Nilesh Patra pushed to branch upstream at Debian Med / python-nanomath
Commits: 461e5d26 by Nilesh Patra at 2021-05-16T18:56:01+05:30 New upstream version 1.2.1+ds - - - - - 4 changed files: - PKG-INFO - nanomath.egg-info/PKG-INFO - nanomath/nanomath.py - nanomath/version.py Changes: ===================================== PKG-INFO ===================================== @@ -1,6 +1,6 @@ Metadata-Version: 1.2 Name: nanomath -Version: 1.2.0 +Version: 1.2.1 Summary: A few simple math function for other Oxford Nanopore processing scripts Home-page: https://github.com/wdecoster/nanomath Author: Wouter De Coster ===================================== nanomath.egg-info/PKG-INFO ===================================== @@ -1,6 +1,6 @@ Metadata-Version: 1.2 Name: nanomath -Version: 1.2.0 +Version: 1.2.1 Summary: A few simple math function for other Oxford Nanopore processing scripts Home-page: https://github.com/wdecoster/nanomath Author: Wouter De Coster ===================================== nanomath/nanomath.py ===================================== @@ -53,6 +53,11 @@ class Stats(object): col="quals", values=["quals", "lengths"]) self._reads_above_qual = [reads_above_qual(df, q) for q in self._qualgroups] + else: + self._top5_lengths = get_top_5(df=df, + col="lengths", + values=["lengths"], + fill='quals') def long_features_as_string(self): """formatting long features to a string to print for legacy stats output""" @@ -95,12 +100,16 @@ class Stats(object): def unwind_long_features_top5(self, feature, name): """for tsv stats output""" + if feature not in self.__dict__: + return for entry, label in zip(self.__dict__[feature], range(1, 6)): self.__dict__[name + ':' + str(label)] = '{} ({})'.format(round(entry[0], ndigits=1), round(entry[1], ndigits=1)) def unwind_long_features_above_qual(self, feature, name): """for tsv stats output""" + if feature not in self.__dict__: + return for entry, label in zip(self.__dict__[feature], ['>Q{}:'.format(q) for q in self._qualgroups]): numberAboveQ, megAboveQ = entry @@ -148,13 +157,20 @@ def ave_qual(quals, qround=False, tab=errs_tab(128)): return None -def get_top_5(df, col, values): +def get_top_5(df, col, values, fill=False): if "readIDs" in df: values.append("readIDs") - return df.sort_values(col, ascending=False) \ - .head(5)[values] \ - .reset_index(drop=True) \ - .itertuples(index=False, name=None) + if fill: + return df.sort_values(col, ascending=False) \ + .head(5)[values] \ + .assign(fill=[0]*5) \ + .reset_index(drop=True) \ + .itertuples(index=False, name=None) + else: + return df.sort_values(col, ascending=False) \ + .head(5)[values] \ + .reset_index(drop=True) \ + .itertuples(index=False, name=None) def reads_above_qual(df, qual): ===================================== nanomath/version.py ===================================== @@ -1 +1 @@ -__version__ = "1.2.0" +__version__ = "1.2.1" View it on GitLab: https://salsa.debian.org/med-team/python-nanomath/-/commit/461e5d26467062fbb1c665e294418b4ec57eea30 -- View it on GitLab: https://salsa.debian.org/med-team/python-nanomath/-/commit/461e5d26467062fbb1c665e294418b4ec57eea30 You're receiving this email because of your account on salsa.debian.org.
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