psiPerEvent error - Githubissues

comprna / SUPPA

SUPPA: Fast quantification of splicing and differential splicing

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psiPerEvent error #56

Closed SukanyaPanja closed 5 years ago

SukanyaPanja commented 5 years ago

Hi, I am trying to calculate psiPerEvent using Suppa. My transcript per million file looks as follows:

sample1 sample2 sample3 sample4 sample5 sample6 sample7 sample8 sample9 sample10 sample11 sample12 sample13 sample14 sample15 sample16 sample17 sample18 sample19 sample20 sample21 sample22 sample23 sample24 sample25 sample26 sample27 sample28 sample29 sample30 sample31 sample32 sample33 sample34 sample35 sample36 sample37 sample38 sample39 sample40 sample41 sample42 sample43 sample44 sample45 sample46 sample47 sample48 sample49 sample50 sample51 sample52 sample53 sample54 sample55 sample56 sample57 sample58 sample59 sample60 sample61 sample62 sample63 sample64 sample65 sample66 sample67 sample68 sample69 sample70 sample71 sample72 sample73 sample74 sample75 sample76 sample77 sample78 sample79 sample80
NR_046018 0.146696232 0 0.02246929 0 0.043484372 0 0.064345526 0 0 0.641447528 0.070457715 0 0 0 0.288446756 0 0.018291742 0.098839876 0 0 0 0.060880505 0.125044033 0 0 0.162726933 0.056250345 0 0.04533607 0.111419096 0.25858868 0 0.10616014 0.081480545 0 0.320725657 0.24226526 0.091504489 0.528826249 0.194352761 0.046725318 0.151982368 0 0 0.226697819 0.084641889 0 0.566318677 0.1484086 0 0.268734574 0.220563037 0 0.109770725 0.05704479 0 NA NA 0 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NR_024540 19.19284277 53.37251412 32.7337806 74.98841145 11.89824843 33.80215601 10.03499221 45.43118253 83.04926565 22.62463001 47.85138289 15.54743843 3.433399326 39.67863222 46.35756323 27.33616404 16.91112386 54.79703587 31.89242283 21.97120496 0 21.57606474 13.35599624 0 4.456391694 28.82763272 66.00394482 32.31343683 11.47348555 52.37874052 57.88761215 11.796335 31.4022174 20.15156518 23.12214838 31.36330696 67.39185448 32.57448068 45.41363924 23.18642724 41.86773395 131.0017562 64.54765994 83.05975972 40.50607761 25.76826385 7.357259576 54.52854758 35.24881828 12.15573145 38.36113881 36.43888614 36.29433057 84.0586856 29.09977577 106.9131704 NA NA 78.02340573 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA

I have attached my complete file. samples_file.txt

And my ioe file as follows: seqname gene_id event_id alternative_transcripts total_transcripts chr17 MIR22HG MIR22HG;A3:chr17:1616189-1616997:1615693-1616997:- NR_028503 NR_028503,NR_028504,NR_028505 chr17 FAM104A FAM104A;A3:chr17:71223403-71228225:71223321-71228225:- NM_032837,NM_001098832 NM_032837,NM_001098832,NM_001289411

However I am getting an error INFO:lib.tools:samples_file.txt opened in reading mode. INFO:psiCalculator:Buffering transcript expression levels. ERROR:lib.tools:1, in line 2. Skipping line... ERROR:lib.tools:2, in line 3. Skipping line... ERROR:lib.tools:3, in line 4. Skipping line...

I tried to look for leading/trailing spaces however I could not find any. Is there a way by which I can solve this issue.

Thanks in advance!!!

EduEyras commented 5 years ago

Hi Sukanya,

Thanks for your message

what is your command line?

Your separations are tabs or single spaces?

best

Eduardo

On Fri, 19 Jul 2019 at 04:33, Sukanya Panja notifications@github.com wrote:

Hi, I am trying to calculate psiPerEvent using Suppa. My transcript per million file looks as follows:

