Merge pull request #52 from jonasscheid/feature_write-idxml

Read and write idXML files using pyopenms
compomics · Oct 25, 2023 · 483f304 · 483f304
2 parents e7f0bfb + cdeefdf
commit 483f304
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Showing 18 changed files with 987 additions and 65 deletions.
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -21,6 +21,7 @@
     "sphinx.ext.autodoc",
     "sphinx.ext.autosectionlabel",
     "sphinx.ext.autosummary",
+    "sphinx.ext.intersphinx",
     "sphinx.ext.napoleon",
     "sphinx_rtd_theme",
     "sphinx_mdinclude",
@@ -40,6 +41,15 @@
 autodoc_member_order = "bysource"
 autoclass_content = "init"
 
+# Intersphinx options
+intersphinx_mapping = {
+    "python": ("https://docs.python.org/3", None),
+    "pandas": ("https://pandas.pydata.org/pandas-docs/stable/", None),
+    "numpy": ("https://numpy.org/doc/stable/", None),
+    "pyteomics": ("https://pyteomics.readthedocs.io/en/latest/", None),
+    "pyopenms": ("https://pyopenms.readthedocs.io/en/latest/", None),
+}
+
 
 def setup(app):
     config = {

diff --git a/online/pages/2_PSM_file_conversion.py b/online/pages/2_PSM_file_conversion.py
@@ -68,9 +68,10 @@ def _convert(self):
                 st.success("PSM file successfully converted!")
 
                 # Construct output filename with new extension
-                output_filename = Path(
-                    st.session_state["convert_input_file"].name
-                ).stem + FILETYPES[st.session_state["convert_output_filetype"]]["extension"]
+                output_filename = (
+                    Path(st.session_state["convert_input_file"].name).stem
+                    + FILETYPES[st.session_state["convert_output_filetype"]]["extension"]
+                )
 
                 # Open converted file in memory for download button
                 with open("output_filename", "rb") as file:

diff --git a/psm_utils/io/__init__.py b/psm_utils/io/__init__.py
@@ -28,7 +28,7 @@
 FILETYPES = {
     "idxml": {
         "reader": idxml.IdXMLReader,
-        "writer": None,
+        "writer": idxml.IdXMLWriter,
         "extension": ".idXML",
         "filename_pattern": r"^.*\.idxml$",
     },
@@ -127,7 +127,7 @@ def _supports_write_psm(writer: WriterBase):
             supports_write_psm = True
         else:
             supports_write_psm = True
-        Path(temp_file.name).unlink()
+            Path(temp_file.name).unlink()
         return supports_write_psm
 
 

diff --git a/psm_utils/io/_pd_msf_tables.py b/psm_utils/io/_pd_msf_tables.py
@@ -17,6 +17,7 @@
     UniqueConstraint,
     text,
 )
+
 try:
     from sqlalchemy.orm import declarative_base
 except ImportError:
-Original file line number
+Diff line change
@@ Expand Up / @@ -17,6 +17,7 @@ @@
         UniqueConstraint,
         text,
     )
     try:
         from sqlalchemy.orm import declarative_base
     except ImportError:
@@ Expand Down @@