From 8d360b0facbbef87d8faafb797fd34a5db65a472 Mon Sep 17 00:00:00 2001 From: Celine Mercier Date: Fri, 19 Aug 2016 17:49:22 +0200 Subject: [PATCH] Minor improvements to obi export command --- python/obitools3/commands/export.pyx | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/python/obitools3/commands/export.pyx b/python/obitools3/commands/export.pyx index 50f1c9f..d64450c 100644 --- a/python/obitools3/commands/export.pyx +++ b/python/obitools3/commands/export.pyx @@ -48,6 +48,8 @@ def run(config): DEFINITION_COLUMN = "DEFINITION" QUALITY_COLUMN = "QUALITY" + special_columns = [NUC_SEQUENCE_COLUMN, ID_COLUMN, DEFINITION_COLUMN, QUALITY_COLUMN] + # Open DMS d = OBIDMS(config['obi']['defaultdms']) @@ -64,7 +66,7 @@ def run(config): toprint = ">"+seq.get_id()+" " for col_name in seq : - if col_name != NUC_SEQUENCE_COLUMN and col_name != ID_COLUMN and col_name != DEFINITION_COLUMN and col_name != QUALITY_COLUMN : + if col_name not in special_columns : toprint = toprint + col_name + "=" + str(seq[col_name]) + "; " if DEFINITION_COLUMN in seq :