sample1 sample2 sample3 sample4 sample5 sample6 sample7 sample8 sample9 sample10 sample11 sample12 sample13 sample14 sample15 sample16 sample17 sample18 sample19 sample20 sample21 sample22 sample23 sample24 sample25 sample26 sample27 sample28 sample29 sample30 sample31 sample32 sample33 sample34 sample35 sample36 sample37 sample38 sample39 sample40 sample41 sample42 sample43 sample44 sample45 sample46 sample47 sample48 sample49 sample50 sample51 sample52 sample53 sample54 sample55 sample56 sample57 sample58 sample59 sample60 sample61 sample62 sample63 sample64 sample65 sample66 sample67 sample68 sample69 sample70 sample71 sample72 sample73 sample74 sample75 sample76 sample77 sample78 sample79 sample80 NR_046018 0.146696232 0 0.02246929 0 0.043484372 0 0.064345526 0 0 0.641447528 0.070457715 0 0 0 0.288446756 0 0.018291742 0.098839876 0 0 0 0.060880505 0.125044033 0 0 0.162726933 0.056250345 0 0.04533607 0.111419096 0.25858868 0 0.10616014 0.081480545 0 0.320725657 0.24226526 0.091504489 0.528826249 0.194352761 0.046725318 0.151982368 0 0 0.226697819 0.084641889 0 0.566318677 0.1484086 0 0.268734574 0.220563037 0 0.109770725 0.05704479 0 NA NA 0 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NR_024540 19.19284277 53.37251412 32.7337806 74.98841145 11.89824843 33.80215601 10.03499221 45.43118253 83.04926565 22.62463001 47.85138289 15.54743843 3.433399326 39.67863222 46.35756323 27.33616404 16.91112386 54.79703587 31.89242283 21.97120496 0 21.57606474 13.35599624 0 4.456391694 28.82763272 66.00394482 32.31343683 11.47348555 52.37874052 57.88761215 11.796335 31.4022174 20.15156518 23.12214838 31.36330696 67.39185448 32.57448068 45.41363924 23.18642724 41.86773395 131.0017562 64.54765994 83.05975972 40.50607761 25.76826385 7.357259576 54.52854758 35.24881828 12.15573145 38.36113881 36.43888614 36.29433057 84.0586856 29.09977577 106.9131704 NA NA 78.02340573 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA

I have attached my complete file. tpm_for_promote.txt https://github.com/comprna/SUPPA/files/3407923/tpm_for_promote.txt And my ioe file as follows: seqname gene_id event_id alternative_transcripts total_transcripts chr17 MIR22HG MIR22HG;A3:chr17:1616189-1616997:1615693-1616997:- NR_028503 NR_028503,NR_028504,NR_028505 chr17 FAM104A FAM104A;A3:chr17:71223403-71228225:71223321-71228225:- NM_032837,NM_001098832 NM_032837,NM_001098832,NM_001289411

However I am getting an error INFO:lib.tools:sample_file.txt opened in reading mode. INFO:psiCalculator:Buffering transcript expression levels. ERROR:lib.tools:1, in line 2. Skipping line... ERROR:lib.tools:2, in line 3. Skipping line... ERROR:lib.tools:3, in line 4. Skipping line...

I tried to look for leading/trailing spaces however could not find any. Is there a way by which I can solve this issue.

Thanks in advance!!!

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/comprna/SUPPA/issues/56?email_source=notifications&email_token=ADCZKB2TYYFXJLSBMTOX2BLQACZOTA5CNFSM4IE6PKFKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HACPVTQ, or mute the thread https://github.com/notifications/unsubscribe-auth/ADCZKB4MBJNGGZODGAC3DT3QACZOTANCNFSM4IE6PKFA .

-- Prof. E Eyras EMBL Group Leader The John Curtin School of Medical Research - Australian National University https://github.com/comprna http://scholar.google.com/citations?user=LiojlGoAAAAJ

SukanyaPanja commented 5 years ago

Hi,

My command line is

python3 /cache/home/.local/lib/python3.5/site-packages/SUPPA/suppa.py psiPerEvent --ioe-file allevents.ioe --expression-file tpm_for_promote -o psi_for_all_events_in_promote

and it is tab delimited

From: Eduardo Eyras notifications@github.com Sent: Thursday, July 18, 2019 9:46:36 PM To: comprna/SUPPA SUPPA@noreply.github.com Cc: Sukanya Panja sp1388@shp.rutgers.edu; State change state_change@noreply.github.com Subject: Re: [comprna/SUPPA] psiPerEvent error (#56)

Hi Sukanya,

Thanks for your message

what is your command line?

Your separations are tabs or single spaces?

best

Eduardo

On Fri, 19 Jul 2019 at 04:33, Sukanya Panja notifications@github.com wrote:

Hi, I am trying to calculate psiPerEvent using Suppa. My transcript per million file looks as follows:

sample1 sample2 sample3 sample4 sample5 sample6 sample7 sample8 sample9 sample10 sample11 sample12 sample13 sample14 sample15 sample16 sample17 sample18 sample19 sample20 sample21 sample22 sample23 sample24 sample25 sample26 sample27 sample28 sample29 sample30 sample31 sample32 sample33 sample34 sample35 sample36 sample37 sample38 sample39 sample40 sample41 sample42 sample43 sample44 sample45 sample46 sample47 sample48 sample49 sample50 sample51 sample52 sample53 sample54 sample55 sample56 sample57 sample58 sample59 sample60 sample61 sample62 sample63 sample64 sample65 sample66 sample67 sample68 sample69 sample70 sample71 sample72 sample73 sample74 sample75 sample76 sample77 sample78 sample79 sample80 NR_046018 0.146696232 0 0.02246929 0 0.043484372 0 0.064345526 0 0 0.641447528 0.070457715 0 0 0 0.288446756 0 0.018291742 0.098839876 0 0 0 0.060880505 0.125044033 0 0 0.162726933 0.056250345 0 0.04533607 0.111419096 0.25858868 0 0.10616014 0.081480545 0 0.320725657 0.24226526 0.091504489 0.528826249 0.194352761 0.046725318 0.151982368 0 0 0.226697819 0.084641889 0 0.566318677 0.1484086 0 0.268734574 0.220563037 0 0.109770725 0.05704479 0 NA NA 0 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NR_024540 19.19284277 53.37251412 32.7337806 74.98841145 11.89824843 33.80215601 10.03499221 45.43118253 83.04926565 22.62463001 47.85138289 15.54743843 3.433399326 39.67863222 46.35756323 27.33616404 16.91112386 54.79703587 31.89242283 21.97120496 0 21.57606474 13.35599624 0 4.456391694 28.82763272 66.00394482 32.31343683 11.47348555 52.37874052 57.88761215 11.796335 31.4022174 20.15156518 23.12214838 31.36330696 67.39185448 32.57448068 45.41363924 23.18642724 41.86773395 131.0017562 64.54765994 83.05975972 40.50607761 25.76826385 7.357259576 54.52854758 35.24881828 12.15573145 38.36113881 36.43888614 36.29433057 84.0586856 29.09977577 106.9131704 NA NA 78.02340573 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA

