starting to add doc of new mqlive version

analysis/mqlivelib/load_log.py

@@ -0,0 +1,40 @@
+import pandas as pd
+import sys
+from scipy import *
+from scipy import ndimage
+from numpy import *
+from pylab import *
+
+def isfloat(value):
+    try:
+        float(value)
+        return True
+    except ValueError:
+        return False
+
+
+def parseLogFile(fName):
+    fl = open(fName)
+    data = [i.split()[3:] for i in fl.readlines() if i.find("PEPTIDE_FOUND_MS1") != -1]
+    data = [["rt:", i[0]] + i[2:] for i in data]
+    fl.close()
+
+    keys, idz, values = [], [], []
+    for c, s in enumerate(data[0]):
+        if (s[-1] == ":"): keys.append(s.replace(":", ""))
+
+    for s in data:
+        v = []
+        for c, i in enumerate(s):
+            if (i[-1] == ":"): v.append(s[c + 1])
+        if (len(v) == len(keys)):      values.append(v)
+
+    values = [[float(v) if isfloat(v) else v for v in val] for val in values]
+
+    peptides = pd.DataFrame(values, columns=keys)
+    peptideLengths = peptides.groupby('id')['rt'].max() - peptides.groupby('id')['rt'].min()
+
+    peptides = peptides.loc[peptides.groupby('id')['intensity'].idxmax()]
+    peptides['length'] = peptideLengths.values
+
+    return peptides.sort_values('rt')

docs/appTargeting.rst

@@ -1,7 +1,7 @@
 Targeting
 =========
 
-.. figure:: figures/image036.png
+.. figure:: figures/TargetingApp.png
     :width: 200px
     :align: left