Example #1
0
def Linnaeus2YASDBF(params):
    db_name = params['DB Name']
    linnaeus = '/home/d3y034/chembio_svn/Proteomics/Linnaeus/Linnaeus.py'
    if os.path.exists(linnaeus):
        yasdbf_main.runCmd( "%s %s %s" % (linnaeus, 'compile2YASDBF', db_name) )
    else:
        sys.exit('Linnaeus is not in the specifed location.')
Example #2
0
def insertSpectraSTData(con, pepXML):
    # NOTE: consider avoiding hardcoding this
    spectraST = "/usr/bin/spectrast"
    if os.path.exists(spectraST):
        # keep relative path in base
        path, base = os.path.split(pepXML)
        base = base.split('.')[0]
        yasdbf_main.runCmd( "%s -c -cP0 %s" % (spectraST, pepXML) )
        
        sptxt = os.path.join(path, base + '.sptxt')
        specST_dict = parseSPTXT(sptxt)
       
        # NOTE: try to alter table 
        # TODO: remove!
        try:
            alter_table(con)
        except sqlite3.OperationalError, ex:
            if "duplicate column name" in str(ex):
                pass
            else:
                raise

        data = []
        for k, v in specST_dict.iteritems():
            data.append( (';'.join(v[0]), ';'.join(v[1]) , ';'.join(v[2]), v[3], v[4], v[5], k) )
       
        con.executemany("UPDATE spectra SET x=?, y=?, labels=?, precur_int=?, total_int=?, matched_int=? WHERE name=?", data) 
        con.commit()
Example #3
0
def runMSGF(msgfPre, dirname, enzyme):
    if os.path.exists(msgfPre):
        msgfPath = "/home/yasdbf/apps/msgf.jar"
        msgf = os.path.join(dirname, msgfPre[:-3]) #make this a path
        if len(dirname) is 0:
            dirname = "."
        params = (msgfPath, msgfPre, dirname, msgf, enzyme)
        cmdStr = "java -Xmx2000M -jar %s -i %s -d %s -o %s -fixMod 0 -e %s" % params
        # "-fixMod 0" sets default mods to none
        # execute command
        yasdbf_main.runCmd(cmdStr)
        return msgf
    #else
    return None
Example #4
0
def Tandem2XML(tandemXML):
    Tandem2XML = "/home/d3y034/chembio_svn/Proteomics/Kraftwerk/apps/Tandem2XML"
    if os.path.exists(Tandem2XML):
        d = os.path.dirname(tandemXML)
        base = os.path.basename(tandemXML).split('.')[0]
        # NOTE: need to copy tandem file to new name for it to relate to mzXML
        newTandemXML = os.path.join(d, base + '.xml') 
        yasdbf_main.runCmd( "cp %s %s" % (tandemXML, newTandemXML) )
        # NOTE: this means pepXMLs follow naming of pepXMLs
        pepXML = os.path.join(d, base + '.pep.xml') 
        yasdbf_main.runCmd( "%s %s %s" % (Tandem2XML, newTandemXML, pepXML) )
        # NOTE: remove copy
        yasdbf_main.runCmd( "rm %s" % newTandemXML )
        return pepXML
    else:
        sys.exit("Tandem2XML does not appear to be installed")
Example #5
0
        if "duplicate column name" in str(ex):
            #NOTE: maybe log some kind of error here
            pass
        else:
            raise

    enzyme = params['Enzyme']
    filename = filename.split('.')[0] + '.mzXML'
    filename = os.path.basename(filename) # make sure you have basename (important for structured mode)
    
    file_id, dirname = con.execute("SELECT id, dirname FROM files WHERE basename=?", (filename,) ).fetchone()
    con.row_factory = sqlite3.Row

    msgfPre = writePrefile(con, file_id, filename)
    msgf = runMSGF(msgfPre, dirname, enzyme)
    yasdbf_main.runCmd("rm %s" % msgfPre) # clean-up
    importMSGF(con, msgf)

def writePrefile(con, file_id, basename):
    # use basename to find name for msgfPre file
    basename = basename.split('.')[0] + '.mzXML'
    filename = basename.split('.')[0] + '.msgfPre'

    # write msgfPre file
    with open(filename, 'w') as f:
        # write headers
        f.write("#SpectrumFile\tScanName\tScan#\tAnnotation\tCharge\n")
        
        select = """SELECT name, n_terminal, peptide, peptide_modded, c_terminal, charge 
                    FROM spectra WHERE file_id = ? ORDER BY name"""
        for record in con.execute(select, (file_id,)):