Rename profiles consistently to new db version

biobakery · Apr 2, 2024 · fea9440 · fea9440
1 parent baa6606
commit fea9440
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Showing 2 changed files with 2 additions and 5 deletions.
diff --git a/metaphlan/utils/fix_relab_mpa4.py b/metaphlan/utils/fix_relab_mpa4.py
@@ -61,7 +61,7 @@ def fix_relab_mpa4(input, output):
             for line in rf:
                 if line.startswith('#mpa_v'):
                     release = line.strip()[1:]
-                    wf.write('{}_fixed\n'.format(line.strip()))
+                    wf.write('{}_202403\n'.format(line.strip()))
                 elif line.startswith('#') or line.startswith('UNCLASSIFIED'):
                     wf.write(line)
                 else:

diff --git a/metaphlan/utils/oct22_fix_tax.tsv b/metaphlan/utils/oct22_fix_tax.tsv
@@ -2120,12 +2120,9 @@ k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g
 k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella_copri_clade_B|t__SGB1613	k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella_copri_clade_B|t__SGB1613	2|976|200643|171549|171552|838|165179|
 k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella_copri_clade_C|t__SGB1644	k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella_copri_clade_C|t__SGB1644	2|976|200643|171549|171552|838|165179|
 k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella_copri_clade_D|t__SGB1636	k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella_copri_clade_D|t__SGB1636	2|976|200643|171549|171552|838|165179|
-k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella_clade_D|t__SGB1635	k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella_clade_D|t__SGB1635	2|976|200643|171549|171552|838|165179|
-k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella_hominis|t__SGB1617	k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella_hominis|t__SGB1617	2|976|200643|171549|171552|838|2518605|
-k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella_hominis|t__SGB1615	k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella_hominis|t__SGB1615	2|976|200643|171549|171552|838|2518605|
 k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Catenibacterium|s__Candidatus_Catenibacterium_tridentinum|t__SGB6783	k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Catenibacterium|s__Candidatus_Catenibacterium_tridentinum|t__SGB6783	2|1239|526524|526525|128827|135858|2292991|
 k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Clostridiales_unclassified|g__Lawsonibacter|s__Lawsonibacter_asaccharolyticus|t__SGB15154	k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Clostridiales_unclassified|g__Lawsonibacter|s__Lawsonibacter_asaccharolyticus|t__SGB15154	2|1239|186801|186802||2172004|2108523|
-k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Ruminococcaceae|g__Candidatus_Cibionibacter|s__Candidatus_Cibionibacter_quicibialis|t__SGB15286	k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Ruminococcaceae|g__Candidatus_Cibionibacter|s__Candidatus_Cibionibacter_quicibialis|t__SGB15286	2|976|200643|171549|171550|2527773|2500537|
+k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Ruminococcaceae|g__Candidatus_Cibionibacter|s__Candidatus_Cibionibacter_quicibialis|t__SGB15286	k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Ruminococcaceae|g__Candidatus_Cibionibacter|s__Candidatus_Cibionibacter_quicibialis|t__SGB15286	2|1239|186801|186802|541000|2527773|2500537|
 k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella_copri_clade_M|t__SGB20113	k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella_copri_clade_M|t__SGB20113	2|976|200643|171549|171552|838|165179|
 k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella_copri_clade_I|t__SGB1623	k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella_copri_clade_I|t__SGB1623	2|976|200643|171549|171552|838|165179|
 k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella_copri_clade_J|t__SGB20123	k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella_copri_clade_J|t__SGB20123	2|976|200643|171549|171552|838|165179|