Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

problem in GenBankWriter with Definition #615

Closed
bneron opened this issue Sep 18, 2015 · 1 comment
Closed

problem in GenBankWriter with Definition #615

bneron opened this issue Sep 18, 2015 · 1 comment

Comments

@bneron
Copy link
Contributor

bneron commented Sep 18, 2015

There is a problem in the GenBankWriter.
Some sequence write using SeqIO.write in 'genbank'
format are not recognize by sequence format detector tool.
The problem come from the DEFINITION field, it must ends with a period

ftp://ftp.ncbi.nih.gov/genbank/gbrel.txt

[...]
3.4.5 DEFINITION Format

The DEFINITION record gives a brief description of the sequence,
proceeding from general to specific. It starts with the common name of
the source organism, then gives the criteria by which this sequence is
distinguished from the remainder of the source genome, such as the
gene name and what it codes for, or the protein name and mRNA, or some
description of the sequence's function (if the sequence is
non-coding). If the sequence has a coding region, the description may
be followed by a completeness qualifier, such as cds (complete coding
sequence). There is no limit on the number of lines that may be part
of the DEFINITION. The last line must end with a period.
[...]

when I convert a fasta file in genbank format see use case
(https://gist.github.com/bneron/884b30a0a00f330c6eeb)
the definition does not ends with a period which induce trouble on some
sequence format detector. I propose to patch GenBankWriter to ensure that
DEFINITION field ends with a period. Thus it will follow strictly the GenBank specifications.

bneron added a commit to bneron/biopython that referenced this issue Sep 18, 2015
biopython#615
ensure that the filed DEFINITION ends with a period as in Genbank
format specifications.
@bneron bneron mentioned this issue Sep 18, 2015
peterjc pushed a commit to peterjc/biopython that referenced this issue Feb 1, 2016
biopython#615
ensure that the filed DEFINITION ends with a period as in Genbank
format specifications.
peterjc added a commit to peterjc/biopython that referenced this issue Feb 1, 2016
peterjc added a commit to peterjc/biopython that referenced this issue Feb 1, 2016
peterjc pushed a commit to peterjc/biopython that referenced this issue Aug 29, 2016
biopython#615
ensure that the filed DEFINITION ends with a period as in Genbank
format specifications.
peterjc added a commit to peterjc/biopython that referenced this issue Aug 29, 2016
peterjc added a commit to peterjc/biopython that referenced this issue Aug 29, 2016
@peterjc
Copy link
Member

peterjc commented Aug 29, 2016

Fixed by 3231fa0 from pull request #616

@peterjc peterjc closed this as completed Aug 29, 2016
MarkusPiotrowski pushed a commit to MarkusPiotrowski/biopython that referenced this issue Oct 31, 2017
biopython#615
ensure that the filed DEFINITION ends with a period as in Genbank
format specifications.
MarkusPiotrowski pushed a commit to MarkusPiotrowski/biopython that referenced this issue Oct 31, 2017
MarkusPiotrowski pushed a commit to MarkusPiotrowski/biopython that referenced this issue Oct 31, 2017
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants