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problem in GenBankWriter with Definition #615
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bneron
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biopython#615 ensure that the filed DEFINITION ends with a period as in Genbank format specifications.
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peterjc
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biopython#615 ensure that the filed DEFINITION ends with a period as in Genbank format specifications.
peterjc
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peterjc
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Closes GitHub biopython#615.
peterjc
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biopython#615 ensure that the filed DEFINITION ends with a period as in Genbank format specifications.
peterjc
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peterjc
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Closes GitHub biopython#615.
MarkusPiotrowski
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biopython#615 ensure that the filed DEFINITION ends with a period as in Genbank format specifications.
MarkusPiotrowski
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MarkusPiotrowski
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Closes GitHub biopython#615.
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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.
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