abutils - npm Package Compare versions

Comparing version 0.4.15 to 0.4.16

abutils.egg-info/PKG-INFO

 Metadata-Version: 2.1
 Name: abutils
-Version: 0.4.15
+Version: 0.4.16
 Summary: Utilities for analysis of adaptive immune receptor repertoire (AIRR) data
@@ -5,0 +5,0 @@ Home-page: https://github.com/briney/abutils

abutils/core/sequence.py

@@ -1027,1 +1027,44 @@ #!/usr/bin/env python
     return fastq_file
+
+
+def to_csv(
+    sequences: Iterable[Sequence],
+    csv_file: str,
+    sep: str = ",",
+    header: bool = True,
+    columns: Optional[Iterable] = None,
+    index: bool = False,
+) -> None:
+    """
+    Saves a list of ``Sequence`` objects to a CSV file.
+
+    Parameters
+    ----------
+    sequences : Iterable[Sequence]
+        List of ``Sequence`` objects to be saved to a CSV file. Required.
+
+    csv_file : str
+        Path to the output CSV file. Required.
+
+    sep : str, default=","
+        Column delimiter. Default is ``","``.
+
+    header : bool, default=True
+        If ``True``, the CSV file will contain a header row. Default is ``True``.
+
+    columns : list, default=None
+        A list of fields to be retained in the output CSV file. Fields must be column
+        names in the input file.
+
+    index : bool, default=False
+        If ``True``, the CSV file will contain an index column. Default is ``False``.
+
+    """
+    d = []
+    for s in sequences:
+        if not s.annotations:
+            d.append({"sequence_id": s.id, "sequence": s.sequence})
+        else:
+            d.append(s.annotations)
+    df = pd.DataFrame(d)
+    df.to_csv(csv_file, sep=sep, index=index, columns=columns, header=header)

abutils/io.py

@@ -28,12 +28,12 @@ #!/usr/bin/env python
 from .core.sequence import (
+    from_mongodb,
+    read_airr,
     read_csv,
-    read_airr,
     read_fasta,
     read_fastq,
     read_json,
-    from_mongodb,
+    to_csv,
     to_fasta,
     to_fastq,
 )
-
 from .utils.convert import abi_to_fasta
@@ -67,3 +67,3 @@ from .utils.pipeline import list_files, make_dir
     sep (str): character used to separate fields in ``'tabular'`` input files. This option is
-        only used when ``format`` is ``'tabular'``. Default is ``'\t'``, which conforms with the 
+        only used when ``format`` is ``'tabular'``. Default is ``'\t'``, which conforms with the
         default format for AIRR-compatible sequence annotation.
@@ -79,6 +79,6 @@
 
-    mongodb_kwargs (dict): dictionary containing additional keyword arguments that will be passed to 
+    mongodb_kwargs (dict): dictionary containing additional keyword arguments that will be passed to
         ``abutils.io.from_mongodb``.
-    
 
+
     Returns:
@@ -118,2 +118,1 @@ --------
         raise ValueError(error)
-

abutils/version.py

@@ -6,2 +6,2 @@ # Store the version here so:
 
-__version__ = "0.4.15"
+__version__ = "0.4.16"

PKG-INFO

 Metadata-Version: 2.1
 Name: abutils
-Version: 0.4.15
+Version: 0.4.16
 Summary: Utilities for analysis of adaptive immune receptor repertoire (AIRR) data
@@ -5,0 +5,0 @@ Home-page: https://github.com/briney/abutils

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