update: tpa

bigbio · Nov 27, 2024 · 9068fd1 · 9068fd1
1 parent b5e324e
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Showing 4 changed files with 529 additions and 5 deletions.
diff --git a/README.md b/README.md
@@ -194,7 +194,7 @@ Options:
 #### Compute TPA
 
 ```asciidoc
-python compute_tpa --fasta Homo-sapiens-uniprot-reviewed-contaminants-decoy-202210.fasta --organism 'human' --peptides PXD003947-peptides.csv --ruler --ploidy 2 --cpc 200 --output PXD003947-tpa.tsv --verbose
+ibaqpy tpa --fasta Homo-sapiens-uniprot-reviewed-contaminants-decoy-202210.fasta --organism human --peptides PXD003947-peptides.csv --ruler --ploidy 2 --cpc 200 --output PXD003947-tpa.tsv --verbose
 ```
 
 ```asciidoc

diff --git a/ibaqpy/commands/compute_tpa.py b/ibaqpy/commands/compute_tpa.py
@@ -4,6 +4,7 @@
 import pandas as pd
 from matplotlib.backends.backend_pdf import PdfPages
 from pyopenms import *
+from ibaqpy.data.data import histones
 
 from ibaqpy.ibaq.ibaqpy_commons import (
     CONDITION,
@@ -156,11 +157,8 @@ def get_protein_group_mw(group: str) -> float:
     if ruler:
         avogadro = 6.02214129e23
         average_base_pair_mass = 617.96  # 615.8771
-
         organism = organism.lower()
-        histone_df = pd.read_json(
-            open(os.path.split(__file__)[0] + "../data/histones.json", "rb")
-        ).T
+        histone_df = pd.DataFrame(histones).T
         target_histones = histone_df[histone_df["name"] == organism.lower()]
         genome_size = target_histones["genome_size"].values[0]
         histones_list = target_histones["histone_entries"].values[0]

diff --git a/ibaqpy/ibaq/__init__.py → ibaqpy/data/__init__.py b/ibaqpy/ibaq/__init__.py → ibaqpy/data/__init__.py