I have attached my complete file. tpm_for_promote.txt https://github.com/comprna/SUPPA/files/3407923/tpm_for_promote.txt And my ioe file as follows: seqname gene_id event_id alternative_transcripts total_transcripts chr17 MIR22HG MIR22HG;A3:chr17:1616189-1616997:1615693-1616997:- NR_028503 NR_028503,NR_028504,NR_028505 chr17 FAM104A FAM104A;A3:chr17:71223403-71228225:71223321-71228225:- NM_032837,NM_001098832 NM_032837,NM_001098832,NM_001289411

However I am getting an error INFO:lib.tools:sample_file.txt opened in reading mode. INFO:psiCalculator:Buffering transcript expression levels. ERROR:lib.tools:1, in line 2. Skipping line... ERROR:lib.tools:2, in line 3. Skipping line... ERROR:lib.tools:3, in line 4. Skipping line...

I tried to look for leading/trailing spaces however could not find any. Is there a way by which I can solve this issue.

Thanks in advance!!!

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/comprna/SUPPA/issues/56?email_source=notifications&email_token=ADCZKB2TYYFXJLSBMTOX2BLQACZOTA5CNFSM4IE6PKFKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HACPVTQ, or mute the thread https://github.com/notifications/unsubscribe-auth/ADCZKB4MBJNGGZODGAC3DT3QACZOTANCNFSM4IE6PKFA .

-- Prof. E Eyras EMBL Group Leader The John Curtin School of Medical Research - Australian National University https://github.com/comprna http://scholar.google.com/citations?user=LiojlGoAAAAJ

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EduEyras commented 5 years ago

Thanks Sukanya,

I cannot see any obvious problem from the command line. Things to check could be a possible issue with the python version or the interpretation of NA.

I cc JC and JL who developed the code and might be able to tell you more about where to look for potential problems.

best

On Sat, 20 Jul 2019 at 08:24, Sukanya Panja notifications@github.com wrote:

Hi,

My command line is

python3 /cache/home/.local/lib/python3.5/site-packages/SUPPA/suppa.py psiPerEvent --ioe-file allevents.ioe --expression-file tpm_for_promote -o psi_for_all_events_in_promote

and it is tab delimited

From: Eduardo Eyras notifications@github.com Sent: Thursday, July 18, 2019 9:46:36 PM To: comprna/SUPPA SUPPA@noreply.github.com Cc: Sukanya Panja sp1388@shp.rutgers.edu; State change < state_change@noreply.github.com> Subject: Re: [comprna/SUPPA] psiPerEvent error (#56)

Hi Sukanya,

Thanks for your message

what is your command line?

Your separations are tabs or single spaces?

best

Eduardo

On Fri, 19 Jul 2019 at 04:33, Sukanya Panja notifications@github.com wrote:

Hi, I am trying to calculate psiPerEvent using Suppa. My transcript per million file looks as follows:

sample1 sample2 sample3 sample4 sample5 sample6 sample7 sample8 sample9 sample10 sample11 sample12 sample13 sample14 sample15 sample16 sample17 sample18 sample19 sample20 sample21 sample22 sample23 sample24 sample25 sample26 sample27 sample28 sample29 sample30 sample31 sample32 sample33 sample34 sample35 sample36 sample37 sample38 sample39 sample40 sample41 sample42 sample43 sample44 sample45 sample46 sample47 sample48 sample49 sample50 sample51 sample52 sample53 sample54 sample55 sample56 sample57 sample58 sample59 sample60 sample61 sample62 sample63 sample64 sample65 sample66 sample67 sample68 sample69 sample70 sample71 sample72 sample73 sample74 sample75 sample76 sample77 sample78 sample79 sample80 NR_046018 0.146696232 0 0.02246929 0 0.043484372 0 0.064345526 0 0 0.641447528 0.070457715 0 0 0 0.288446756 0 0.018291742 0.098839876 0 0 0 0.060880505 0.125044033 0 0 0.162726933 0.056250345 0 0.04533607 0.111419096 0.25858868 0 0.10616014 0.081480545 0 0.320725657 0.24226526 0.091504489 0.528826249 0.194352761 0.046725318 0.151982368 0 0 0.226697819 0.084641889 0 0.566318677 0.1484086 0 0.268734574 0.220563037 0 0.109770725 0.05704479 0 NA NA 0 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NR_024540 19.19284277 53.37251412 32.7337806 74.98841145 11.89824843 33.80215601 10.03499221 45.43118253 83.04926565 22.62463001 47.85138289 15.54743843 3.433399326 39.67863222 46.35756323 27.33616404 16.91112386 54.79703587 31.89242283 21.97120496 0 21.57606474 13.35599624 0 4.456391694 28.82763272 66.00394482 32.31343683 11.47348555 52.37874052 57.88761215 11.796335 31.4022174 20.15156518 23.12214838 31.36330696 67.39185448 32.57448068 45.41363924 23.18642724 41.86773395 131.0017562 64.54765994 83.05975972 40.50607761 25.76826385 7.357259576 54.52854758 35.24881828 12.15573145 38.36113881 36.43888614 36.29433057 84.0586856 29.09977577 106.9131704 NA NA 78.02340573 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA

I have attached my complete file. tpm_for_promote.txt https://github.com/comprna/SUPPA/files/3407923/tpm_for_promote.txt And my ioe file as follows: seqname gene_id event_id alternative_transcripts total_transcripts chr17 MIR22HG MIR22HG;A3:chr17:1616189-1616997:1615693-1616997:- NR_028503 NR_028503,NR_028504,NR_028505 chr17 FAM104A FAM104A;A3:chr17:71223403-71228225:71223321-71228225:- NM_032837,NM_001098832 NM_032837,NM_001098832,NM_001289411

However I am getting an error INFO:lib.tools:sample_file.txt opened in reading mode. INFO:psiCalculator:Buffering transcript expression levels. ERROR:lib.tools:1, in line 2. Skipping line... ERROR:lib.tools:2, in line 3. Skipping line... ERROR:lib.tools:3, in line 4. Skipping line...

I tried to look for leading/trailing spaces however could not find any. Is there a way by which I can solve this issue.

Thanks in advance!!!

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub < https://github.com/comprna/SUPPA/issues/56?email_source=notifications&email_token=ADCZKB2TYYFXJLSBMTOX2BLQACZOTA5CNFSM4IE6PKFKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HACPVTQ , or mute the thread < https://github.com/notifications/unsubscribe-auth/ADCZKB4MBJNGGZODGAC3DT3QACZOTANCNFSM4IE6PKFA

.

-- Prof. E Eyras EMBL Group Leader The John Curtin School of Medical Research - Australian National University https://github.com/comprna http://scholar.google.com/citations?user=LiojlGoAAAAJ

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— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/comprna/SUPPA/issues/56?email_source=notifications&email_token=ADCZKB2SSJTP5NHQK2F5US3QAI5IRA5CNFSM4IE6PKFKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD2M5J4A#issuecomment-513398000, or mute the thread https://github.com/notifications/unsubscribe-auth/ADCZKB6JS2R7UXAPYIVHPVDQAI5IRANCNFSM4IE6PKFA .

-- Prof. E Eyras EMBL Group Leader The John Curtin School of Medical Research - Australian National University https://github.com/comprna http://scholar.google.com/citations?user=LiojlGoAAAAJ

SukanyaPanja commented 5 years ago

Hi ,

Thank you so much. How do i check if the problem is with the python version

From: Eduardo Eyras notifications@github.com Sent: Saturday, July 20, 2019 12:38:43 AM To: comprna/SUPPA SUPPA@noreply.github.com Cc: Sukanya Panja sp1388@shp.rutgers.edu; State change state_change@noreply.github.com Subject: Re: [comprna/SUPPA] psiPerEvent error (#56)

Thanks Sukanya,

I cannot see any obvious problem from the command line. Things to check could be a possible issue with the python version or the interpretation of NA.

I cc JC and JL who developed the code and might be able to tell you more about where to look for potential problems.

best

On Sat, 20 Jul 2019 at 08:24, Sukanya Panja notifications@github.com wrote:

Hi,

My command line is

python3 /cache/home/.local/lib/python3.5/site-packages/SUPPA/suppa.py psiPerEvent --ioe-file allevents.ioe --expression-file tpm_for_promote -o psi_for_all_events_in_promote

and it is tab delimited

From: Eduardo Eyras notifications@github.com Sent: Thursday, July 18, 2019 9:46:36 PM To: comprna/SUPPA SUPPA@noreply.github.com Cc: Sukanya Panja sp1388@shp.rutgers.edu; State change < state_change@noreply.github.com> Subject: Re: [comprna/SUPPA] psiPerEvent error (#56)

Hi Sukanya,

Thanks for your message

what is your command line?

