Working on a local fork

[abhi18av]

Hey, I'm working on a patch here

https://github.com/abhi18av/cellworks/tree/patch-1

I think the issue is that there are multiple variants within a genome so that's maybe that's why it takes a lot of time.

But I'm diagnosing it still.

[saamm]

its not about taking a lot of time if you check the file thats getting created it has the same data in it i.e. its printing the same line again and again and not iterating properly because of which I concluded that somehow the code has entered an infinite loop.

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On Mon, Sep 11, 2017 at 4:41 PM, Abhinav Sharma ***@***.***> wrote: Hey, I'm working on a patch here https://github.com/abhi18av/cellworks/tree/patch-1 I think the issue is that there are multiple variants within a genome so that's maybe that's why it takes a lot of time. But I'm diagnosing it still. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#1>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AG2zCR3pTkTqhxIy5u3dkcRAX5SLPRIrks5shRVwgaJpZM4PS_-Y> .

[saamm]

because till the time i want to print it out on the screen its all cool, only when I want to write it onto the csv file its printing only one row in repetition. I have been at it for a while, but I cant seem to figure out the problem. I thought fresh eyes can do me good. On Mon, Sep 11, 2017 at 4:45 PM, Soumya sinha <soumyasinha161093@gmail.com> wrote:

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its not about taking a lot of time if you check the file thats getting created it has the same data in it i.e. its printing the same line again and again and not iterating properly because of which I concluded that somehow the code has entered an infinite loop. On Mon, Sep 11, 2017 at 4:41 PM, Abhinav Sharma ***@***.***> wrote: > Hey, I'm working on a patch here > > https://github.com/abhi18av/cellworks/tree/patch-1 > > I think the issue is that there are multiple variants within a genome so > that's maybe that's why it takes a lot of time. > > But I'm diagnosing it still. > > — > You are receiving this because you are subscribed to this thread. > Reply to this email directly, view it on GitHub > <#1>, or mute the thread > <https://github.com/notifications/unsubscribe-auth/AG2zCR3pTkTqhxIy5u3dkcRAX5SLPRIrks5shRVwgaJpZM4PS_-Y> > . >

[abhi18av]

Hey, so I've done some basic debugging and I've placed the output with the corresponding code ( commit ) on the readme.

I think at some point, the logic fails to find the other variants.

It's probably before this line
https://github.com/abhi18av/cellworks/blob/e8f8b979ee344250a40e52fff5d2f5df0d51a93f/ckb3.py#L55

[saamm]

The RE I am using is because I just want to catch the 8-digit numbers which is written in the format (PMID: 12345678) and I just want the numbers in the last column. On Mon, Sep 11, 2017 at 4:56 PM, Soumya sinha <soumyasinha161093@gmail.com> wrote:

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because till the time i want to print it out on the screen its all cool, only when I want to write it onto the csv file its printing only one row in repetition. I have been at it for a while, but I cant seem to figure out the problem. I thought fresh eyes can do me good. On Mon, Sep 11, 2017 at 4:45 PM, Soumya sinha ***@***.*** > wrote: > its not about taking a lot of time if you check the file thats getting > created it has the same data in it i.e. its printing the same line again > and again and not iterating properly because of which I concluded that > somehow the code has entered an infinite loop. > > On Mon, Sep 11, 2017 at 4:41 PM, Abhinav Sharma ***@***.*** > > wrote: > >> Hey, I'm working on a patch here >> >> https://github.com/abhi18av/cellworks/tree/patch-1 >> >> I think the issue is that there are multiple variants within a genome so >> that's maybe that's why it takes a lot of time. >> >> But I'm diagnosing it still. >> >> — >> You are receiving this because you are subscribed to this thread. >> Reply to this email directly, view it on GitHub >> <#1>, or mute the thread >> <https://github.com/notifications/unsubscribe-auth/AG2zCR3pTkTqhxIy5u3dkcRAX5SLPRIrks5shRVwgaJpZM4PS_-Y> >> . >> > >

[saamm]

but say if at line 68 we print(ckblist) we get the answer perfectly. I have checked by selecting a particular gene and just iterating the variants. its only when I am trying to push it into a a csv file its not writing, I can figure out where to put that in, cause at other positions of the loop I am getting an IndexList error. On Mon, Sep 11, 2017 at 5:05 PM, Soumya sinha <soumyasinha161093@gmail.com> wrote:

