Error using '-ps averages' #22
Comments
|
Hey!
Can you send me the complete commands you are using ?
Thanks!
…Sent from my iPhone
On Apr 7, 2023, at 3:37 PM, Joe Bowness ***@***.***> wrote:
CAUTION: This email originated from outside the organization. DO NOT CLICK ON LINKS or OPEN ATTACHMENTS unless you know and trust the sender.
Hello!
Thanks for making this tool! I have recently discovered it, and mostly it is working great for how I want to visualise my tracks.
The only thing I have not been able to work yet is that when using the '-ps averages' mode, I get this error:
Traceback (most recent call last):
File "SparK.py", line 622, in
coords.append([get_relative_hight(np.average(averages)), x_pos])
File "SparK.py", line 181, in get_relative_hight
return((raw_value * hight * relative_track_hight_percentage) / max_value) # to not go up to the max
TypeError: unsupported operand type(s) for /: 'float' and 'NoneType'
The same command works perfectly well if I omit the '-ps averages' flag (but it overlays separate tracks for each replicate). Can you give me any insight on what might be going wrong for me here?
Cheers!
—
Reply to this email directly, view it on GitHub<#22>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AHANDYRBUFMCX7YWE5SLBWLXABUILANCNFSM6AAAAAAWW3SZGI>.
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Hi,
Thanks for your quick reply!
This is an example of a command I am using which works - it generates a plot that looks similar to the one I attach here, with the replicates for each condition overlain separately.
#plot Mecp2
python ~/Resources/Software/SparK/SparK.py \
-pr chrX:74082000-74088000 \
-cf ~/SparK_tracks/bedGraph/ATAC_A11B2/17_A11B2_ES_ATAC.sort.chrX.bw.bedGraph.gz \
~/SparK_tracks/bedGraph/ATAC_A11B2/17_A11B2_ES_ATAC.genome1.sort.chrX1.bw.bedGraph.gz \
~/SparK_tracks/bedGraph/ATAC_A11B2/NPC_1d_Rep1.genome1.chrX1.sort.bw.bedGraph.gz ~/SparK_tracks/bedGraph/ATAC_A11B2/NPC_1d_Rep2.genome1.chrX1.sort.bw.bedGraph.gz \
~/SparK_tracks/bedGraph/ATAC_A11B2/NPC_3d_Rep1.genome1.chrX1.sort.bw.bedGraph.gz ~/SparK_tracks/bedGraph/ATAC_A11B2/NPC_3d_Rep2.genome1.chrX1.sort.bw.bedGraph.gz \
~/SparK_tracks/bedGraph/ATAC_A11B2/NPC_6d_Rep1.genome1.chrX1.sort.bw.bedGraph.gz ~/SparK_tracks/bedGraph/ATAC_A11B2/NPC_6d_Rep2.genome1.chrX1.sort.bw.bedGraph.gz \
~/SparK_tracks/bedGraph/ATAC_A11B2/NPC_17d_Rep1.genome1.chrX1.sort.bw.bedGraph.gz ~/SparK_tracks/bedGraph/ATAC_A11B2/NPC_17d_Rep2.genome1.chrX1.sort.bw.bedGraph.gz \
-tf ~/SparK_tracks/bedGraph/ATAC_A11B2/17_A11B2_ES_ATAC.genome2.sort.chrX1.bw.bedGraph.gz \
~/SparK_tracks/bedGraph/ATAC_A11B2/NPC_1d_Rep1.genome2.chrX1.sort.bw.bedGraph.gz ~/SparK_tracks/bedGraph/ATAC_A11B2/NPC_1d_Rep2.genome2.chrX1.sort.bw.bedGraph.gz \
~/SparK_tracks/bedGraph/ATAC_A11B2/NPC_3d_Rep1.genome2.chrX1.sort.bw.bedGraph.gz ~/SparK_tracks/bedGraph/ATAC_A11B2/NPC_3d_Rep2.genome2.chrX1.sort.bw.bedGraph.gz \
~/SparK_tracks/bedGraph/ATAC_A11B2/NPC_6d_Rep1.genome2.chrX1.sort.bw.bedGraph.gz ~/SparK_tracks/bedGraph/ATAC_A11B2/NPC_6d_Rep2.genome2.chrX1.sort.bw.bedGraph.gz \
~/SparK_tracks/bedGraph/ATAC_A11B2/NPC_17d_Rep1.genome2.chrX1.sort.bw.bedGraph.gz ~/SparK_tracks/bedGraph/ATAC_A11B2/NPC_17d_Rep2.genome2.chrX1.sort.bw.bedGraph.gz \
-cg 1 2 3 3 4 4 5 5 6 6 -tg 2 3 3 4 4 5 5 6 6 \
-gl unsplit_ES ES d1 d3 d6 d17 \
-l g1 g2 -f 191b80 56fcf1 \
-gtf ~/Resources/gencode.vM25.annotation.chrX.gtf -dg Mecp2 \
-o plots/A11B2_ATAC_Mecp2
However, when I include the flag "-ps averages” into the command, it produces the error I described.
