seer-pas-sdk 0.1.2__py3-none-any.whl → 0.1.3__py3-none-any.whl

seer_pas_sdk/objects/__init__.py

@@ -1,129 +1 @@
-import pandas as pd
-
-
-class PlateMap:
-    """
-    Plate map object containing information about samples and corresponding MS data files.
-    """
-
-    def __init__(
-        self,
-        ms_file_name=None,
-        sample_name=None,
-        sample_id=None,
-        well_location=None,
-        nanoparticle=None,
-        nanoparticle_id=None,
-        control=None,
-        control_id=None,
-        instrument_name=None,
-        date_sample_preparation=None,
-        sample_volume=None,
-        peptide_concentration=None,
-        peptide_mass_sample=None,
-        dilution_factor=None,
-        kit_id=None,
-        plate_id=None,
-        plate_name=None,
-    ):
-
-        if not ms_file_name:
-            raise ValueError("MS file name(s) must be provided.")
-
-        self.ms_file_name = ms_file_name
-        self.length = len(ms_file_name)
-
-        self.sample_name = sample_name
-        self.sample_id = sample_id
-        self.well_location = well_location
-        self.nanoparticle = nanoparticle
-        self.nanoparticle_id = nanoparticle_id
-        self.control = control
-        self.control_id = control_id
-        self.instrument_name = instrument_name
-        self.date_sample_preparation = date_sample_preparation
-        self.sample_volume = sample_volume
-        self.peptide_concentration = peptide_concentration
-        self.peptide_mass_sample = peptide_mass_sample
-        self.dilution_factor = dilution_factor
-        self.kit_id = kit_id
-        self.plate_id = plate_id
-        self.plate_name = plate_name
-
-        self.__cols = [
-            "MS file name",
-            "Sample name",
-            "Sample ID",
-            "Well location",
-            "Nanoparticle",
-            "Nanoparticle ID",
-            "Control",
-            "Control ID",
-            "Instrument name",
-            "Date sample preparation",
-            "Sample volume",
-            "Peptide concentration",
-            "Peptide mass sample",
-            "Dilution factor",
-            "Kit ID",
-            "Plate ID",
-            "Plate Name",
-        ]
-
-        self.__attrs = [
-            "ms_file_name",
-            "sample_name",
-            "sample_id",
-            "well_location",
-            "nanoparticle",
-            "nanoparticle_id",
-            "control",
-            "control_id",
-            "instrument_name",
-            "date_sample_preparation",
-            "sample_volume",
-            "peptide_concentration",
-            "peptide_mass_sample",
-            "dilution_factor",
-            "kit_id",
-            "plate_id",
-            "plate_name",
-        ]
-
-        for attr in self.__attrs:
-            if not getattr(self, attr):
-                # Replace falsey values with empty lists
-                setattr(self, attr, [])
-
-            attr_len = len(getattr(self, attr))
-
-            if attr_len > self.length:
-                raise ValueError(
-                    "Parameter lengths must not exceed the number of MS files."
-                )
-
-            elif attr_len < self.length:
-                for i in range(self.length - attr_len):
-                    getattr(self, attr).append(None)
-
-    def to_dict(self):
-        res = {}
-
-        for i in range(len(self.__attrs)):
-            res[self.__cols[i]] = getattr(self, self.__attrs[i])
-
-        for entry in res:
-            res[entry] = {i: res[entry][i] for i in range(len(res[entry]))}
-
-        return res
-
-    def to_df(self):
-        return pd.DataFrame(self.to_dict())
-
-    def to_csv(self, path=None):
-        if not path:
-            return self.to_df().to_csv(index=False)
-        return self.to_df().to_csv(path_or_buf=path, index=False)
-
-    def __repr__(self):
-        return str(self.to_dict())
+from .platemap import PlateMap

