Timeline for Are there tools for automatically parsing glycan names into tree structures?
Current License: CC BY-SA 3.0
11 events
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| Mar 21, 2014 at 19:56 | comment | added | Atl LED | @ericmjl I hope that points you in the right direction, maybe someone else will have a Python solution. And there might be a way to go directly from IUPAC, I just don't know it. | |
| Mar 21, 2014 at 19:53 | history | edited | Atl LED | CC BY-SA 3.0 |
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| Mar 21, 2014 at 17:49 | comment | added | Atl LED | @ericmjl actually what we have is in C# (I thought it was Java, just checked). I added the logic of it to the answer, hope that helps. | |
| Mar 21, 2014 at 17:47 | history | edited | Atl LED | CC BY-SA 3.0 |
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| Mar 21, 2014 at 17:35 | comment | added | ericmjl | No problem, I can brush up on my Java (it's been 6 years since I last used it). Thank you very much! | |
| Mar 21, 2014 at 17:14 | comment | added | Atl LED | @ericmjl are ok if they're not in Python? KEGG is a Java program. My Python is limited though I have a tech who's ok in it. I'll check with my tech transfer and let you know. Right now I'm looking for published ones, we can't be the only ones who needed to. | |
| Mar 21, 2014 at 17:04 | comment | added | ericmjl | Ah! I misunderstood, my apologies. Would you be kind enough to share that code? | |
| Mar 21, 2014 at 17:03 | comment | added | Atl LED | @ericmjl I was going to show some examples of short scripts used to call KEGG Draw, which is what I thought you would want. If they're in IUPAC, I don't know a good way to get it graphics. Have you asked them if they will give it to you in KEGG? Might be easy on the source side, or parsing then converting might be your only option. | |
| Mar 21, 2014 at 14:35 | comment | added | ericmjl | Update: I tried KEGG Draw, but it doesn't accept glycan IUPAC names. | |
| Mar 21, 2014 at 4:48 | comment | added | ericmjl | Upvote because your answer was helpful, though I still couldn't figure out an answer to my problem. To clarify, I wanted to take a list of glycans, written in the IUPAC condensed nomenclature, and return an image for each glycan. Here, each image would be the "graph" representation (nodes + edges). I will update my original question to clarify that; in the meantime, do you know of any tool to do this? Thanks in advance! | |
| Mar 20, 2014 at 19:09 | history | answered | Atl LED | CC BY-SA 3.0 |