In order to save time and memory, I restrict my bedgraph files to only the region of the genome I am interested in (ie. a ~100Mb region of Chromosome X). Could this potentially produce the issue with the averages function? (Maybe it is trying to divide empty regions?)
Best Wishes,
Joe
[A11B2_ATAC_Mecp2.pdf](https://github.com/harbourlab/SparK/files/11183131/A11B2_ATAC_Mecp2.pdf)
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Maybe.. could you try using the full bedgraphs real quick?
Sent from my iPhone
On Apr 8, 2023, at 5:26 AM, Joe Bowness ***@***.***> wrote:
Hi,
Thanks for your quick reply!
This is an example of a command I am using which works - it generates a plot that looks similar to the one I attach here, with the replicates for each condition overlain separately.
#plot Mecp2
python ~/Resources/Software/SparK/SparK.py \
-pr chrX:74082000-74088000 \
-cf ~/SparK_tracks/bedGraph/ATAC_A11B2/17_A11B2_ES_ATAC.sort.chrX.bw.bedGraph.gz \
~/SparK_tracks/bedGraph/ATAC_A11B2/17_A11B2_ES_ATAC.genome1.sort.chrX1.bw.bedGraph.gz \
~/SparK_tracks/bedGraph/ATAC_A11B2/NPC_1d_Rep1.genome1.chrX1.sort.bw.bedGraph.gz ~/SparK_tracks/bedGraph/ATAC_A11B2/NPC_1d_Rep2.genome1.chrX1.sort.bw.bedGraph.gz \
~/SparK_tracks/bedGraph/ATAC_A11B2/NPC_3d_Rep1.genome1.chrX1.sort.bw.bedGraph.gz ~/SparK_tracks/bedGraph/ATAC_A11B2/NPC_3d_Rep2.genome1.chrX1.sort.bw.bedGraph.gz \
~/SparK_tracks/bedGraph/ATAC_A11B2/NPC_6d_Rep1.genome1.chrX1.sort.bw.bedGraph.gz ~/SparK_tracks/bedGraph/ATAC_A11B2/NPC_6d_Rep2.genome1.chrX1.sort.bw.bedGraph.gz \
~/SparK_tracks/bedGraph/ATAC_A11B2/NPC_17d_Rep1.genome1.chrX1.sort.bw.bedGraph.gz ~/SparK_tracks/bedGraph/ATAC_A11B2/NPC_17d_Rep2.genome1.chrX1.sort.bw.bedGraph.gz \
-tf ~/SparK_tracks/bedGraph/ATAC_A11B2/17_A11B2_ES_ATAC.genome2.sort.chrX1.bw.bedGraph.gz \
~/SparK_tracks/bedGraph/ATAC_A11B2/NPC_1d_Rep1.genome2.chrX1.sort.bw.bedGraph.gz ~/SparK_tracks/bedGraph/ATAC_A11B2/NPC_1d_Rep2.genome2.chrX1.sort.bw.bedGraph.gz \
~/SparK_tracks/bedGraph/ATAC_A11B2/NPC_3d_Rep1.genome2.chrX1.sort.bw.bedGraph.gz ~/SparK_tracks/bedGraph/ATAC_A11B2/NPC_3d_Rep2.genome2.chrX1.sort.bw.bedGraph.gz \
~/SparK_tracks/bedGraph/ATAC_A11B2/NPC_6d_Rep1.genome2.chrX1.sort.bw.bedGraph.gz ~/SparK_tracks/bedGraph/ATAC_A11B2/NPC_6d_Rep2.genome2.chrX1.sort.bw.bedGraph.gz \
~/SparK_tracks/bedGraph/ATAC_A11B2/NPC_17d_Rep1.genome2.chrX1.sort.bw.bedGraph.gz ~/SparK_tracks/bedGraph/ATAC_A11B2/NPC_17d_Rep2.genome2.chrX1.sort.bw.bedGraph.gz \
-cg 1 2 3 3 4 4 5 5 6 6 -tg 2 3 3 4 4 5 5 6 6 \
-gl unsplit_ES ES d1 d3 d6 d17 \