seer_pas_sdk/objects/platemap.py

@@ -0,0 +1,129 @@
+import pandas as pd
+
+
+class PlateMap:
+    """
+    Plate map object containing information about samples and corresponding MS data files.
+    """
+
+    def __init__(
+        self,
+        ms_file_name=None,
+        sample_name=None,
+        sample_id=None,
+        well_location=None,
+        nanoparticle=None,
+        nanoparticle_id=None,
+        control=None,
+        control_id=None,
+        instrument_name=None,
+        date_sample_preparation=None,
+        sample_volume=None,
+        peptide_concentration=None,
+        peptide_mass_sample=None,
+        dilution_factor=None,
+        kit_id=None,
+        plate_id=None,
+        plate_name=None,
+    ):
+
+        if not ms_file_name:
+            raise ValueError("MS file name(s) must be provided.")
+
+        self.ms_file_name = ms_file_name
+        self.length = len(ms_file_name)
+
+        self.sample_name = sample_name
+        self.sample_id = sample_id
+        self.well_location = well_location
+        self.nanoparticle = nanoparticle
+        self.nanoparticle_id = nanoparticle_id
+        self.control = control
+        self.control_id = control_id
+        self.instrument_name = instrument_name
+        self.date_sample_preparation = date_sample_preparation
+        self.sample_volume = sample_volume
+        self.peptide_concentration = peptide_concentration
+        self.peptide_mass_sample = peptide_mass_sample
+        self.dilution_factor = dilution_factor
+        self.kit_id = kit_id
+        self.plate_id = plate_id
+        self.plate_name = plate_name
+
+        self.__cols = [
+            "MS file name",
+            "Sample name",
+            "Sample ID",
+            "Well location",
+            "Nanoparticle",
+            "Nanoparticle ID",
+            "Control",
+            "Control ID",
+            "Instrument name",
+            "Date sample preparation",
+            "Sample volume",
+            "Peptide concentration",
+            "Peptide mass sample",
+            "Dilution factor",
+            "Kit ID",
+            "Plate ID",
+            "Plate Name",
+        ]
+
+        self.__attrs = [
+            "ms_file_name",
+            "sample_name",
+            "sample_id",
+            "well_location",
+            "nanoparticle",
+            "nanoparticle_id",
+            "control",
+            "control_id",
+            "instrument_name",
+            "date_sample_preparation",
+            "sample_volume",
+            "peptide_concentration",
+            "peptide_mass_sample",
+            "dilution_factor",
+            "kit_id",
+            "plate_id",
+            "plate_name",
+        ]
+
+        for attr in self.__attrs:
+            if not getattr(self, attr):
+                # Replace falsey values with empty lists
+                setattr(self, attr, [])
+
+            attr_len = len(getattr(self, attr))
+
+            if attr_len > self.length:
+                raise ValueError(
+                    "Parameter lengths must not exceed the number of MS files."
+                )
+
+            elif attr_len < self.length:
+                for i in range(self.length - attr_len):
+                    getattr(self, attr).append(None)
+
+    def to_dict(self):
+        res = {}
+
+        for i in range(len(self.__attrs)):
+            res[self.__cols[i]] = getattr(self, self.__attrs[i])
+
+        for entry in res:
+            res[entry] = {i: res[entry][i] for i in range(len(res[entry]))}
+
+        return res
+
+    def to_df(self):
+        return pd.DataFrame(self.to_dict())
+
+    def to_csv(self, path=None):
+        if not path:
+            return self.to_df().to_csv(index=False)
+        return self.to_df().to_csv(path_or_buf=path, index=False)
+
+    def __repr__(self):
+        return str(self.to_dict())