Your separations are tabs or single spaces?

best

Eduardo

On Fri, 19 Jul 2019 at 04:33, Sukanya Panja notifications@github.com wrote:

Hi, I am trying to calculate psiPerEvent using Suppa. My transcript per million file looks as follows:

sample1 sample2 sample3 sample4 sample5 sample6 sample7 sample8 sample9 sample10 sample11 sample12 sample13 sample14 sample15 sample16 sample17 sample18 sample19 sample20 sample21 sample22 sample23 sample24 sample25 sample26 sample27 sample28 sample29 sample30 sample31 sample32 sample33 sample34 sample35 sample36 sample37 sample38 sample39 sample40 sample41 sample42 sample43 sample44 sample45 sample46 sample47 sample48 sample49 sample50 sample51 sample52 sample53 sample54 sample55 sample56 sample57 sample58 sample59 sample60 sample61 sample62 sample63 sample64 sample65 sample66 sample67 sample68 sample69 sample70 sample71 sample72 sample73 sample74 sample75 sample76 sample77 sample78 sample79 sample80 NR_046018 0.146696232 0 0.02246929 0 0.043484372 0 0.064345526 0 0 0.641447528 0.070457715 0 0 0 0.288446756 0 0.018291742 0.098839876 0 0 0 0.060880505 0.125044033 0 0 0.162726933 0.056250345 0 0.04533607 0.111419096 0.25858868 0 0.10616014 0.081480545 0 0.320725657 0.24226526 0.091504489 0.528826249 0.194352761 0.046725318 0.151982368 0 0 0.226697819 0.084641889 0 0.566318677 0.1484086 0 0.268734574 0.220563037 0 0.109770725 0.05704479 0 NA NA 0 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NR_024540 19.19284277 53.37251412 32.7337806 74.98841145 11.89824843 33.80215601 10.03499221 45.43118253 83.04926565 22.62463001 47.85138289 15.54743843 3.433399326 39.67863222 46.35756323 27.33616404 16.91112386 54.79703587 31.89242283 21.97120496 0 21.57606474 13.35599624 0 4.456391694 28.82763272 66.00394482 32.31343683 11.47348555 52.37874052 57.88761215 11.796335 31.4022174 20.15156518 23.12214838 31.36330696 67.39185448 32.57448068 45.41363924 23.18642724 41.86773395 131.0017562 64.54765994 83.05975972 40.50607761 25.76826385 7.357259576 54.52854758 35.24881828 12.15573145 38.36113881 36.43888614 36.29433057 84.0586856 29.09977577 106.9131704 NA NA 78.02340573 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA

I have attached my complete file. tpm_for_promote.txt https://github.com/comprna/SUPPA/files/3407923/tpm_for_promote.txt And my ioe file as follows: seqname gene_id event_id alternative_transcripts total_transcripts chr17 MIR22HG MIR22HG;A3:chr17:1616189-1616997:1615693-1616997:- NR_028503 NR_028503,NR_028504,NR_028505 chr17 FAM104A FAM104A;A3:chr17:71223403-71228225:71223321-71228225:- NM_032837,NM_001098832 NM_032837,NM_001098832,NM_001289411

However I am getting an error INFO:lib.tools:sample_file.txt opened in reading mode. INFO:psiCalculator:Buffering transcript expression levels. ERROR:lib.tools:1, in line 2. Skipping line... ERROR:lib.tools:2, in line 3. Skipping line... ERROR:lib.tools:3, in line 4. Skipping line...

I tried to look for leading/trailing spaces however could not find any. Is there a way by which I can solve this issue.

Thanks in advance!!!

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EduEyras commented 5 years ago

I was wondering whether you need to use explicitly python3.4

On Sun, 21 Jul 2019 at 02:17, Sukanya Panja notifications@github.com wrote:

Hi ,

Thank you so much. How do i check if the problem is with the python version

From: Eduardo Eyras notifications@github.com Sent: Saturday, July 20, 2019 12:38:43 AM To: comprna/SUPPA SUPPA@noreply.github.com Cc: Sukanya Panja sp1388@shp.rutgers.edu; State change < state_change@noreply.github.com> Subject: Re: [comprna/SUPPA] psiPerEvent error (#56)

Thanks Sukanya,

I cannot see any obvious problem from the command line. Things to check could be a possible issue with the python version or the interpretation of NA.

I cc JC and JL who developed the code and might be able to tell you more about where to look for potential problems.

best

E.

On Sat, 20 Jul 2019 at 08:24, Sukanya Panja notifications@github.com wrote:

Hi,

My command line is

python3 /cache/home/.local/lib/python3.5/site-packages/SUPPA/suppa.py psiPerEvent --ioe-file allevents.ioe --expression-file tpm_for_promote -o psi_for_all_events_in_promote

and it is tab delimited

From: Eduardo Eyras notifications@github.com Sent: Thursday, July 18, 2019 9:46:36 PM To: comprna/SUPPA SUPPA@noreply.github.com Cc: Sukanya Panja sp1388@shp.rutgers.edu; State change < state_change@noreply.github.com> Subject: Re: [comprna/SUPPA] psiPerEvent error (#56)

Hi Sukanya,

Thanks for your message

what is your command line?

