signalP integration

micronota/bfillings/signalp.py

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+# ----------------------------------------------------------------------------
+# Copyright (c) 2015--, micronota development team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+# ----------------------------------------------------------------------------
+
+from os import makedirs
+from os.path import join
+import re
+
+from burrito.parameters import FlagParameter, ValuedParameter
+from burrito.util import CommandLineApplication, ResultPath
+
+
+class SignalP(CommandLineApplication):
+    '''SignalP (version 4.1) application controller.'''
+    _command = 'signalp'
+    _valued_path_options = [
+        # Logfile if -v is defined. Default: 'STDERR'
+        '-l',
+        # Specify temporary file directory. Default: /var/tmp
+        '-T',
+        # Make fasta file with mature sequence. Default: None
+        '-m',
+        # Make gff file of processed sequences. Default: 'Off'
+        '-n'
+    ]
+    _valued_nonpath_options = [
+        # Setting the output format ('short', 'long', 'summary' or 'all').
+        # Default: 'short'
+        '-f',
+        # Graphics 'png' or 'png+eps'. Requires GNUPLOT. Default: 'Off'
+        '-g',
+        # Signal peptide networks to use ('best' or 'notm'). Default: 'best'
+        '-s',
+        # Organism type> (euk, gram+, gram-). Default: 'euk'
+        '-t',
+        # user defined D-cutoff for noTM networks
+        '-u',
+        # user defined D-cutoff for TM networks
+        '-U',
+        # Minimal predicted signal peptide length. Default: [10]
+        '-M',
+        # truncate to sequence length - 0 means no truncation. Default '70'
+        '-c'
+    ]
+    _flag_options = [
+        # Output this handy help message
+        '-h',
+        # Print SignalP version and exit
+        '-V',
+        # Verbose mode
+        '-v',
+        # Keep temporary directory. Default: 'Off'
+        '-k',
+        # web predictions. Default: 'Off'
+        '-w'
+    ]
+
+    _parameters = {}
+    _parameters.update({
+        i: ValuedParameter(
+            Prefix=i[0], Name=i[1:], Delimiter=' ',
+            IsPath=True)
+        for i in _valued_path_options})
+    _parameters.update({
+        i: ValuedParameter(
+            Prefix=i[0], Name=i[1:], Delimiter=' ')
+        for i in _valued_nonpath_options})
+    _parameters.update({
+        i: FlagParameter(
+            Prefix=i[0], Name=i[1:])
+        for i in _flag_options})
+    _suppress_stderr = False
+
+    def _accept_exit_status(self, exit_status):
+        return exit_status == 0
+
+    def _get_result_paths(self, data):
+        result = {}
+
+        # if `-k` flag is defined get temporaty file dir from `-T`
+        if self.Parameters['-k'].isOn():
+            if self.Parameters['-T'].isOn():
+                tmp_fp = self._absolute(self.Parameters['-T'].Value)
+            else:
+                # taken from default definition in `_valued_path_options`
+                tmp_fp = '/var/tmp/'
+            result['tmp'] = ResultPath(Path=tmp_fp, IsWritten=True)
+
+        # get log, fasta and gff file paths
+        for option, vals in [('-l', 'log'), ('-m', 'fasta'), ('-n', 'gff')]:
+            if self.Parameters[option].isOn():
+                fp = self._absolute(self.Parameters[option].Value)
+                result[vals] = ResultPath(Path=fp, IsWritten=True)
+
+        # get png (and eps) files
+        if self.Parameters['-g'].isOn():
+            # get inp_fp GI_IDs
+            gis = []
+            with open(data[0]) as f:
+                for line in f.readlines():
+                    if line.startswith('>'):
+                        line = re.sub('^>\ *', '', line)
+                        gis.append(line.split()[0])
+            g_fp = self.WorkingDir
+            # get png files
+            for i, gi in enumerate(gis):
+                png_fp = join(g_fp, '.'.join([gi, 'png']))
+                result['png'+str(i)] = ResultPath(Path=png_fp, IsWritten=True)
+                if self.Parameters['-g'].Value is 'gff+eps':
+                    # get eps files
+                    eps_fp = join(g_fp, '.'.join([gi, 'eps']))
+                    result['eps'+str(i)] = ResultPath(Path=eps_fp,
+                                                      IsWritten=True)
+        return result
+
+
+def predict_signal(in_fp, out_dir, prefix, params=None):
+    '''Predict signal peptide cleavage sites for the input file.
+
+    Notes
+    -----
+    It will create an output, depending on the selected parameter:
+        A. short
+        B. long
+        C. summary
+        D. all
+    SignalP accepts any input and does not raise input file errors.
+    Please check for correct input before running SignalP.
+
+    Parameters
+    ----------
+    in_fp : str
+        input file path
+    out_dir : str
+        output file directory path
+    prefix : str
+        name of the output file
+    params : dict
+        Other command line parameters for SignalP. key is the option
+        (e.g. "-t") and value is the value for the option (e.g. "euk").
+        If the option is a flag, set the value to None.
+
+    Returns
+    -------
+    burrito.util.CommandLineAppResult
+        It contains opened file handlers of stdout, stderr, and the
+        output files, which can be accessed in a dict style with the
+        keys of "StdOut", "StdErr", "tmp" (if specified), "gff" (if specified),
+        "fasta" (if specified), "png[0-9]" & "eps[0-9]" (if specified)
+        and "log" (if specified). Main output is passed to "StdOut".
+        The exit status can be similarly fetched with the key "ExitStatus".
+    '''
+    # create dir if does not exist
+    makedirs(out_dir, exist_ok=True)
+
+    if params is None:
+        params = {}
+
+    # change -m, -n and -l options to include path if there isn't one!
+    for i in ['-l', '-m', '-n']:
+        if i in params:
+            if '/' not in params[i]:
+                params[i] = join(out_dir, params[i])
+
+    app = SignalP(InputHandler='_input_as_paths', WorkingDir=out_dir,
+                  params=params)
+    return app([in_fp])

