Forum: [META] Noticed an issue with code markup and open parentheses (
1
gravatar for jrj.healey
10 months ago by
jrj.healey2.9k
United Kingdom
jrj.healey2.9k wrote:

I'm fairly new to the forum (actively participating that is!) but I've noticed in 2 or 3 threads so far that some elements of code syntax don't seem to be being marked up properly.

For example in my answer in the following thread, this code fails to show the ( between open and rec.id - despite the fact it is there in the raw post content. I copy and pasted the code directly too so it's not an error in copying over.

C: Splitting and Extracting Features in fasta format from Genbank Files using Biopy

# splitgenbank.py

from Bio import SeqIO
import sys

for rec in SeqIO.parse(sys.argv[1], "genbank"):
    SeqIO.write([rec], openrec.id + ".gbk", "w"), "genbank")
                           ^
                        Bracket
                      disappearing

Similarly, I cant see tpaisie91's raw content, but in the code in their question in this thread: A: Fixing a biopython script

the print and gb_record.name should have an ( . Their code works (just doesn't output exactly what they wanted) so I think I can reasonably safely assume it's a markup error. And the exact same thing occurs with that string pattern in my answer, which, again, was a direct cut and paste of working code.

Is this a known problem?

markup code forum meta • 345 views
ADD COMMENTlink modified 10 months ago by Ram12k • written 10 months ago by jrj.healey2.9k
1

Tagging Istvan Albert

ADD REPLYlink written 10 months ago by WouterDeCoster23k
1

That is one weird error for sure. The original raw content does contain an extra parenthesis that disappears here.

I will investigate. I'll open a github issue for it:

https://github.com/ialbert/biostar-central/issues/421

ADD REPLYlink written 10 months ago by Istvan Albert ♦♦ 74k
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