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Commit 3fbb71e9 authored by Blaise Li's avatar Blaise Li
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Allow custom info columns in counts table.

parent 4f5b9211
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...@@ -280,16 +280,18 @@ might be excluded. ...@@ -280,16 +280,18 @@ might be excluded.
def make_counts_only( def make_counts_only(
counts_table, counts_table,
seq_id_kw="locus_tag", alt_tag_kw="old_locus_tag"): seq_id_kw="locus_tag", alt_tag_kw="old_locus_tag",
ref_info_cols=None):
""" """
Integrate "informative" columns of *counts_table* into the index. Integrate "informative" columns of *counts_table* into the index.
""" """
# To ensure a stable order: # To ensure a stable order:
ref_info_cols = [ if ref_info_cols is None:
alt_tag_kw, seq_id_kw, ref_info_cols = [
"start", "end", "length", alt_tag_kw, seq_id_kw,
"start_codon", "expected_start_aa", "start", "end", "length",
"first_stop", "nb_stops", "start_upstream", "end_downstream"] "start_codon", "expected_start_aa",
"first_stop", "nb_stops", "start_upstream", "end_downstream"]
# To ensure no info columns are lost: # To ensure no info columns are lost:
info_cols = [ info_cols = [
counts_table.index.name, counts_table.index.name,
......
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