10 AM, "Marc Jan Bonder" ***@***.***> wrote: Hi, When trying to prepare the leafcutt cluster output to run a splice QTL analysis I get the following error: Traceback (most recent call last): File "../scripts/prepare_phenotype_table.py", line 166, in main(args[0], int(options.npcs) ) File "../scripts/prepare_phenotype_table.py", line 58, in main chrom = dic['chrom'].replace("chr",'') KeyError: 'chrom' What can cause this error? Cheers, Marc — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#21>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AE1piV0ePj7EDN-RAtrivte5t-XsSZedks5rp-G4gaJpZM4Mqf5p> .

Hi Marc, could you check that you have the correct input? Yang On Mar 27, 2017 11:10 AM, "Marc Jan Bonder" ***@***.***> wrote: > Hi, > > When trying to prepare the leafcutt cluster output to run a splice QTL > analysis I get the following error: > > Traceback (most recent call last): > File "../scripts/prepare_phenotype_table.py", line 166, in > main(args[0], int(options.npcs) ) > File "../scripts/prepare_phenotype_table.py", line 58, in main > chrom = dic['chrom'].replace("chr",'') > KeyError: 'chrom' > > What can cause this error? > > Cheers, > Marc > > — > You are receiving this because you are subscribed to this thread. > Reply to this email directly, view it on GitHub > <#21>, or mute the > thread > <https://github.com/notifications/unsubscribe-auth/AE1piV0ePj7EDN- RAtrivte5t-XsSZedks5rp-G4gaJpZM4Mqf5p> > . > — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#21 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ADyAM9q2OiYewfM4xRqtpmwgk7TQFctYks5rp_G3gaJpZM4Mqf5p> .

On Mar 27, 2017 1:13 PM, "Marc Jan Bonder" ***@***.***> wrote: Hi Yang, Thanks for the reply. I used exactly the commands as presented in the example. Cheers, Marc On Mon, Mar 27, 2017 at 7:28 PM, goldenflaw ***@***.***> wrote: > Hi Marc, could you check that you have the correct input? > > Yang > > On Mar 27, 2017 11:10 AM, "Marc Jan Bonder" ***@***.***> > wrote: > > > Hi, > > > > When trying to prepare the leafcutt cluster output to run a splice QTL > > analysis I get the following error: > > > > Traceback (most recent call last): > > File "../scripts/prepare_phenotype_table.py", line 166, in > > main(args[0], int(options.npcs) ) > > File "../scripts/prepare_phenotype_table.py", line 58, in main > > chrom = dic['chrom'].replace("chr",'') > > KeyError: 'chrom' > > > > What can cause this error? > > > > Cheers, > > Marc > > > > — > > You are receiving this because you are subscribed to this thread. > > Reply to this email directly, view it on GitHub > > <#21>, or mute the > > thread > > <https://github.com/notifications/unsubscribe-auth/AE1piV0ePj7EDN- > RAtrivte5t-XsSZedks5rp-G4gaJpZM4Mqf5p> > > . > > > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub > <#21 (comment)- 289524572>, > or mute the thread > <https://github.com/notifications/unsubscribe-auth/ ADyAM9q2OiYewfM4xRqtpmwgk7TQFctYks5rp_G3gaJpZM4Mqf5p> > . > — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#21 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AE1piRogi1IlywtRq2CUuGIwi4nGQyc7ks5rqAIAgaJpZM4Mqf5p> .