-l g1 g2 -f 191b80 56fcf1 \
-gtf ~/Resources/gencode.vM25.annotation.chrX.gtf -dg Mecp2 \
-o plots/A11B2_ATAC_Mecp2
However, when I include the flag "-ps averages” into the command, it produces the error I described.
In order to save time and memory, I restrict my bedgraph files to only the region of the genome I am interested in (ie. a ~100Mb region of Chromosome X). Could this potentially produce the issue with the averages function? (Maybe it is trying to divide empty regions?)
Best Wishes,
Joe
On 7 Apr 2023, at 22:59, harbourlab ***@***.***> wrote:
Hey!
Can you send me the complete commands you are using ?
Thanks!
Sent from my iPhone
On Apr 7, 2023, at 3:37 PM, Joe Bowness ***@***.***> wrote:
CAUTION: This email originated from outside the organization. DO NOT CLICK ON LINKS or OPEN ATTACHMENTS unless you know and trust the sender.
Hello!
Thanks for making this tool! I have recently discovered it, and mostly it is working great for how I want to visualise my tracks.
The only thing I have not been able to work yet is that when using the '-ps averages' mode, I get this error:
Traceback (most recent call last):
File "SparK.py", line 622, in
coords.append([get_relative_hight(np.average(averages)), x_pos])
File "SparK.py", line 181, in get_relative_hight
return((raw_value * hight * relative_track_hight_percentage) / max_value) # to not go up to the max
TypeError: unsupported operand type(s) for /: 'float' and 'NoneType'
The same command works perfectly well if I omit the '-ps averages' flag (but it overlays separate tracks for each replicate). Can you give me any insight on what might be going wrong for me here?
Cheers!
—
Reply to this email directly, view it on GitHub<#22>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AHANDYRBUFMCX7YWE5SLBWLXABUILANCNFSM6AAAAAAWW3SZGI>.
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|
I just tried with some full genome-wide bedGraphs, and yes, the averaging seems to work fine. So it probably is a problem related to the fact I was trying to use pre-cropped bedGraph files - I guess I will just have to use the full-size ones.
Thanks again for your help.
… On 8 Apr 2023, at 13:36, harbourlab ***@***.***> wrote:
Maybe.. could you try using the full bedgraphs real quick?
Sent from my iPhone
On Apr 8, 2023, at 5:26 AM, Joe Bowness ***@***.***> wrote:
Hi,
Thanks for your quick reply!
This is an example of a command I am using which works - it generates a plot that looks similar to the one I attach here, with the replicates for each condition overlain separately.