{seer_pas_sdk-0.1.2.dist-info → seer_pas_sdk-0.1.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: seer-pas-sdk
-Version: 0.1.2
+Version: 0.1.3
 Summary: SDK for Seer Proteograph Analysis Suite (PAS)
 Home-page: https://github.com/seerbio/seer-pas-sdk
 Author: Agam Jolly
@@ -45,6 +45,6 @@ from seer_pas_sdk import SeerSDK
 sdk = SeerSDK(USERNAME, PASSWORD)
 ```
 
-You can then use the SDK's functions to create, query, or retrieve projects, plates, samples, and analyses.
+You can then use the SDK's methods to create, query, or retrieve projects, plates, samples, and analyses.
 
 For complete documentation of this SDK, visit [https://seerbio.github.io/seer-pas-sdk/](https://seerbio.github.io/seer-pas-sdk/ "Documentation").

seer_pas_sdk-0.1.3.dist-info/RECORD

@@ -0,0 +1,19 @@
+seer_pas_sdk/__init__.py,sha256=Ie6atdmdBV-OmdHHXjhrGhdFGXiyP3JKhKrr3hyvSsA,563
+seer_pas_sdk/auth/__init__.py,sha256=e_eM4jJnnyKUdg4Nggzi9ypt2MLWcEJ8CmCPkUaQDSs,23
+seer_pas_sdk/auth/auth.py,sha256=DZcbkYel11GvIn-iiutt9UOVfj9URZ_f89QMHhyGfRg,2277
+seer_pas_sdk/common/__init__.py,sha256=QnBup2dT6okt62Yjdhik4DmLf36Ozgv6KybdvFAULaA,12260
+seer_pas_sdk/core/__init__.py,sha256=rxbKgg-Qe24OaxX2zyHHYPYgDCTEKE_-41bB2wvpvL4,25
+seer_pas_sdk/core/sdk.py,sha256=IlTFn09nZ21iHffh502qAvKUhWcO_bcR6c9723AJckw,45291
+seer_pas_sdk/objects/__init__.py,sha256=ljq6G4yeE3GoefDPqEYx1tLrDuD_9H_7_hedo6-OAuk,31
+seer_pas_sdk/objects/platemap.py,sha256=DosquJu2-XvDjVj4JFKoXa0DBVS8OroYCDeS5Np4U8Q,3693
+tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+tests/conftest.py,sha256=nu5Qu8CHwgJEwFpLQ0iX8e5csz4HGIC2oe50AdkA2Ms,317
+tests/test_auth.py,sha256=np4XXbEzoSFf-zXKaZQFL4Ry1ehMtjbXtHG3J6D-zzc,933
+tests/test_common.py,sha256=3VgHPbeLVJCh8V0kBGMvkhTKMd6sN_eLJF3AgvbyH0I,3433
+tests/test_objects.py,sha256=BcQtE8CbGUAnFlbkwsaJalUV6D8WbdwN2aWiQddh3k4,2521
+tests/test_sdk.py,sha256=ZNfsRAe_YHIXfteVugfkcds_lmYb0emIfDbJz7jpqR4,239
+seer_pas_sdk-0.1.3.dist-info/LICENSE.txt,sha256=DVQuDIgE45qn836wDaWnYhSdxoLXgpRRKH4RuTjpRZQ,10174
+seer_pas_sdk-0.1.3.dist-info/METADATA,sha256=3OrGnwgKw2ECRB-LTulbhxFAlbVw7ialPFQdfR39ddg,1714
+seer_pas_sdk-0.1.3.dist-info/WHEEL,sha256=Mdi9PDNwEZptOjTlUcAth7XJDFtKrHYaQMPulZeBCiQ,91
+seer_pas_sdk-0.1.3.dist-info/top_level.txt,sha256=gMffZ5LfTF87Sr-oiyl-rtY6omfBslYCA2S4DM7YNC8,19
+seer_pas_sdk-0.1.3.dist-info/RECORD,,

seer_pas_sdk-0.1.2.dist-info/RECORD

@@ -1,16 +0,0 @@
-seer_pas_sdk/__init__.py,sha256=Ie6atdmdBV-OmdHHXjhrGhdFGXiyP3JKhKrr3hyvSsA,563
-seer_pas_sdk/auth/__init__.py,sha256=DZcbkYel11GvIn-iiutt9UOVfj9URZ_f89QMHhyGfRg,2277
-seer_pas_sdk/common/__init__.py,sha256=QnBup2dT6okt62Yjdhik4DmLf36Ozgv6KybdvFAULaA,12260
-seer_pas_sdk/core/__init__.py,sha256=J8dAiYsvNbc11zN1mgp7KqjHSVPw9CVwI-uc85UHw5s,47488
-seer_pas_sdk/objects/__init__.py,sha256=DosquJu2-XvDjVj4JFKoXa0DBVS8OroYCDeS5Np4U8Q,3693
-tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-tests/conftest.py,sha256=nu5Qu8CHwgJEwFpLQ0iX8e5csz4HGIC2oe50AdkA2Ms,317
-tests/test_auth.py,sha256=np4XXbEzoSFf-zXKaZQFL4Ry1ehMtjbXtHG3J6D-zzc,933
-tests/test_common.py,sha256=3VgHPbeLVJCh8V0kBGMvkhTKMd6sN_eLJF3AgvbyH0I,3433
-tests/test_objects.py,sha256=BcQtE8CbGUAnFlbkwsaJalUV6D8WbdwN2aWiQddh3k4,2521
-tests/test_sdk.py,sha256=ZNfsRAe_YHIXfteVugfkcds_lmYb0emIfDbJz7jpqR4,239
-seer_pas_sdk-0.1.2.dist-info/LICENSE.txt,sha256=DVQuDIgE45qn836wDaWnYhSdxoLXgpRRKH4RuTjpRZQ,10174
-seer_pas_sdk-0.1.2.dist-info/METADATA,sha256=VuuOZGQuA6LaN6MgYSZEHKBJXKRuVZxXNDFLLM63shk,1716
-seer_pas_sdk-0.1.2.dist-info/WHEEL,sha256=Mdi9PDNwEZptOjTlUcAth7XJDFtKrHYaQMPulZeBCiQ,91
-seer_pas_sdk-0.1.2.dist-info/top_level.txt,sha256=gMffZ5LfTF87Sr-oiyl-rtY6omfBslYCA2S4DM7YNC8,19
-seer_pas_sdk-0.1.2.dist-info/RECORD,,