Can you post the top 2 lines of your input file? Yang On Mar 27, 2017 1:13 PM, "Marc Jan Bonder" ***@***.***> wrote: > Hi Yang, > > Thanks for the reply. I used exactly the commands as presented in the > example. > > Cheers, > Marc > > On Mon, Mar 27, 2017 at 7:28 PM, goldenflaw ***@***.***> > wrote: > > > Hi Marc, could you check that you have the correct input? > > > > Yang > > > > On Mar 27, 2017 11:10 AM, "Marc Jan Bonder" ***@***.***> > > wrote: > > > > > Hi, > > > > > > When trying to prepare the leafcutt cluster output to run a splice QTL > > > analysis I get the following error: > > > > > > Traceback (most recent call last): > > > File "../scripts/prepare_phenotype_table.py", line 166, in > > > main(args[0], int(options.npcs) ) > > > File "../scripts/prepare_phenotype_table.py", line 58, in main > > > chrom = dic['chrom'].replace("chr",'') > > > KeyError: 'chrom' > > > > > > What can cause this error? > > > > > > Cheers, > > > Marc > > > > > > — > > > You are receiving this because you are subscribed to this thread. > > > Reply to this email directly, view it on GitHub > > > <#21>, or mute the > > > thread > > > <https://github.com/notifications/unsubscribe-auth/AE1piV0ePj7EDN- > > RAtrivte5t-XsSZedks5rp-G4gaJpZM4Mqf5p> > > > . > > > > > > > — > > You are receiving this because you authored the thread. > > Reply to this email directly, view it on GitHub > > <#21 (comment)- > 289524572>, > > or mute the thread > > <https://github.com/notifications/unsubscribe-auth/ > ADyAM9q2OiYewfM4xRqtpmwgk7TQFctYks5rp_G3gaJpZM4Mqf5p> > > . > > > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub > <#21 (comment)- 289544942>, > or mute the thread > <https://github.com/notifications/unsubscribe-auth/ AE1piRogi1IlywtRq2CUuGIwi4nGQyc7ks5rqAIAgaJpZM4Mqf5p> > . > — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#21 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ADyAMxpu2mpktwVZ_GUX5GHDILLGWJ5hks5rqAtYgaJpZM4Mqf5p> .

Hi Yang, I try to put in the "testYRIvsEU_perind_numers.counts.gz" file. Which were generated using: python ../clustering/leafcutter_cluster.py -j test_juncfiles.txt -m 50 -o testYRIvsEU -l 500000 The first two rows look like this: RNA.NA06986_CEU.chr1.bam RNA.NA06994_CEU.chr1.bam RNA.NA18486_YRI.chr1.bam RNA.NA06985_CEU.chr1.bam RNA.NA18487_YRI.chr1.bam RNA.NA06989_CEU.chr1.bam RNA.NA06984_CEU.chr1.bam RNA.NA18488_YRI.chr1.bam RNA.NA18489_YRI.chr1.bam RNA.NA18498_YRI.chr1.bam chr1:17055:17233:clu_1 21 13 18 20 17 12 11 8 15 25 Cheers, Marc On Mon, Mar 27, 2017 at 8:17 PM, goldenflaw ***@***.***> wrote: > Can you post the top 2 lines of your input file? > > Yang > > > On Mar 27, 2017 1:13 PM, "Marc Jan Bonder" ***@***.***> > wrote: > > > Hi Yang, > > > > Thanks for the reply. I used exactly the commands as presented in the > > example. > > > > Cheers, > > Marc > > > > On Mon, Mar 27, 2017 at 7:28 PM, goldenflaw ***@***.***> > > wrote: > > > > > Hi Marc, could you check that you have the correct input? > > > > > > Yang > > > > > > On Mar 27, 2017 11:10 AM, "Marc Jan Bonder" ***@***.*** > > > > > wrote: > > > > > > > Hi, > > > > > > > > When trying to prepare the leafcutt cluster output to run a splice > QTL > > > > analysis I get the following error: > > > > > > > > Traceback (most recent call last): > > > > File "../scripts/prepare_phenotype_table.py", line 166, in > > > > main(args[0], int(options.npcs) ) > > > > File "../scripts/prepare_phenotype_table.py", line 58, in main > > > > chrom = dic['chrom'].replace("chr",'') > > > > KeyError: 'chrom' > > > > > > > > What can cause this error? > > > > > > > > Cheers, > > > > Marc > > > > > > > > — > > > > You are receiving this because you are subscribed to this thread. > > > > Reply to this email directly, view it on GitHub > > > > <#21>, or mute > the > > > > thread > > > > <https://github.com/notifications/unsubscribe-auth/AE1piV0ePj7EDN- > > > RAtrivte5t-XsSZedks5rp-G4gaJpZM4Mqf5p> > > > > . > > > > > > > > > > — > > > You