#200 :pep in cDNA file

[Valerie Wood]

I cant remember if this was done or not and my connection is too slow to access the file via ftp
but lat time I looked the cDNA file had :pep in the IDs (which were establised to come from chado)

ftp://ftp.ensemblgenomes.org/pub/fungi/current/fasta/schizosaccharomyces_pombe/cdna/

(If this makes no sense, assign to me and I'll figure out what it was meant to be when I get back)

val

[Kim Rutherford]

We were going to change the peptide IDs but as far as I know we haven't decided what to change them to.

I originally went with ":pep" (ie. ":<feature_type>" because that's what the Sanger PSU/PGG use and colon was a delimiter we weren't using elsewhere in the IDs. We also have colons in IDs like: "SPBP8B7.20c:allele-1" and "SPAC1556.06.1:exon:1" which I'm guessing will cause problems for the Ensembl code too one day.

(That exon ID is inconsistent. We should have used "-1", "-2" like the allele IDs: "SPAC1556.06.1:exon-1")

If we need to change, I suggest changing to ".pep", "-pep" or "/pep". The first has the disadvantage that we'll be overloading "." even more. The second would also be a overloading in the allele case. The third has the disadvantage that it looks weird (no offence meant to FlyBase).

The "." is overloaded in that we use it within gene identifiers ("SPBP8B7.20c") and we use it for the transcripts IDs ("SPAC1556.06.1" vs "SPAC1556.06.2").

If we use ".pep" we'll end up with "SPAC1556.06.1.pep" and "SPAC1556.06.1.exon-1" which looks a bit like we couldn't found any other keys on the keyboard.

While we're on the subject, I think I originally suggested using "-" for the transcript case (eg. ""SPAC1556.06-1"), but for some reason we couldn't do that.

[Valerie Wood]

I don't have a big problem with :pep (although we should think about if
this is the best way to do this, I think it is probably fine but we
should chat about the details - vs . vs : etc).

I was wondering why the cDNA file referred to :pep ids at all as these
are cDNA not proteins?

val

On 04/07/2013 23:15, Kim Rutherford wrote:

We were going to change the peptide IDs but as far as I know we
haven't decided what to change them to.

I originally went with ":pep" (ie. ":" because that's what the Sanger
PSU/PGG use and colon was a delimiter we weren't using elsewhere in
the IDs. We also have colons in IDs like: "SPBP8B7.20c:allele-1" and
"SPAC1556.06.1:exon:1" which I'm guessing will cause problems for the
Ensembl code too one day.

(That exon ID is inconsistent. We should have used "-1", "-2" like the
allele IDs: "SPAC1556.06.1:exon-1")

If we need to change, I suggest changing to ".pep", "-pep" or "/pep".
The first has the disadvantage that we'll be overloading "." even
more. The second would also be a overloading in the allele case. The
third has the disadvantage that it looks weird (no offence meant to
FlyBase).

The "." is overloaded in that we use it within gene identifiers
("SPBP8B7.20c") and we use it for the transcripts IDs ("SPAC1556.06.1"
vs "SPAC1556.06.2").

If we use ".pep" we'll end up with "SPAC1556.06.1.pep" and
"SPAC1556.06.1.exon-1" which looks a bit like we couldn't found any
other keys on the keyboard.

While we're on the subject, I think I originally suggested using "-"
for the transcript case (eg. ""SPAC1556.06-1"), but for some reason we
couldn't do that.

---

[chado:#200] http://sourceforge.net/p/pombase/chado/200/ :pep in
cDNA file

Status: open
Created: Thu Jul 04, 2013 12:17 PM UTC by Valerie Wood
Last Updated: Thu Jul 04, 2013 12:17 PM UTC
Owner: nobody

I cant remember if this was done or not and my connection is too slow
to access the file via ftp
but lat time I looked the cDNA file had :pep in the IDs (which were
establised to come from chado)

ftp://ftp.ensemblgenomes.org/pub/fungi/current/fasta/schizosaccharomyces_pombe/cdna/

(If this makes no sense, assign to me and I'll figure out what it was
meant to be when I get back)

val

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[Kim Rutherford]

I was wondering why the cDNA file referred to :pep ids at all as these
are cDNA not proteins?

I don't know. I'm assigning this to Mark to investigate.