Your separations are tabs or single spaces?

best

Eduardo

On Fri, 19 Jul 2019 at 04:33, Sukanya Panja notifications@github.com wrote:

Hi, I am trying to calculate psiPerEvent using Suppa. My transcript per million file looks as follows:

sample1 sample2 sample3 sample4 sample5 sample6 sample7 sample8 sample9 sample10 sample11 sample12 sample13 sample14 sample15 sample16 sample17 sample18 sample19 sample20 sample21 sample22 sample23 sample24 sample25 sample26 sample27 sample28 sample29 sample30 sample31 sample32 sample33 sample34 sample35 sample36 sample37 sample38 sample39 sample40 sample41 sample42 sample43 sample44 sample45 sample46 sample47 sample48 sample49 sample50 sample51 sample52 sample53 sample54 sample55 sample56 sample57 sample58 sample59 sample60 sample61 sample62 sample63 sample64 sample65 sample66 sample67 sample68 sample69 sample70 sample71 sample72 sample73 sample74 sample75 sample76 sample77 sample78 sample79 sample80 NR_046018 0.146696232 0 0.02246929 0 0.043484372 0 0.064345526 0 0 0.641447528 0.070457715 0 0 0 0.288446756 0 0.018291742 0.098839876 0 0 0 0.060880505 0.125044033 0 0 0.162726933 0.056250345 0 0.04533607 0.111419096 0.25858868 0 0.10616014 0.081480545 0 0.320725657 0.24226526 0.091504489 0.528826249 0.194352761 0.046725318 0.151982368 0 0 0.226697819 0.084641889 0 0.566318677 0.1484086 0 0.268734574 0.220563037 0 0.109770725 0.05704479 0 NA NA 0 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NR_024540 19.19284277 53.37251412 32.7337806 74.98841145 11.89824843 33.80215601 10.03499221 45.43118253 83.04926565 22.62463001 47.85138289 15.54743843 3.433399326 39.67863222 46.35756323 27.33616404 16.91112386 54.79703587 31.89242283 21.97120496 0 21.57606474 13.35599624 0 4.456391694 28.82763272 66.00394482 32.31343683 11.47348555 52.37874052 57.88761215 11.796335 31.4022174 20.15156518 23.12214838 31.36330696 67.39185448 32.57448068 45.41363924 23.18642724 41.86773395 131.0017562 64.54765994 83.05975972 40.50607761 25.76826385 7.357259576 54.52854758 35.24881828 12.15573145 38.36113881 36.43888614 36.29433057 84.0586856 29.09977577 106.9131704 NA NA 78.02340573 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA

I have attached my complete file. tpm_for_promote.txt https://github.com/comprna/SUPPA/files/3407923/tpm_for_promote.txt And my ioe file as follows: seqname gene_id event_id alternative_transcripts total_transcripts chr17 MIR22HG MIR22HG;A3:chr17:1616189-1616997:1615693-1616997:- NR_028503 NR_028503,NR_028504,NR_028505 chr17 FAM104A FAM104A;A3:chr17:71223403-71228225:71223321-71228225:- NM_032837,NM_001098832 NM_032837,NM_001098832,NM_001289411

However I am getting an error INFO:lib.tools:sample_file.txt opened in reading mode. INFO:psiCalculator:Buffering transcript expression levels. ERROR:lib.tools:1, in line 2. Skipping line... ERROR:lib.tools:2, in line 3. Skipping line... ERROR:lib.tools:3, in line 4. Skipping line...

I tried to look for leading/trailing spaces however could not find any. Is there a way by which I can solve this issue.

Thanks in advance!!!

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EduEyras commented 5 years ago

Hello Sukanya,

I am JC, one of the developers of SUPPA. I will take a look at the error and I will get back at you as soon as possible!

Kind regards JC

On Sat, 20 Jul 2019 at 05:38, Eduardo Eyras eduardo.eyras@anu.edu.au wrote:

Thanks Sukanya,

I cannot see any obvious problem from the command line. Things to check could be a possible issue with the python version or the interpretation of NA.

I cc JC and JL who developed the code and might be able to tell you more about where to look for potential problems.

best

E.

On Sat, 20 Jul 2019 at 08:24, Sukanya Panja notifications@github.com wrote:

Hi,

My command line is

python3 /cache/home/.local/lib/python3.5/site-packages/SUPPA/suppa.py psiPerEvent --ioe-file allevents.ioe --expression-file tpm_for_promote -o psi_for_all_events_in_promote

and it is tab delimited

From: Eduardo Eyras notifications@github.com Sent: Thursday, July 18, 2019 9:46:36 PM To: comprna/SUPPA SUPPA@noreply.github.com Cc: Sukanya Panja sp1388@shp.rutgers.edu; State change < state_change@noreply.github.com> Subject: Re: [comprna/SUPPA] psiPerEvent error (#56)

Hi Sukanya,

Thanks for your message

what is your command line?

