SEA-PHAGES | Phams

Link to this post \| posted 18 Nov, 2015 02:22
jparker	Hello, I am having trouble getting the Phams to load in Phamerator. I Click on Phams on the left and it hangs, just showing the continual spinny wheel. I would really like to create a Pham Circle. Any thoughts or advice? Thanks, Jordan

Link to this post \| posted 19 Nov, 2015 04:29
cdshaffer	Maybe Steve or Dan can confirm but I believe the database has grown too large for the tasks you want. Looking at Actino_draft there are over 1100 phage and almost 12,000 phams. I don't think I have been able to get a pham circle since the phage count went above about 200. I can't image how small the font would need to be to have the names of 1100 phage around a circle. There are other ways of looking at pham data [but it won't be pretty pictures]. Its fairly easy to generate a list of all genes in a pham using either the mysql command line or extracting the data out of the pham table. What pham are you interested in? Would a list of the gene members for a particular pham be helpful?

Link to this post | posted 19 Nov, 2015 04:29

cdshaffer

Maybe Steve or Dan can confirm but I believe the database has grown too large for the tasks you want. Looking at Actino_draft there are over 1100 phage and almost 12,000 phams. I don't think I have been able to get a pham circle since the phage count went above about 200. I can't image how small the font would need to be to have the names of 1100 phage around a circle.

There are other ways of looking at pham data [but it won't be pretty pictures]. Its fairly easy to generate a list of all genes in a pham using either the mysql command line or extracting the data out of the pham table. What pham are you interested in? Would a list of the gene members for a particular pham be helpful?

Link to this post \| posted 23 Nov, 2015 16:26
edgingtonn1	The "pham circle" tool is broken in Phamerator, and I believe that Steve C. is aware of this. In the meanwhile, if you can do some programming, Circos is an option to draw something similar.

Link to this post \| posted 24 Nov, 2015 01:39
jparker	Thanks Nick and cdshaffer! I only know enough coding language to frustrate myself, so I'll probably leave that to the experts. Is there a straightforward way to generate lists of pham members without opening the pham circle tool? This may be a more complicated question than can be easily answered here. I'm headed to the in silico workshop in two weeks, so I should be able to get more info there. Thanks for your help! Jordan

Link to this post | posted 24 Nov, 2015 01:39

jparker

Thanks Nick and cdshaffer! I only know enough coding language to frustrate myself, so I'll probably leave that to the experts. Is there a straightforward way to generate lists of pham members without opening the pham circle tool? This may be a more complicated question than can be easily answered here. I'm headed to the in silico workshop in two weeks, so I should be able to get more info there.
Thanks for your help!
Jordan

Link to this post \| posted 24 Nov, 2015 20:07
cdshaffer	There is a way to get the info but I am not sure i would call it easy. You can export the complete pham table from phamerator. Open up phamerator, in the file menu select export pham table, select the file location, give the file a name and hit save. This will take a bit, depends on your machine, but you will eventually end up with a file of all genes cross referenced for all phage and all phams (take my computer about 3-4 minutes to create the file). The file is currently running about 15mb but it does compress down quite a bit. The pham table is essentially a giant excel spreadsheet with a couple of columns of summary data, then each phage in a single column, each pham as a row. The sheet is then filled with genes names where each gene is placed in the cell that intersects the proper column (i.e. phage the gene came from) with the proper row (i.e which pham it is in). I have created the current pham table from the most recent Actino_Draft database, you can download it with this link. That file will work for now but of course it will soon be out of date. But for now, just download the file, double click on it to uncompress, and import into excel. You will need to tell excel during the import that the data is in a text file, that the data is delimited, and that the delimiter is Tab (at least that is how it works on my mac version of excel). This is a lot of data, so be patient with excel, some commands could take 20 or 30 seconds to complete, there are something like 14 million cells to process in the whole spreadsheet. Once you have it open in excel, I would recommend you scroll down until you find the pham you are interested in, select the whole row, copy it, move to a new blank spreadsheet and use "Paste special…" to paste a "transposed" version into your new sheet (that will create a much, much smaller and faster spreadsheet). Transposition will convert the row to a single column which will be much easier to deal with. You can then use excel "sort" or "filter" on the column to bring all the gene names to the top. good luck, most more questions if you get stuck at any point. Edited 24 Nov, 2015 20:19

Link to this post | posted 24 Nov, 2015 20:07

cdshaffer

There is a way to get the info but I am not sure i would call it easy. You can export the complete pham table from phamerator. Open up phamerator, in the file menu select export pham table, select the file location, give the file a name and hit save. This will take a bit, depends on your machine, but you will eventually end up with a file of all genes cross referenced for all phage and all phams (take my computer about 3-4 minutes to create the file). The file is currently running about 15mb but it does compress down quite a bit. The pham table is essentially a giant excel spreadsheet with a couple of columns of summary data, then each phage in a single column, each pham as a row. The sheet is then filled with genes names where each gene is placed in the cell that intersects the proper column (i.e. phage the gene came from) with the proper row (i.e which pham it is in).