are receiving this because you authored the thread. > > > Reply to this email directly, view it on GitHub > > > <#21 (comment)- > > 289524572>, > > > or mute the thread > > > <https://github.com/notifications/unsubscribe-auth/ > > ADyAM9q2OiYewfM4xRqtpmwgk7TQFctYks5rp_G3gaJpZM4Mqf5p> > > > . > > > > > > > — > > You are receiving this because you commented. > > Reply to this email directly, view it on GitHub > > <#21# > issuecomment-289544942>, > > or mute the thread > > <https://github.com/notifications/unsubscribe-auth/AE1piRogi > 1IlywtRq2CUuGIwi4nGQyc7ks5rqAIAgaJpZM4Mqf5p> > > > . > > > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub > <#21 (comment)>, > or mute the thread > <https://github.com/notifications/unsubscribe-auth/ADyAMxpu2mpktwVZ_GUX5GHDILLGWJ5hks5rqAtYgaJpZM4Mqf5p> > . >

On Mar 28, 2017 3:13 AM, "Marc Jan Bonder" ***@***.***> wrote: Hi Yang, I try to put in the "testYRIvsEU_perind_numers.counts.gz" file. Which were generated using: python ../clustering/leafcutter_cluster.py -j test_juncfiles.txt -m 50 -o testYRIvsEU -l 500000 The first two rows look like this: RNA.NA06986_CEU.chr1.bam RNA.NA06994_CEU.chr1.bam RNA.NA18486_YRI.chr1.bam RNA.NA06985_CEU.chr1.bam RNA.NA18487_YRI.chr1.bam RNA.NA06989_CEU.chr1.bam RNA.NA06984_CEU.chr1.bam RNA.NA18488_YRI.chr1.bam RNA.NA18489_YRI.chr1.bam RNA.NA18498_YRI.chr1.bam chr1:17055:17233:clu_1 21 13 18 20 17 12 11 8 15 25 Cheers, Marc On Mon, Mar 27, 2017 at 8:17 PM, goldenflaw ***@***.***> wrote: > Can you post the top 2 lines of your input file? > > Yang > > > On Mar 27, 2017 1:13 PM, "Marc Jan Bonder" ***@***.***> > wrote: > > > Hi Yang, > > > > Thanks for the reply. I used exactly the commands as presented in the > > example. > > > > Cheers, > > Marc > > > > On Mon, Mar 27, 2017 at 7:28 PM, goldenflaw ***@***.***> > > wrote: > > > > > Hi Marc, could you check that you have the correct input? > > > > > > Yang > > > > > > On Mar 27, 2017 11:10 AM, "Marc Jan Bonder" < ***@***.***> > > > wrote: > > > > > > > Hi, > > > > > > > > When trying to prepare the leafcutt cluster output to run a splice > QTL > > > > analysis I get the following error: > > > > > > > > Traceback (most recent call last): > > > > File "../scripts/prepare_phenotype_table.py", line 166, in > > > > main(args[0], int(options.npcs) ) > > > > File "../scripts/prepare_phenotype_table.py", line 58, in main > > > > chrom = dic['chrom'].replace("chr",'') > > > > KeyError: 'chrom' > > > > > > > > What can cause this error? > > > > > > > > Cheers, > > > > Marc > > > > > > > > — > > > > You are receiving this because you are subscribed to this thread. > > > > Reply to this email directly, view it on GitHub > > > > <#21>, or mute the > > > > thread > > > > <https://github.com/notifications/unsubscribe-auth/AE1piV0ePj7EDN- > > > RAtrivte5t-XsSZedks5rp-G4gaJpZM4Mqf5p> > > > > . > > > > > > > > > > — > > > You are receiving this because you authored the thread. > > > Reply to this email directly, view it on GitHub > > > <#21 (comment)- > > 289524572>, > > > or mute the thread > > > <https://github.com/notifications/unsubscribe-auth/ > > ADyAM9q2OiYewfM4xRqtpmwgk7TQFctYks5rp_G3gaJpZM4Mqf5p> > > > . > > > > > > > — > > You are receiving this because you commented. > > Reply to this email directly, view it on GitHub > > <#21 (comment)- > 289544942>, > > or mute the thread > > <https://github.com/notifications/unsubscribe-auth/ > AE1piRogi1IlywtRq2CUuGIwi4nGQyc7ks5rqAIAgaJpZM4Mqf5p> > > > . > > > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub > <#21 (comment)- 289556511>, > or mute the thread > <https://github.com/notifications/unsubscribe-auth/ADyAMxpu2mpktwVZ_ GUX5GHDILLGWJ5hks5rqAtYgaJpZM4Mqf5p> > . > — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#21 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AE1piZQuaMxsR3STyiKRKi1IfJhXKUi8ks5rqM9LgaJpZM4Mqf5p> .

