docs: Add FlashLFQ

compomics · Sep 5, 2024 · b501930 · b501930
1 parent a873aca
commit b501930
Show file tree

Hide file tree

Showing 4 changed files with 30 additions and 3 deletions.
diff --git a/README.rst b/README.rst
@@ -89,6 +89,7 @@ Supported file formats
 ===================================================================================================================== ======================== =============== ===============
  File format psm_utils tag Read support Write support
 ===================================================================================================================== ======================== =============== ===============
+ `FlashLFQ generic TSV <https://github.com/smith-chem-wisc/FlashLFQ/wiki/Identification-Input-Formats>`_ ``flashlfq`` ✅ ✅
  `ionbot CSV <https://ionbot.cloud/>`_ ``ionbot`` ✅ ❌
  `OpenMS idXML <https://www.openms.de/>`_ ``idxml`` ✅ ✅
  `MaxQuant msms.txt <https://www.maxquant.org/>`_ ``msms`` ✅ ❌

diff --git a/docs/source/api/psm_utils.io.rst b/docs/source/api/psm_utils.io.rst
@@ -7,6 +7,14 @@ psm_utils.io
 
 
 
+psm_utils.io.flashlfq
+##################
+
+.. automodule:: psm_utils.io.flashlfq
+ :members:
+ :inherited-members:
+
+
 psm_utils.io.idxml
 ##################
 

diff --git a/example_files/example.flashlfq.tsv b/example_files/example.flashlfq.tsv
@@ -0,0 +1,18 @@
+File Name Scan Retention Time Precursor Charge Base Sequence Full Sequence Peptide Monoisotopic Mass Protein Accession
+SmallCalibratible_Yeast 24.80555 2 KAPAGGAADAAAK KAPAGGAADAAAK 
+SmallCalibratible_Yeast 24.95372 2 KAPAAAPAASK KAPAAAPAASK 
+SmallCalibratible_Yeast 24.77032 2 KQAIETANK KQAIETANK 
+SmallCalibratible_Yeast 24.17319 2 RVDEGGAQDK RVDEGGAQDK 
+SmallCalibratible_Yeast 24.26695 2 KDAEPQSDSTTSK KDAEPQSDSTTSK 
+SmallCalibratible_Yeast 24.10798 2 EKAEAEAEK EKAEAEAEK 
+SmallCalibratible_Yeast 24.06874 2 EKAEAEAEK EKAEAEAEK 
+SmallCalibratible_Yeast 24.77398 2 FKEEDEKESQR FKEEDEKESQR 
+SmallCalibratible_Yeast 24.90638 2 YDHEASSSYK YDHEASSSYK 
+SmallCalibratible_Yeast 24.40345 3 SKDVTDSATTKK SKDVTDSATTKK 
+SmallCalibratible_Yeast 24.71679 2 FKEEDEKESQR FKEEDEKESQR 
+SmallCalibratible_Yeast 24.39968 2 ALKQEGAANK ALKQEGAANK 
+SmallCalibratible_Yeast 24.67303 2 SKDVTDSATTK SKDVTDSATTK 
+SmallCalibratible_Yeast 24.45053 2 KLEDHPK KLEDHPK 
+SmallCalibratible_Yeast 24.77398 1 HIDAGAK HIDAGAK 
+SmallCalibratible_Yeast 24.9022 2 YLAKEEEKK YLAKEEEKK 
+SmallCalibratible_Yeast 24.76278 2 YAGEVSHDDK YAGEVSHDDK 
diff --git a/psm_utils/io/flashlfq.py b/psm_utils/io/flashlfq.py
@@ -7,11 +7,11 @@
 Notes
 -----
 - The FlashLFQ format does not contain the actual spectrum identifier. When reading a FlashLFQ
-file, the spectrum identifier is set to the row number in the file.
+ file, the spectrum identifier is set to the row number in the file.
 - The FlashLFQ format does not contain the precursor m/z, but the theoretical monoisotopic mass.
-This value is not read into the PSM object, but can be calculated from the peptidoform.
+ This value is not read into the PSM object, but can be calculated from the peptidoform.
 - To read from a FlashLFQ file, the ``Full Sequence`` column is expected to contain a ProForma v2
-compatible peptidoform notation.
+ compatible peptidoform notation.
 
 """