I have created the current pham table from the most recent Actino_Draft database, you can download it with this link. That file will work for now but of course it will soon be out of date. But for now, just download the file, double click on it to uncompress, and import into excel. You will need to tell excel during the import that the data is in a text file, that the data is delimited, and that the delimiter is Tab (at least that is how it works on my mac version of excel). This is a lot of data, so be patient with excel, some commands could take 20 or 30 seconds to complete, there are something like 14 million cells to process in the whole spreadsheet.

Once you have it open in excel, I would recommend you scroll down until you find the pham you are interested in, select the whole row, copy it, move to a new blank spreadsheet and use "Paste special…" to paste a "transposed" version into your new sheet (that will create a much, much smaller and faster spreadsheet). Transposition will convert the row to a single column which will be much easier to deal with. You can then use excel "sort" or "filter" on the column to bring all the gene names to the top.

good luck, most more questions if you get stuck at any point.

Edited 24 Nov, 2015 20:19

Link to this post \| posted 07 Dec, 2015 05:31
DanRussell	jparker Thanks Nick and cdshaffer! I only know enough coding language to frustrate myself, so I'll probably leave that to the experts. Is there a straightforward way to generate lists of pham members without opening the pham circle tool? This may be a more complicated question than can be easily answered here. I'm headed to the in silico workshop in two weeks, so I should be able to get more info there. Thanks for your help! Jordan Hi Jordan, Depending on exactly what you want, you may be able to do this on PhagesDB as well. The Pham page lets you select a Pham of interest and view its members: http://phagesdb.org/phams/ For example: http://phagesdb.org/phams/1728/ –Dan

Link to this post | posted 07 Dec, 2015 05:31

DanRussell

jparker
Thanks Nick and cdshaffer! I only know enough coding language to frustrate myself, so I'll probably leave that to the experts. Is there a straightforward way to generate lists of pham members without opening the pham circle tool? This may be a more complicated question than can be easily answered here. I'm headed to the in silico workshop in two weeks, so I should be able to get more info there.
Thanks for your help!
Jordan

Hi Jordan,

Depending on exactly what you want, you may be able to do this on PhagesDB as well. The Pham page lets you select a Pham of interest and view its members:

http://phagesdb.org/phams/

For example:

http://phagesdb.org/phams/1728/

–Dan

Link to this post \| posted 07 Dec, 2015 16:05
jparker	Eureka! Exactly what I need. I have never seen that page. What menu is it under? I can't seem to be find a link for it on PhagesDB. Now that I know it exists, i'll bookmark it, but it would be good to know how to direct students to the page. Thanks! Jordan

Link to this post \| posted 07 Dec, 2015 20:47
cdshaffer	I always just type out phagesdb.org/pham speaking of which, Dan, I know from that page I can search for words in the notes field but is there a way to see all notes for a given pham? This would be nice, I have run across a problem with finding functional annotations if they are relatively recent (i.e very few phage have that annotation) and the pham is particularly large. The function just doesn't end up in the top 100 proteins listed in the blast result but you can find them if you search all the notes. I have my full semester students look directly for annotations using a mysql query of the notes field but it would be really nice to have a web bases system for our mini-phage class. I looked for this kind of function before but could not find in on phages.db. Does such a search exist?

Link to this post | posted 07 Dec, 2015 20:47

cdshaffer

I always just type out phagesdb.org/pham

speaking of which, Dan, I know from that page I can search for words in the notes field but is there a way to see all notes for a given pham? This would be nice, I have run across a problem with finding functional annotations if they are relatively recent (i.e very few phage have that annotation) and the pham is particularly large. The function just doesn't end up in the top 100 proteins listed in the blast result but you can find them if you search all the notes. I have my full semester students look directly for annotations using a mysql query of the notes field but it would be really nice to have a web bases system for our mini-phage class. I looked for this kind of function before but could not find in on phages.db. Does such a search exist?

Link to this post \| posted 07 Dec, 2015 21:05
DanRussell	jparker Eureka! Exactly what I need. I have never seen that page. What menu is it under? I can't seem to be find a link for it on PhagesDB. Now that I know it exists, i'll bookmark it, but it would be good to know how to direct students to the page. Thanks! Jordan Hi Jordan, I think I removed the menu link about 6 months ago when the Phamerator database on PhagesDB was out-of-date. But now that it's re-synced, I've put it back in. Now there's a "Phams" item in the Phages dropdown menu. Thanks for the reminder! –Dan

Link to this post | posted 07 Dec, 2015 21:05

DanRussell

jparker
Eureka! Exactly what I need. I have never seen that page. What menu is it under? I can't seem to be find a link for it on PhagesDB. Now that I know it exists, i'll bookmark it, but it would be good to know how to direct students to the page.
Thanks!
Jordan

Hi Jordan,

I think I removed the menu link about 6 months ago when the Phamerator database on PhagesDB was out-of-date. But now that it's re-synced, I've put it back in. Now there's a "Phams" item in the Phages dropdown menu. Thanks for the reminder!

–Dan

Link to this post \| posted 27 Sep, 2017 17:20
grosej	Hi Dan, I am wondering if there is a way to merge two PhamDB databases, such as by merging the mysql files? thanks! Julianne Grose

Recent Activity

Phams