ctrl_events_ids & reg_events_ids files

[JamalELH]

Dear Eduardo,

First of all, thank you so much for sharing your expertise with us!

I have a simple question about the two input files used in step A of the anlysis.
these files in this file : MoSEA/test_files/infile/
control_events_chr22.ids
reg_events_chr22.ids

I know that they contain event ids detected by SUPPA, but I just want make sure I correctly understood the difference between them:
Does this file "control_events_chr22.ids" contain all SE events regardless if they are or not significant?
Does the second file "reg_events_chr22.ids" contain regulated SE events found to be significant according to SUPPA pipeline?

if not, could you please clarify what these files are?
Thank you so much in advance!
Respectfully,
Jamal.

[EduEyras]

Hi Jamal, thanks a lot for your email. The control events should be those that do not change significantly. You can select those by keeping those events that have e.g. | deltaPSI | < 0.05 and p-value > 0.05 The regulated events are those that change significantly. Both sets should not overlap. I cc Babita Singh in case she wants to add anything else I hope this helps Thanks a lot for your interest in our work Best Eduardo

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On Thu, 10 Jan 2019 at 20:20, JamalELH ***@***.***> wrote: Dear Eduardo, First of all, thank you so much for sharing your expertise with us! I have a simple question about the two input files used in step A of the anlysis. these files in this file : MoSEA/test_files/infile/ control_events_chr22.ids reg_events_chr22.ids I know that they contain event ids detected by SUPPA, but I just want make sure I correctly understood the difference between them: Does this file "control_events_chr22.ids" contain all SE events regardless if they are or not significant? Does the second file "reg_events_chr22.ids" contain regulated SE events found to be significant according to SUPPA pipeline? if not, could you please clarify what these files are? Thank you so much in advance! Respectfully, Jamal. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#2>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AMWVB4cQudF78kL7po69ogpHcVuw1IM7ks5vB5KGgaJpZM4Z6JgH> .

-- Dr E Eyras ICREA Research Professor PRBB, Dr Aiguader 88 Tel: +34 93 316 0502 (ext 1502) E08003 Barcelona - Spain Fax: +34 93 316 0550 http://scholar.google.com/citations?user=LiojlGoAAAAJ http://www.researcherid.com/rid/L-1053-2014

[JamalELH]

Dear team,

While trying to run the following command to get enrichment results between my two conditions I got the following error:
"Error in parsing: invalid literal for int() with base 10: '0.0'"

my command line was the following:
#Regulated files : Fasta sequences and Motif count table
reg_file_fa=$fafile_reg
reg_file_count="$fafile_reg.tab"

#Control files : Fasta sequences and Motif count table
control_file_fa=$fafile_control
control_file_count="$fafile_control.tab"

#Zscore Output file name
outfile="$path_outdir/zscore_outfile.tab"

#perform enrichment
python2.7 $path/mosea.py enrich --reg_fa_file $reg_file_fa --reg_count_file $reg_file_count
--bg_fa_file $control_file_fa --bg_count_file $control_file_count
--out_file $outfile
As you can see I'm using python2.7, but I'm not sure if I still need to import some library(es) to deal with "0.0" in my input files. Should I modify something within the script of mosea.py?

Thank you so much in advance for your help!
Best regards,
Jamal.

[EduEyras]

Hi Babita, could you please take a look at this request? Thanks E.

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On Mon, 4 Feb 2019 at 08:40, JamalELH ***@***.***> wrote: Dear team, While trying to run the following command to get enrichment results between my two conditions I got the following error: "Error in parsing: invalid literal for int() with base 10: '0.0'" my command line was the following: #Regulated files : Fasta sequences and Motif count table reg_file_fa=$fafile_reg reg_file_count="$fafile_reg.tab" #Control files : Fasta sequences and Motif count table control_file_fa=$fafile_control control_file_count="$fafile_control.tab" #Zscore Output file name outfile="$path_outdir/zscore_outfile.tab" #perform enrichment python2.7 $path/mosea.py enrich --reg_fa_file $reg_file_fa --reg_count_file $reg_file_count --bg_fa_file $control_file_fa --bg_count_file $control_file_count --out_file $outfile As you can see I'm using python2.7, but I'm not sure if I still need to import some library(es) to deal with "0.0" in my input files. Should I modify something within the script of mosea.py? Thank you so much in advance for your help! Best regards, Jamal. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#2 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AMWVB50Ig7x6ulIa6w7X_5HcZNtRQhQiks5vJ1dJgaJpZM4Z6JgH> .

-- Dr E Eyras ICREA Research Professor PRBB, Dr Aiguader 88 Tel: +34 93 316 0502 (ext 1502) E08003 Barcelona - Spain Fax: +34 93 316 0550 http://scholar.google.com/citations?user=LiojlGoAAAAJ http://www.researcherid.com/rid/L-1053-2014

[babisingh]

Dear Jamal,

Is it possible to send a dummy version of your files you're using? It will help me to better understand the error. It could be arising due to a non-integer value entered in an integer field.

You can send the files at babita.singh [at] upf [dot] edu

[JamalELH]

Dear Babita,
Thank you for your reply!

I got this error even when I run the analysis on the test files included in the MoSEA algorithm folder. That's why I think it is not related to my files. I will send you a copy of my files in a while in private.

best regards,
Jamal.

[JamalELH]

Dear Eduardo and Babita,
I've discovered the source of the error above ""Error in parsing: invalid literal for int() with base 10: '0.0'". It is happening when I run the enrichment command because it tries to convert a string literal to an int, because in input files I have '0.0' instead of '0', which can't be parsed to an integer because it contains a decimal point and therefore is unparseable as an integer. I will try to fix this and let you know how it goes.

Thank you both again your help!
Cheers,
Jamal.