SEA-PHAGES | DNA Master Note Parsing Bugs

Link to this post \| posted 05 Jul, 2017 22:15
ClaireRinehart	Lee Hughes and his students pointed out that when quotes were entered into the notes section of PECAAN and then the data was exported to DNA Master that the text imported into the Notes field in DNA Master were truncated at the first quote. Therefore, putting 5' or 3' designations into the notes would cause truncations. We tried additional testing and also found that when we put CR-LF (carriage return & line feed symbols) into the notes during our PECAAN GenBank format export that DNA Master also truncated the GenBank import at the first CR-LF. We tried importing PECAAN's GenBank export into Geneious and found no truncations with either the quotes or the CR-LF. This appears to be a DNA Master-specific quirk (or bug). We are therefore removing the CR-LF from the GenBank export and substituting ` for ' in all other exports from PECAAN.

Link to this post | posted 05 Jul, 2017 22:15

Lee Hughes and his students pointed out that when quotes were entered into the notes section of PECAAN and then the data was exported to DNA Master that the text imported into the Notes field in DNA Master were truncated at the first quote. Therefore, putting 5' or 3' designations into the notes would cause truncations. We tried additional testing and also found that when we put CR-LF (carriage return & line feed symbols) into the notes during our PECAAN GenBank format export that DNA Master also truncated the GenBank import at the first CR-LF. We tried importing PECAAN's GenBank export into Geneious and found no truncations with either the quotes or the CR-LF. This appears to be a DNA Master-specific quirk (or bug). We are therefore removing the CR-LF from the GenBank export and substituting ` for ' in all other exports from PECAAN.

Link to this post \| posted 28 Apr, 2019 16:13
jmclean2@sunyrockland.edu	I am having this issue importing full annotations of phage Dieselweasel to DNA Master from PECAAN. I have tried to replace all quotes as described in Claire's post, I have tried cutting and pasting the notes in pieces, I have tried creating several DNA Master files each containing chunks of the notes and merging them. Regardless of technique DNA Master will only paste in the first 33 genes into the documentation. Functions-only export from PECAAN to DNA master works just fine. Help? Thanks, Jeff

Link to this post | posted 28 Apr, 2019 16:13

jmclean2@sunyrockland.edu

I am having this issue importing full annotations of phage Dieselweasel to DNA Master from PECAAN. I have tried to replace all quotes as described in Claire's post, I have tried cutting and pasting the notes in pieces, I have tried creating several DNA Master files each containing chunks of the notes and merging them. Regardless of technique DNA Master will only paste in the first 33 genes into the documentation. Functions-only export from PECAAN to DNA master works just fine.
Help?
Thanks,
Jeff

Link to this post \| posted 28 Apr, 2019 17:52
jmclean2@sunyrockland.edu	Just tried with a different phage (Phaded) and all worked well with the export of full annotation from PECAAN to DNA Master, tried dieselweasel again and same truncation as before. i'm at a loss….any information greatly appreciated! Jeff

Link to this post \| posted 28 Apr, 2019 22:19
ClaireRinehart	Jeff, Sorry for the problems that you are experiencing. I downloaded the Dieselweasel.fasta file from Phagesdb and opened it in DNA Master. I then plasted in the Full Annotation export from PECAAN and Parsed it. It all went in up through gene 85. I have attached the DNA Master file. We have noticed that successfully pasting text into DNA Master and then Parsing is very dependant on the text editor that you use to copy and paste with. I use Textwrangler or BBedit because they are text only editors. No control codes are embedded. Certainly Word or even Apple's own TextEdit will slip control codes into the text, almost unseen, that will cause DNA Master to abort the Parsing. In the future, you might try another text editor. Thanks, Claire 63Kb

Link to this post | posted 28 Apr, 2019 22:19

ClaireRinehart

Jeff,
Sorry for the problems that you are experiencing.
I downloaded the Dieselweasel.fasta file from Phagesdb and opened it in DNA Master. I then plasted in the Full Annotation export from PECAAN and Parsed it. It all went in up through gene 85. I have attached the DNA Master file.

We have noticed that successfully pasting text into DNA Master and then Parsing is very dependant on the text editor that you use to copy and paste with. I use Textwrangler or BBedit because they are text only editors. No control codes are embedded. Certainly Word or even Apple's own TextEdit will slip control codes into the text, almost unseen, that will cause DNA Master to abort the Parsing. In the future, you might try another text editor.
Thanks,
Claire

Link to this post \| posted 06 May, 2019 20:54
jmclean2@sunyrockland.edu	This is all a tremendous help. Thank you very much for everything!! Jeff

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DNA Master Note Parsing Bugs