Your separations are tabs or single spaces?

best

Eduardo

On Fri, 19 Jul 2019 at 04:33, Sukanya Panja notifications@github.com wrote:

Hi, I am trying to calculate psiPerEvent using Suppa. My transcript per million file looks as follows:

sample1 sample2 sample3 sample4 sample5 sample6 sample7 sample8 sample9 sample10 sample11 sample12 sample13 sample14 sample15 sample16 sample17 sample18 sample19 sample20 sample21 sample22 sample23 sample24 sample25 sample26 sample27 sample28 sample29 sample30 sample31 sample32 sample33 sample34 sample35 sample36 sample37 sample38 sample39 sample40 sample41 sample42 sample43 sample44 sample45 sample46 sample47 sample48 sample49 sample50 sample51 sample52 sample53 sample54 sample55 sample56 sample57 sample58 sample59 sample60 sample61 sample62 sample63 sample64 sample65 sample66 sample67 sample68 sample69 sample70 sample71 sample72 sample73 sample74 sample75 sample76 sample77 sample78 sample79 sample80 NR_046018 0.146696232 0 0.02246929 0 0.043484372 0 0.064345526 0 0 0.641447528 0.070457715 0 0 0 0.288446756 0 0.018291742 0.098839876 0 0 0 0.060880505 0.125044033 0 0 0.162726933 0.056250345 0 0.04533607 0.111419096 0.25858868 0 0.10616014 0.081480545 0 0.320725657 0.24226526 0.091504489 0.528826249 0.194352761 0.046725318 0.151982368 0 0 0.226697819 0.084641889 0 0.566318677 0.1484086 0 0.268734574 0.220563037 0 0.109770725 0.05704479 0 NA NA 0 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NR_024540 19.19284277 53.37251412 32.7337806 74.98841145 11.89824843 33.80215601 10.03499221 45.43118253 83.04926565 22.62463001 47.85138289 15.54743843 3.433399326 39.67863222 46.35756323 27.33616404 16.91112386 54.79703587 31.89242283 21.97120496 0 21.57606474 13.35599624 0 4.456391694 28.82763272 66.00394482 32.31343683 11.47348555 52.37874052 57.88761215 11.796335 31.4022174 20.15156518 23.12214838 31.36330696 67.39185448 32.57448068 45.41363924 23.18642724 41.86773395 131.0017562 64.54765994 83.05975972 40.50607761 25.76826385 7.357259576 54.52854758 35.24881828 12.15573145 38.36113881 36.43888614 36.29433057 84.0586856 29.09977577 106.9131704 NA NA 78.02340573 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA

I have attached my complete file. tpm_for_promote.txt https://github.com/comprna/SUPPA/files/3407923/tpm_for_promote.txt And my ioe file as follows: seqname gene_id event_id alternative_transcripts total_transcripts chr17 MIR22HG MIR22HG;A3:chr17:1616189-1616997:1615693-1616997:- NR_028503 NR_028503,NR_028504,NR_028505 chr17 FAM104A FAM104A;A3:chr17:71223403-71228225:71223321-71228225:- NM_032837,NM_001098832 NM_032837,NM_001098832,NM_001289411

However I am getting an error INFO:lib.tools:sample_file.txt opened in reading mode. INFO:psiCalculator:Buffering transcript expression levels. ERROR:lib.tools:1, in line 2. Skipping line... ERROR:lib.tools:2, in line 3. Skipping line... ERROR:lib.tools:3, in line 4. Skipping line...

I tried to look for leading/trailing spaces however could not find any. Is there a way by which I can solve this issue.

Thanks in advance!!!

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub < https://github.com/comprna/SUPPA/issues/56?email_source=notifications&email_token=ADCZKB2TYYFXJLSBMTOX2BLQACZOTA5CNFSM4IE6PKFKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HACPVTQ , or mute the thread < https://github.com/notifications/unsubscribe-auth/ADCZKB4MBJNGGZODGAC3DT3QACZOTANCNFSM4IE6PKFA

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-- Prof. E Eyras EMBL Group Leader The John Curtin School of Medical Research - Australian National University https://github.com/comprna http://scholar.google.com/citations?user=LiojlGoAAAAJ

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SukanyaPanja commented 5 years ago

Thank you so much.

Sukanya

From: Eduardo Eyras notifications@github.com Sent: Monday, July 22, 2019 6:19:53 AM To: comprna/SUPPA SUPPA@noreply.github.com Cc: Sukanya Panja sp1388@shp.rutgers.edu; State change state_change@noreply.github.com Subject: Re: [comprna/SUPPA] psiPerEvent error (#56)

Hello Sukanya,

I am JC, one of the developers of SUPPA. I will take a look at the error and I will get back at you as soon as possible!

Kind regards JC

On Sat, 20 Jul 2019 at 05:38, Eduardo Eyras eduardo.eyras@anu.edu.au wrote:

Thanks Sukanya,

I cannot see any obvious problem from the command line. Things to check could be a possible issue with the python version or the interpretation of NA.

I cc JC and JL who developed the code and might be able to tell you more about where to look for potential problems.

best

E.

