Merge pull request #102 from sbslee/0.21.0-dev

0.21.0 dev

Author: sbslee

CHANGELOG.rst

@@ -1,6 +1,14 @@
 Changelog
 *********
 
+0.21.0 (2023-08-25)
+-------------------
+
+* :issue:`96`: Fix bug in :command:`compute-copy-number` command where it threw an error "Different sample sets found" when the sample name consists of only numbers with one or more leading zeros.
+* :issue:`97`: Fix bug in IFNL3 genotyping where certain variants were not considered because they were located outside of the target region.
+* :issue:`99`: Refresh the CPIC table for :meth:`api.core.load_cpic_table` method. The table's latest update was on February 6, 2022.
+* :issue:`63`: Fix bug in :meth:`api.utils.estimate_phase_beagle` method where Beagle throws an error "Window has only one position" even when multiple overlapping variants exist.
+
 0.20.0 (2023-01-12)
 -------------------
 

docs/genes.rst

@@ -413,8 +413,8 @@ Below is a summary table:
      -
      -
      - Other
-     - `chr19:39731245-39738646 <https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr19%3A39731245%2D39738646&hgsid=1251392659_FCwuNEZja7PPePnsIvfT1wF8Ke9Y>`__
-     - `chr19:39240552-39248006 <https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr19%3A39240552%2D39248006&hgsid=1251392659_FCwuNEZja7PPePnsIvfT1wF8Ke9Y>`__
+     - `chr19:39731245-39744165 <https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr19%3A39731245%2D39744165&hgsid=1251392659_FCwuNEZja7PPePnsIvfT1wF8Ke9Y>`__
+     - `chr19:39240552-39253525 <https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr19%3A39240552%2D39253525&hgsid=1251392659_FCwuNEZja7PPePnsIvfT1wF8Ke9Y>`__
      -
    * - NAT1
      - ✅

pypgx/api/core.py

@@ -1138,6 +1138,10 @@ def load_cpic_table():
     """
     Load the CPIC table.
 
+    The copy of the CPIC table in PyPGx is current as of August 19, 2023. To 
+    obtain the latest CPIC table, you can visit the Genes-Drugs page on the 
+    CPIC website.
+
     Returns
     -------
     pandas.DataFrame
@@ -1149,12 +1153,12 @@ def load_cpic_table():
     >>> import pypgx
     >>> df = pypgx.load_cpic_table()
     >>> df.head()
-          Gene           Drug                                          Guideline CPICLevel CPICLevelStatus PharmGKBLevel             FDALabel               PMID
-    0    HLA-B       abacavir  https://cpicpgx.org/guidelines/guideline-for-a...         A           Final            1A     Testing required  24561393;22378157
-    1    HLA-B    allopurinol  https://cpicpgx.org/guidelines/guideline-for-a...         A           Final            1A  Testing recommended  23232549;26094938
-    2  MT-RNR1       amikacin  https://cpicpgx.org/guidelines/cpic-guideline-...         A           Final             3                  NaN           34032273
-    3  CYP2C19  amitriptyline  https://cpicpgx.org/guidelines/guideline-for-t...         A           Final            1A                  NaN  23486447;27997040
-    4   CYP2D6  amitriptyline  https://cpicpgx.org/guidelines/guideline-for-t...         A           Final            1A       Actionable PGx  23486447;27997040
+        Gene           Drug    RxNorm                                 ATC                                          Guideline CPICLevel CPICLevelStatus PharmGKBLevel             FDALabel               PMID
+    0    HLA-B       abacavir  190521.0  J05AF06, J05AR02, J05AR13, J05AR04  https://cpicpgx.org/guidelines/guideline-for-a...         A           Final            1A     Testing required  24561393;22378157
+    1    HLA-B    allopurinol     519.0                    M04AA01, M04AA51  https://cpicpgx.org/guidelines/guideline-for-a...         A           Final            1A  Testing recommended  23232549;26094938
+    2  MT-RNR1       amikacin     641.0           D06AX12, J01GB06, S01AA21  https://cpicpgx.org/guidelines/cpic-guideline-...         A           Final            1A                  NaN           34032273
+    3  CYP2C19  amitriptyline     704.0                    N06AA09, N06CA01  https://cpicpgx.org/guidelines/guideline-for-t...         A           Final            1A                  NaN  23486447;27997040
+    4   CYP2D6  amitriptyline     704.0                    N06AA09, N06CA01  https://cpicpgx.org/guidelines/guideline-for-t...         A           Final            1A       Actionable PGx  23486447;27997040
     """
     b = BytesIO(pkgutil.get_data(__name__, 'data/cpic-table.csv'))
     return pd.read_csv(b)