Source code for emzed.utils.utils

import emzed.core.data_types

[docs]def toTable(colName, iterable, format_="", type_=None, title="", meta=None): return emzed.core.Table.toTable(colName, iterable, format_, type_, title, meta)
toTable.__doc__ = emzed.core.Table.toTable.__doc__
[docs]def formula(mf): """ Creates formula object which allows addition and subtraction: .. pycon:: import emzed mf1 = emzed.utils.formula("H2O") mf2 = emzed.utils.formula("NaOH") mf3 = mf1 + mf2 print str(mf3) print str(mf3 - mf1) Mass calculation is supported too: .. pycon:: print mf1.mass() If you need some internal representation, you can get a dictionary. Keys are pairs of *(symbol, massnumber)*, where *massnumber = None* refers to the lowest massnumber. Values of the dictionary are counts: .. pycon:: print mf1.asDict() mixed = emzed.utils.formula("[13]C2[14]C3") print mixed.asDict() """ from emzed.core.chemistry import MolecularFormula return MolecularFormula(mf)
[docs]def addmf(formula0, *formulas): """ Combines molecular formulas by addition and subtraction: .. pycon:: import emzed print emzed.utils.addmf("H2O", "COOH") print emzed.utils.addmf("H2O", "COOH", "NaCl") A leading minus sign subtracts the formula following this sign: .. pycon:: print emzed.utils.addmf("H2O2", "-H2O") print emzed.utils.addmf("H2O", "COOH", "NaCl", "-H2O2") print emzed.utils.addmf("(CH2)7COOH", "-C7") """ mf0 = formula(formula0) for f in formulas: if f.startswith("-"): mf0 -= formula(f[1:]) else: mf0 += formula(f) return str(mf0)
[docs]def openInBrowser(urlPath): """ opens *urlPath* in browser, eg: .. pycon:: emzed.utils.openInBrowser("") !noexec """ from PyQt4.QtGui import QDesktopServices from PyQt4.QtCore import QUrl import os.path url = QUrl(urlPath) scheme = url.scheme() if scheme not in ["http", "ftp", "mailto"]: # C:/ or something simiar: if os.path.splitdrive(urlPath)[0] != "": url = QUrl("file:///"+urlPath) ok = QDesktopServices.openUrl(url) if not ok: raise Exception("could not open '%s'" % url.toString())
def _recalculateMzPeakFor(postfix): def calculator(table, row, name, postfix=postfix): mzmin = table.getValue(row, "mzmin"+postfix) mzmax = table.getValue(row, "mzmax"+postfix) rtmin = table.getValue(row, "rtmin"+postfix) rtmax = table.getValue(row, "rtmax"+postfix) pm = table.getValue(row, "peakmap"+postfix) mz = pm.representingMzPeak(mzmin, mzmax, rtmin, rtmax) return mz if mz is not None else (mzmin+mzmax)/2.0 return calculator def _hasRangeColumns(table, postfix): return all([table.hasColumn(n + postfix) for n in ["rtmin", "rtmax", "mzmin", "mzmax", "peakmap"]])
[docs]def recalculateMzPeaks(table): """Adds mz value for peaks not detected with centwaves algorithm based on rt and mz window: needed are columns mzmin, mzmax, rtmin, rtmax and peakmap mz, postfixes are automaticaly taken into account""" postfixes = [ "" ] + [ "__%d" % i for i in range(len(table._colNames))] for postfix in postfixes: if _hasRangeColumns(table, postfix): mz_col = "mz" + postfix if table.hasColumn(mz_col): table.replaceColumn(mz_col, _recalculateMzPeakFor(postfix), format_="%.5f", type_=float) else: table.addColumn(mz_col, _recalculateMzPeakFor(postfix), format_="%.5f", type_=float)
[docs]def startfile(path): import sys, os if sys.platform == "win32": path = path.replace("/", "\\") # needed for network paths return os.startfile(path)