On Sat, 20 Jul 2019 at 08:24, Sukanya Panja notifications@github.com wrote:

Hi,

My command line is

python3 /cache/home/.local/lib/python3.5/site-packages/SUPPA/suppa.py psiPerEvent --ioe-file allevents.ioe --expression-file tpm_for_promote -o psi_for_all_events_in_promote

and it is tab delimited

From: Eduardo Eyras notifications@github.com Sent: Thursday, July 18, 2019 9:46:36 PM To: comprna/SUPPA SUPPA@noreply.github.com Cc: Sukanya Panja sp1388@shp.rutgers.edu; State change < state_change@noreply.github.com> Subject: Re: [comprna/SUPPA] psiPerEvent error (#56)

Hi Sukanya,

Thanks for your message

what is your command line?

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Eduardo

On Fri, 19 Jul 2019 at 04:33, Sukanya Panja notifications@github.com wrote:

Hi, I am trying to calculate psiPerEvent using Suppa. My transcript per million file looks as follows:

sample1 sample2 sample3 sample4 sample5 sample6 sample7 sample8 sample9 sample10 sample11 sample12 sample13 sample14 sample15 sample16 sample17 sample18 sample19 sample20 sample21 sample22 sample23 sample24 sample25 sample26 sample27 sample28 sample29 sample30 sample31 sample32 sample33 sample34 sample35 sample36 sample37 sample38 sample39 sample40 sample41 sample42 sample43 sample44 sample45 sample46 sample47 sample48 sample49 sample50 sample51 sample52 sample53 sample54 sample55 sample56 sample57 sample58 sample59 sample60 sample61 sample62 sample63 sample64 sample65 sample66 sample67 sample68 sample69 sample70 sample71 sample72 sample73 sample74 sample75 sample76 sample77 sample78 sample79 sample80 NR_046018 0.146696232 0 0.02246929 0 0.043484372 0 0.064345526 0 0 0.641447528 0.070457715 0 0 0 0.288446756 0 0.018291742 0.098839876 0 0 0 0.060880505 0.125044033 0 0 0.162726933 0.056250345 0 0.04533607 0.111419096 0.25858868 0 0.10616014 0.081480545 0 0.320725657 0.24226526 0.091504489 0.528826249 0.194352761 0.046725318 0.151982368 0 0 0.226697819 0.084641889 0 0.566318677 0.1484086 0 0.268734574 0.220563037 0 0.109770725 0.05704479 0 NA NA 0 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NR_024540 19.19284277 53.37251412 32.7337806 74.98841145 11.89824843 33.80215601 10.03499221 45.43118253 83.04926565 22.62463001 47.85138289 15.54743843 3.433399326 39.67863222 46.35756323 27.33616404 16.91112386 54.79703587 31.89242283 21.97120496 0 21.57606474 13.35599624 0 4.456391694 28.82763272 66.00394482 32.31343683 11.47348555 52.37874052 57.88761215 11.796335 31.4022174 20.15156518 23.12214838 31.36330696 67.39185448 32.57448068 45.41363924 23.18642724 41.86773395 131.0017562 64.54765994 83.05975972 40.50607761 25.76826385 7.357259576 54.52854758 35.24881828 12.15573145 38.36113881 36.43888614 36.29433057 84.0586856 29.09977577 106.9131704 NA NA 78.02340573 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA

I have attached my complete file. tpm_for_promote.txt https://github.com/comprna/SUPPA/files/3407923/tpm_for_promote.txt And my ioe file as follows: seqname gene_id event_id alternative_transcripts total_transcripts chr17 MIR22HG MIR22HG;A3:chr17:1616189-1616997:1615693-1616997:- NR_028503 NR_028503,NR_028504,NR_028505 chr17 FAM104A FAM104A;A3:chr17:71223403-71228225:71223321-71228225:- NM_032837,NM_001098832 NM_032837,NM_001098832,NM_001289411

However I am getting an error INFO:lib.tools:sample_file.txt opened in reading mode. INFO:psiCalculator:Buffering transcript expression levels. ERROR:lib.tools:1, in line 2. Skipping line... ERROR:lib.tools:2, in line 3. Skipping line... ERROR:lib.tools:3, in line 4. Skipping line...

I tried to look for leading/trailing spaces however could not find any. Is there a way by which I can solve this issue.

Thanks in advance!!!

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EduEyras commented 5 years ago

Are you using the right version? https://github.com/comprna/SUPPA/releases/tag/v2.3

SukanyaPanja commented 5 years ago

Hi Eduardo, Yes i am using the correct version. Thanks Sukanya

On Aug 23, 2019 10:25 AM, Eduardo Eyras notifications@github.com wrote:

Are you using the right version? https://github.com/comprna/SUPPA/releases/tag/v2.3 https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fcomprna%2FSUPPA%2Freleases%2Ftag%2Fv2.3&data=02%7C01%7Csp1388%40shp.rutgers.edu%7C19db4d3d6c3646eb717e08d727d5b38a%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C637021671100405146&sdata=8JsNdjnlA2KSUfPUjiy1xm3DqC%2BxDO5PUOJ35D%2F3BBM%3D&reserved=0

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EduEyras commented 5 years ago

Hi Sukanya, have you checked whether you have transcripts in the ioe/ioi file that are not in the expression file? Is your output completely empty? Or do you still get PSIs for some events? Thanks