From 522b28b46998bacec4fc888d40c3410d8986a0f0 Mon Sep 17 00:00:00 2001
From: Schneider Leo <leo.schneider@etu.ec-lyon.fr>
Date: Fri, 20 Sep 2024 14:20:51 +0200
Subject: [PATCH] local inetgration update
---
local_integration_msms.py | 23 ++++++++++++++++++-----
main_custom.py | 2 +-
2 files changed, 19 insertions(+), 6 deletions(-)
diff --git a/local_integration_msms.py b/local_integration_msms.py
index 0015141..7cc384b 100644
--- a/local_integration_msms.py
+++ b/local_integration_msms.py
@@ -1,20 +1,21 @@
import pyopenms as oms
import numpy as np
+import matplotlib.pyplot as plt
-def compute_chromatograms(rt,charge,intensity,start_c,end_c):
+def compute_chromatograms(rt, mz, intensity, start_c, end_c):
value=[]
for k in range(len(rt)):
- c = np.array(charge[k])
+ c = np.array(mz[k])
i = np.array(intensity[k])
- value.append(np.sum(np.where(end_c > c > start_c, i, 0)))
+ value.append(np.sum(np.where((end_c > c) & (c > start_c), i, 0)))
return value
if __name__ == "__main__":
e = oms.MSExperiment()
- oms.MzMLFile().load("data/STAPH140.mzML", e)
+ oms.MzMLFile().load("data/Staph140.mzML", e)
e.updateRanges()
rt = []
charge = []
@@ -24,4 +25,16 @@ if __name__ == "__main__":
rt.append(s.getRT())
charge.append(s.get_peaks()[0])
intensity.append(s.get_peaks()[1])
- val = compute_chromatograms(rt, charge, intensity, 400. ,400.5)
\ No newline at end of file
+ mz_range = np.linspace(350,1250,4000)
+ for i in range(len(mz_range)-1):
+ print(mz_range[i],'/1250')
+ val = compute_chromatograms(rt, charge, intensity, mz_range[i] ,mz_range[i+1])
+ fig, ax = plt.subplots()
+ ax.plot(val)
+ ax.set_xlabel('Retention time')
+ ax.set_ylabel('Intensity')
+ ax.set_title('mz : {} to {}'.format(mz_range[i] ,mz_range[i+1]))
+ plt.savefig('fig/rt_local/{}_to_{}.png'.format(mz_range[i] ,mz_range[i+1]))
+ plt.clf()
+df = e.get_df()
+#358.1 358.32
\ No newline at end of file
diff --git a/main_custom.py b/main_custom.py
index 1118c9a..cca8c9c 100644
--- a/main_custom.py
+++ b/main_custom.py
@@ -207,7 +207,7 @@ def main(args):
print('\nData loaded')
- model = Model_Common_Transformer_TAPE(encoder_ff=args.encoder_ff, decoder_rt_ff=args.decoder_rt_ff,
+ model = Model_Common_Transformer(encoder_ff=args.encoder_ff, decoder_rt_ff=args.decoder_rt_ff,
decoder_int_ff=args.decoder_int_ff
, n_head=args.n_head, encoder_num_layer=args.encoder_num_layer,
decoder_int_num_layer=args.decoder_int_num_layer,
--
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