Hi Marc, You have to put the _counts file (the other output from leafcutter). Yang On Mar 28, 2017 3:13 AM, "Marc Jan Bonder" ***@***.***> wrote: > Hi Yang, > > I try to put in the "testYRIvsEU_perind_numers.counts.gz" file. > Which were generated using: python ../clustering/leafcutter_cluster.py -j > test_juncfiles.txt -m 50 -o testYRIvsEU -l 500000 > > The first two rows look like this: > > RNA.NA06986_CEU.chr1.bam RNA.NA06994_CEU.chr1.bam RNA.NA18486_YRI.chr1.bam > RNA.NA06985_CEU.chr1.bam RNA.NA18487_YRI.chr1.bam RNA.NA06989_CEU.chr1.bam > RNA.NA06984_CEU.chr1.bam RNA.NA18488_YRI.chr1.bam RNA.NA18489_YRI.chr1.bam > RNA.NA18498_YRI.chr1.bam > chr1:17055:17233:clu_1 21 13 18 20 17 12 11 8 15 25 > > Cheers, > Marc > > On Mon, Mar 27, 2017 at 8:17 PM, goldenflaw ***@***.***> > wrote: > > > Can you post the top 2 lines of your input file? > > > > Yang > > > > > > On Mar 27, 2017 1:13 PM, "Marc Jan Bonder" ***@***.***> > > wrote: > > > > > Hi Yang, > > > > > > Thanks for the reply. I used exactly the commands as presented in the > > > example. > > > > > > Cheers, > > > Marc > > > > > > On Mon, Mar 27, 2017 at 7:28 PM, goldenflaw < ***@***.***> > > > wrote: > > > > > > > Hi Marc, could you check that you have the correct input? > > > > > > > > Yang > > > > > > > > On Mar 27, 2017 11:10 AM, "Marc Jan Bonder" < > ***@***.***> > > > > wrote: > > > > > > > > > Hi, > > > > > > > > > > When trying to prepare the leafcutt cluster output to run a splice > > QTL > > > > > analysis I get the following error: > > > > > > > > > > Traceback (most recent call last): > > > > > File "../scripts/prepare_phenotype_table.py", line 166, in > > > > > main(args[0], int(options.npcs) ) > > > > > File "../scripts/prepare_phenotype_table.py", line 58, in main > > > > > chrom = dic['chrom'].replace("chr",'') > > > > > KeyError: 'chrom' > > > > > > > > > > What can cause this error? > > > > > > > > > > Cheers, > > > > > Marc > > > > > > > > > > — > > > > > You are receiving this because you are subscribed to this thread. > > > > > Reply to this email directly, view it on GitHub > > > > > <#21>, or mute > the > > > > > thread > > > > > <https://github.com/notifications/unsubscribe- auth/AE1piV0ePj7EDN- > > > > RAtrivte5t-XsSZedks5rp-G4gaJpZM4Mqf5p> > > > > > . > > > > > > > > > > > > > — > > > > You are receiving this because you authored the thread. > > > > Reply to this email directly, view it on GitHub > > > > <https://github.com/davidaknowles/leafcutter/ issues/21#issuecomment- > > > 289524572>, > > > > or mute the thread > > > > <https://github.com/notifications/unsubscribe-auth/ > > > ADyAM9q2OiYewfM4xRqtpmwgk7TQFctYks5rp_G3gaJpZM4Mqf5p> > > > > . > > > > > > > > > > — > > > You are receiving this because you commented. > > > Reply to this email directly, view it on GitHub > > > <#21 (comment)- > > 289544942>, > > > or mute the thread > > > <https://github.com/notifications/unsubscribe-auth/ > > AE1piRogi1IlywtRq2CUuGIwi4nGQyc7ks5rqAIAgaJpZM4Mqf5p> > > > > > . > > > > > > > — > > You are receiving this because you authored the thread. > > Reply to this email directly, view it on GitHub > > <#21 (comment)- > 289556511>, > > or mute the thread > > <https://github.com/notifications/unsubscribe-auth/ADyAMxpu2mpktwVZ_ > GUX5GHDILLGWJ5hks5rqAtYgaJpZM4Mqf5p> > > . > > > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub > <#21 (comment)- 289710938>, > or mute the thread > <https://github.com/notifications/unsubscribe-auth/ AE1piZQuaMxsR3STyiKRKi1IfJhXKUi8ks5rqM9LgaJpZM4Mqf5p> > . > — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#21 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ADyAM1wsweoHDTqdgFhkhWXJEwDbZKXgks5rqRrcgaJpZM4Mqf5p> .

On Mon, Jul 16, 2018 at 11:52 AM summike ***@***.***> wrote: *Hi, I am sorry that I met the similar problem when I ran my own data. There are about 350 samples in my data, so I cannot provide the comprehensive information on the first two rows, but I try to provide as much as I can. Please kindly see the details below. Here is my TT_perind.counts file,* chrom KDNY048-Aligned.out.bam ABO8T90-Aligned.out.bam ABT3R48-Aligned.out.bam ABE3T55-Aligned.out.bam ABP9U87-Aligned.out.bam 44ad-0cb35529f2-Aligned.out.bam ABD9C13-Aligned.out.bam ABF4J93-Aligned.out.bam 9d55-8ac6e18fcd-Aligned.out.bam ... chr1:15225:185747:clu_2911_NA 3/3 0/1 53/54 2/2 0/0 0/0 0/0 8/9 0/0 ... chr1:15225:185758:clu_2911_NA 0/3 1/1 1/54 0/2 0/0 0/0 0/0 1/9 0/0 ... ... *After I ran the command,* "python scripts/prepare_phenotype_table.py example_data/TT_perind.counts.gz -p 10". *I got the following error,* " Starting... Traceback (most recent call last): File "scripts/prepare_phenotype_table.py", line 171, in main(args[0], int(options.npcs) ) File "scripts/prepare_phenotype_table.py", line 60, in main chrom = dic['chrom'].replace("chr",'') KeyError: 'chrom' " *I am clear that I input the _counts file and have already sorted by the first column (chrom). May I know what may cause this error?* *Thank you for your patience and kind help!* — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#21 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AE1piZEKBudKdcwexNwlH6FuEQfo_4bxks5uHMTjgaJpZM4Mqf5p> .

On Mon, Jul 16, 2018 at 1:21 PM summike ***@***.***> wrote: Hello Yang, Thank you very much for your reply. However, the error still occurs after taking your advice. command of Line 60, chrom = dic['chrom'].replace("chr",''), is located in one for-loop. I am sorry that my python knowledge is limited. May I know does this command for extract the chromosome number without 'chr'? [image: 2018-07-16 6 43 27] <https://user-images.githubusercontent.com/28684936/42774087-b594d8b4-8928-11e8-8770-b784e53adb6c.png> — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#21 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AE1piTjc1YLG964bf39zJCrE-VaeI1sOks5uHNmNgaJpZM4Mqf5p> .