biopython/biopython

Deprecate record.database_letters, record.query_letters

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#1,000 opened on 2016年11月16日

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From Redminegood first issue

説明

From redmine XML Blast parser: miscellaneous bug fixes and cleanup Most of the cleanup, bug fixes were done. The last comment was:

We could perhaps deprecate record.database_letters immediately, and at a later point, record.query_letters

There is a TODO in the code regarding this.

@peterjc last comment

I've updated CVS as per comment 12 to also use record.query_length, and comment 13 to also use record.database_length.

Before:

from Bio.Blast import NCBIXML for record in NCBIXML.parse(open("xbt007.xml")) :

... print record.query_id ... print record.query_letters, record.query_length ... print record.num_letters_in_database, record.database_letters, record.database_length ... gi|585505|sp|Q08386|MOPB_RHOCA 270 None 13958303 None None gi|129628|sp|P07175.1|PARA_AGRTU 222 None 13958303 None None

Now, with Bio/Blast/NCBIXML.py CVS revision 1.20 or 1.21,

from Bio.Blast import NCBIXML for record in NCBIXML.parse(open("xbt007.xml")) :

... print record.query_id ... print record.query_letters, record.query_length ... print record.num_letters_in_database, record.database_letters, record.database_length ... gi|585505|sp|Q08386|MOPB_RHOCA 270 270 13958303 None 13958303 gi|129628|sp|P07175.1|PARA_AGRTU 222 222 13958303 None 13958303

We could perhaps deprecate record.database_letters immediately, and at a later point, record.query_letters

コントリビューターガイド

技術スタック
python
領域
backenddata
Issue 種別
refactor
難度新しい貢献者にとっての実装難度です。1 は非常に小さな変更、5 は専門的な作業です。
3
推定時間経験ある貢献者が調査、実装、テスト、pull request 準備にかけるおおよその時間範囲です。
half day
活動状況Issue が今どれだけ取り組みやすいかを示します。新しい、活発、古い、ブロック中、またはメンテナー入力待ちなどです。
stale
明確さ期待される変更、受け入れ条件、次の手順がどれだけ明確かを示します。
mostly clear
前提条件
Pythonbasic deprecation patterns
初心者向け度初回貢献者にどれだけ取り組みやすいかを 1-100 で推定したスコアです。
60
調査方針
Review the TODO at line 188 in Bio/Blast/NCBIXML.py. The issue is to add deprecation warnings for record.database letters and record.query letters, likely using Python's warnings module. Consult the earlier discussion in the linked redmine issue and the existing code changes for context. Implement the deprecation and ensure existing tests pass.