#plot Mecp2
python ~/Resources/Software/SparK/SparK.py \
-pr chrX:74082000-74088000 \
-cf ~/SparK_tracks/bedGraph/ATAC_A11B2/17_A11B2_ES_ATAC.sort.chrX.bw.bedGraph.gz \
~/SparK_tracks/bedGraph/ATAC_A11B2/17_A11B2_ES_ATAC.genome1.sort.chrX1.bw.bedGraph.gz \
~/SparK_tracks/bedGraph/ATAC_A11B2/NPC_1d_Rep1.genome1.chrX1.sort.bw.bedGraph.gz ~/SparK_tracks/bedGraph/ATAC_A11B2/NPC_1d_Rep2.genome1.chrX1.sort.bw.bedGraph.gz \
~/SparK_tracks/bedGraph/ATAC_A11B2/NPC_3d_Rep1.genome1.chrX1.sort.bw.bedGraph.gz ~/SparK_tracks/bedGraph/ATAC_A11B2/NPC_3d_Rep2.genome1.chrX1.sort.bw.bedGraph.gz \
~/SparK_tracks/bedGraph/ATAC_A11B2/NPC_6d_Rep1.genome1.chrX1.sort.bw.bedGraph.gz ~/SparK_tracks/bedGraph/ATAC_A11B2/NPC_6d_Rep2.genome1.chrX1.sort.bw.bedGraph.gz \
~/SparK_tracks/bedGraph/ATAC_A11B2/NPC_17d_Rep1.genome1.chrX1.sort.bw.bedGraph.gz ~/SparK_tracks/bedGraph/ATAC_A11B2/NPC_17d_Rep2.genome1.chrX1.sort.bw.bedGraph.gz \
-tf ~/SparK_tracks/bedGraph/ATAC_A11B2/17_A11B2_ES_ATAC.genome2.sort.chrX1.bw.bedGraph.gz \
~/SparK_tracks/bedGraph/ATAC_A11B2/NPC_1d_Rep1.genome2.chrX1.sort.bw.bedGraph.gz ~/SparK_tracks/bedGraph/ATAC_A11B2/NPC_1d_Rep2.genome2.chrX1.sort.bw.bedGraph.gz \
~/SparK_tracks/bedGraph/ATAC_A11B2/NPC_3d_Rep1.genome2.chrX1.sort.bw.bedGraph.gz ~/SparK_tracks/bedGraph/ATAC_A11B2/NPC_3d_Rep2.genome2.chrX1.sort.bw.bedGraph.gz \
~/SparK_tracks/bedGraph/ATAC_A11B2/NPC_6d_Rep1.genome2.chrX1.sort.bw.bedGraph.gz ~/SparK_tracks/bedGraph/ATAC_A11B2/NPC_6d_Rep2.genome2.chrX1.sort.bw.bedGraph.gz \
~/SparK_tracks/bedGraph/ATAC_A11B2/NPC_17d_Rep1.genome2.chrX1.sort.bw.bedGraph.gz ~/SparK_tracks/bedGraph/ATAC_A11B2/NPC_17d_Rep2.genome2.chrX1.sort.bw.bedGraph.gz \
-cg 1 2 3 3 4 4 5 5 6 6 -tg 2 3 3 4 4 5 5 6 6 \
-gl unsplit_ES ES d1 d3 d6 d17 \
-l g1 g2 -f 191b80 56fcf1 \
-gtf ~/Resources/gencode.vM25.annotation.chrX.gtf -dg Mecp2 \
-o plots/A11B2_ATAC_Mecp2
However, when I include the flag "-ps averages” into the command, it produces the error I described.
In order to save time and memory, I restrict my bedgraph files to only the region of the genome I am interested in (ie. a ~100Mb region of Chromosome X). Could this potentially produce the issue with the averages function? (Maybe it is trying to divide empty regions?)
Best Wishes,
Joe
> On 7 Apr 2023, at 22:59, harbourlab ***@***.***> wrote:
>
>
> Hey!
>
> Can you send me the complete commands you are using ?
>
> Thanks!
>
> Sent from my iPhone
>
> On Apr 7, 2023, at 3:37 PM, Joe Bowness ***@***.***> wrote:
>
>
> CAUTION: This email originated from outside the organization. DO NOT CLICK ON LINKS or OPEN ATTACHMENTS unless you know and trust the sender.
>
> Hello!
>
> Thanks for making this tool! I have recently discovered it, and mostly it is working great for how I want to visualise my tracks.
>
> The only thing I have not been able to work yet is that when using the '-ps averages' mode, I get this error:
>
> Traceback (most recent call last):
> File "SparK.py", line 622, in
> coords.append([get_relative_hight(np.average(averages)), x_pos])
> File "SparK.py", line 181, in get_relative_hight
> return((raw_value * hight * relative_track_hight_percentage) / max_value) # to not go up to the max
> TypeError: unsupported operand type(s) for /: 'float' and 'NoneType'
>
> The same command works perfectly well if I omit the '-ps averages' flag (but it overlays separate tracks for each replicate). Can you give me any insight on what might be going wrong for me here?
>
> Cheers!
>
> —
> Reply to this email directly, view it on GitHub<#22>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AHANDYRBUFMCX7YWE5SLBWLXABUILANCNFSM6AAAAAAWW3SZGI>.
> You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>
> —
> Reply to this email directly, view it on GitHub, or unsubscribe.
> You are receiving this because you authored the thread.
>
—
Reply to this email directly, view it on GitHub<#22 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AHANDYXDDZABLVB7DTO7XH3XAEVMHANCNFSM6AAAAAAWW3SZGI>.
You are receiving this because you commented.Message ID: ***@***.***>
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|
Great! Glad it works now!
Cheers
Sent from my iPhone
On Apr 10, 2023, at 6:12 AM, Joe Bowness ***@***.***> wrote:
I just tried with some full genome-wide bedGraphs, and yes, the averaging seems to work fine. So it probably is a problem related to the fact I was trying to use pre-cropped bedGraph files - I guess I will just have to use the full-size ones.
Thanks again for your help.
On 8 Apr 2023, at 13:36, harbourlab ***@***.***> wrote:
Maybe.. could you try using the full bedgraphs real quick?
Sent from my iPhone
On Apr 8, 2023, at 5:26 AM, Joe Bowness ***@***.***> wrote:
Hi,
Thanks for your quick reply!
This is an example of a command I am using which works - it generates a plot that looks similar to the one I attach here, with the replicates for each condition overlain separately.
#plot Mecp2
python ~/Resources/Software/SparK/SparK.py \
-pr chrX:74082000-74088000 \
-cf ~/SparK_tracks/bedGraph/ATAC_A11B2/17_A11B2_ES_ATAC.sort.chrX.bw.bedGraph.gz \
~/SparK_tracks/bedGraph/ATAC_A11B2/17_A11B2_ES_ATAC.genome1.sort.chrX1.bw.bedGraph.gz \
~/SparK_tracks/bedGraph/ATAC_A11B2/NPC_1d_Rep1.genome1.chrX1.sort.bw.bedGraph.gz ~/SparK_tracks/bedGraph/ATAC_A11B2/NPC_1d_Rep2.genome1.chrX1.sort.bw.bedGraph.gz \
~/SparK_tracks/bedGraph/ATAC_A11B2/NPC_3d_Rep1.genome1.chrX1.sort.bw.bedGraph.gz ~/SparK_tracks/bedGraph/ATAC_A11B2/NPC_3d_Rep2.genome1.chrX1.sort.bw.bedGraph.gz \
~/SparK_tracks/bedGraph/ATAC_A11B2/NPC_6d_Rep1.genome1.chrX1.sort.bw.bedGraph.gz ~/SparK_tracks/bedGraph/ATAC_A11B2/NPC_6d_Rep2.genome1.chrX1.sort.bw.bedGraph.gz \
~/SparK_tracks/bedGraph/ATAC_A11B2/NPC_17d_Rep1.genome1.chrX1.sort.bw.bedGraph.gz ~/SparK_tracks/bedGraph/ATAC_A11B2/NPC_17d_Rep2.genome1.chrX1.sort.bw.bedGraph.gz \
-tf ~/SparK_tracks/bedGraph/ATAC_A11B2/17_A11B2_ES_ATAC.genome2.sort.chrX1.bw.bedGraph.gz \
~/SparK_tracks/bedGraph/ATAC_A11B2/NPC_1d_Rep1.genome2.chrX1.sort.bw.bedGraph.gz ~/SparK_tracks/bedGraph/ATAC_A11B2/NPC_1d_Rep2.genome2.chrX1.sort.bw.bedGraph.gz \
~/SparK_tracks/bedGraph/ATAC_A11B2/NPC_3d_Rep1.genome2.chrX1.sort.bw.bedGraph.gz ~/SparK_tracks/bedGraph/ATAC_A11B2/NPC_3d_Rep2.genome2.chrX1.sort.bw.bedGraph.gz \