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The RE I am using is because I just want to catch the 8-digit numbers which is written in the format (PMID: 12345678) and I just want the numbers in the last column. On Mon, Sep 11, 2017 at 4:56 PM, Soumya sinha ***@***.*** > wrote: > because till the time i want to print it out on the screen its all cool, > only when I want to write it onto the csv file its printing only one row in > repetition. I have been at it for a while, but I cant seem to figure out > the problem. I thought fresh eyes can do me good. > > On Mon, Sep 11, 2017 at 4:45 PM, Soumya sinha < > ***@***.***> wrote: > >> its not about taking a lot of time if you check the file thats getting >> created it has the same data in it i.e. its printing the same line again >> and again and not iterating properly because of which I concluded that >> somehow the code has entered an infinite loop. >> >> On Mon, Sep 11, 2017 at 4:41 PM, Abhinav Sharma < >> ***@***.***> wrote: >> >>> Hey, I'm working on a patch here >>> >>> https://github.com/abhi18av/cellworks/tree/patch-1 >>> >>> I think the issue is that there are multiple variants within a genome >>> so that's maybe that's why it takes a lot of time. >>> >>> But I'm diagnosing it still. >>> >>> — >>> You are receiving this because you are subscribed to this thread. >>> Reply to this email directly, view it on GitHub >>> <#1>, or mute the thread >>> <https://github.com/notifications/unsubscribe-auth/AG2zCR3pTkTqhxIy5u3dkcRAX5SLPRIrks5shRVwgaJpZM4PS_-Y> >>> . >>> >> >> >

[abhi18av]

Ah, I see.

Hey, now I've gotta run. Would look into it tonight again.

I have a hunch that the error is related to RE .

For future reference, part of legends in code.

Some people, when confronted with a problem, think "I know, I'll use regular expressions." 

Now they have two problems.

[saamm]

See again maybe the error is related to RE but in the csv it is catching one PMID number(which is another problem that I have to solve as with a column with multiple PMIDs its only catching one,i think) and putting it in the csv, the column doesnt have the full para anymore just the number even if its only the first one. BUT AGAIN!!! in the csv its only pushing the one line!!! P.S. this is why telephonic or vdo conversations works over normal chats, have literally typed the same thing in all the emails and I am still not sure if I was successful in explaining the problem.

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On Mon, Sep 11, 2017 at 5:08 PM, Abhinav Sharma ***@***.***> wrote: Ah, I see. Hey, now I've gotta run. Would look into it tonight again. I have a hunch that the error is related to RE . For future reference, part of legends in code. Some people, when confronted with a problem, think "I know, I'll use regular expressions." Now they have two problems. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#1 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AG2zCflm9CSJvhwz2LiJnhrZV5kpQ1hlks5shRvCgaJpZM4PS_-Y> .

[abhi18av]

Hmmm, but there we don't have a paper trail and would likely make the same mistake in long term. So, could you show me what the ideal Csv looks like for you?

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On Sep 11, 2017 5:14 PM, "saamm" ***@***.***> wrote: See again maybe the error is related to RE but in the csv it is catching one PMID number(which is another problem that I have to solve as with a column with multiple PMIDs its only catching one,i think) and putting it in the csv, the column doesnt have the full para anymore just the number even if its only the first one. BUT AGAIN!!! in the csv its only pushing the one line!!! P.S. this is why telephonic or vdo conversations works over normal chats, have literally typed the same thing in all the emails and I am still not sure if I was successful in explaining the problem. On Mon, Sep 11, 2017 at 5:08 PM, Abhinav Sharma ***@***.***> wrote: > Ah, I see. > > Hey, now I've gotta run. Would look into it tonight again. > > I have a hunch that the error is related to RE . > > For future reference, part of legends in code. > > Some people, when confronted with a problem, think "I know, I'll use regular expressions." > > Now they have two problems. > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub > <#1 (comment)>, or mute > the thread > <https://github.com/notifications/unsubscribe-auth/ AG2zCflm9CSJvhwz2LiJnhrZV5kpQ1hlks5shRvCgaJpZM4PS_-Y> > . > — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#1 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AMNNXrTffQR21_9CZec74dgyYvTZuLbQks5shR0sgaJpZM4PS_-Y> .

[abhi18av]

It's not the regex.

[saamm]

This is one of the test csv that was generated

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On Mon, Sep 11, 2017 at 5:18 PM, Abhinav Sharma ***@***.***> wrote: It's not the regex. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#1 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AG2zCVdm8r4od0Nh_BxHi931QLg7oXKEks5shR3zgaJpZM4PS_-Y> .