~/SparK_tracks/bedGraph/ATAC_A11B2/NPC_6d_Rep1.genome2.chrX1.sort.bw.bedGraph.gz ~/SparK_tracks/bedGraph/ATAC_A11B2/NPC_6d_Rep2.genome2.chrX1.sort.bw.bedGraph.gz \
~/SparK_tracks/bedGraph/ATAC_A11B2/NPC_17d_Rep1.genome2.chrX1.sort.bw.bedGraph.gz ~/SparK_tracks/bedGraph/ATAC_A11B2/NPC_17d_Rep2.genome2.chrX1.sort.bw.bedGraph.gz \
-cg 1 2 3 3 4 4 5 5 6 6 -tg 2 3 3 4 4 5 5 6 6 \
-gl unsplit_ES ES d1 d3 d6 d17 \
-l g1 g2 -f 191b80 56fcf1 \
-gtf ~/Resources/gencode.vM25.annotation.chrX.gtf -dg Mecp2 \
-o plots/A11B2_ATAC_Mecp2
However, when I include the flag "-ps averages” into the command, it produces the error I described.
In order to save time and memory, I restrict my bedgraph files to only the region of the genome I am interested in (ie. a ~100Mb region of Chromosome X). Could this potentially produce the issue with the averages function? (Maybe it is trying to divide empty regions?)
Best Wishes,
Joe
> On 7 Apr 2023, at 22:59, harbourlab ***@***.***> wrote:
>
>
> Hey!
>
> Can you send me the complete commands you are using ?
>
> Thanks!
>
> Sent from my iPhone
>
> On Apr 7, 2023, at 3:37 PM, Joe Bowness ***@***.***> wrote:
>
>
> CAUTION: This email originated from outside the organization. DO NOT CLICK ON LINKS or OPEN ATTACHMENTS unless you know and trust the sender.
>
> Hello!
>
> Thanks for making this tool! I have recently discovered it, and mostly it is working great for how I want to visualise my tracks.
>
> The only thing I have not been able to work yet is that when using the '-ps averages' mode, I get this error:
>
> Traceback (most recent call last):
> File "SparK.py", line 622, in
> coords.append([get_relative_hight(np.average(averages)), x_pos])
> File "SparK.py", line 181, in get_relative_hight
> return((raw_value * hight * relative_track_hight_percentage) / max_value) # to not go up to the max
> TypeError: unsupported operand type(s) for /: 'float' and 'NoneType'
>
> The same command works perfectly well if I omit the '-ps averages' flag (but it overlays separate tracks for each replicate). Can you give me any insight on what might be going wrong for me here?
>
> Cheers!
>
> —
> Reply to this email directly, view it on GitHub<#22>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AHANDYRBUFMCX7YWE5SLBWLXABUILANCNFSM6AAAAAAWW3SZGI>.
> You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>
> —
> Reply to this email directly, view it on GitHub, or unsubscribe.
> You are receiving this because you authored the thread.
>
—
Reply to this email directly, view it on GitHub<#22 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AHANDYXDDZABLVB7DTO7XH3XAEVMHANCNFSM6AAAAAAWW3SZGI>.
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Hello!
Thanks for making this tool! I have recently discovered it, and mostly it is working great for how I want to visualise my tracks.
The only thing I have not been able to work yet is that when using the '-ps averages' mode, I get this error:
Traceback (most recent call last):
File "SparK.py", line 622, in
coords.append([get_relative_hight(np.average(averages)), x_pos])
File "SparK.py", line 181, in get_relative_hight
return((raw_value * hight * relative_track_hight_percentage) / max_value) # to not go up to the max
TypeError: unsupported operand type(s) for /: 'float' and 'NoneType'
The same command works perfectly well if I omit the '-ps averages' flag (but it overlays separate tracks for each replicate). Can you give me any insight on what might be going wrong for me here?
Cheers!
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