micronota/bfillings/tests/data/signalp/euk10.fasta

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+>IPI:IPI00000013.1  SWISS-PROT:O60911 TREMBL:B2R717 ENSEMBL:ENSP00000259470 REFSEQ:NP_001324 H-INV:HIT000252685 VEGA:OTTHUMP00000021738  Tax_Id=9606 Gene_Symbol=CTSL2 Cathepsin L2; MatureChain: 18-334
+VPKFDQNLDTKWYQWKATHRRLYGANEEGWRRAVWEKNMKMIELHNGEYSQGKHGFTMAM
+NAFGDMTNEEFRQMMGCFRNQKFRKGKVFREPLFLDLPKSVDWRKKGYVTPVKNQKQCGS
+CWAFSATGALEGQMFRKTGKLVSLSEQNLVDCSRPQGNQGCNGGFMARAFQYVKENGGLD
+SEESYPYVAVDEICKYRPENSVANDTGFTVVAPGKEKALMKAVATVGPISVAMDAGHSSF
+QFYKSGIYFEPDCSSKNLDHGVLVVGYGFEGANSNNSKYWLVKNSWGPEWGSNGYVKIAK
+DKNNHCGIATAASYPNV
+>IPI:IPI00000023.4  SWISS-PROT:P18507 TREMBL:B4DSA1 ENSEMBL:ENSP00000354651 REFSEQ:NP_000807 H-INV:HIT000263500 VEGA:OTTHUMP00000160874  Tax_Id=9606 Gene_Symbol=GABRG2 Gamma-aminobutyric acid receptor subunit gamma-2; MatureChain: 41-467
+KSDDDYEDYASNKTWVLTPKVPEGDVTVILNNLLEGYDNKLRPDIGVKPTLIHTDMYVNS
+IGPVNAINMEYTIDIFFAQTWYDRRLKFNSTIKVLRLNSNMVGKIWIPDTFFRNSKKADA
+HWITTPNRMLRIWNDGRVLYTLRLTIDAECQLQLHNFPMDEHSCPLEFSSYGYPREEIVY
+QWKRSSVEVGDTRSWRLYQFSFVGLRNTTEVVKTTSGDYVVMSVYFDLSRRMGYFTIQTY
+IPCTLIVVLSWVSFWINKDAVPARTSLGITTVLTMTTLSTIARKSLPKVSYVTAMDLFVS
+VCFIFVFSALVEYGTLHYFVSNRKPSKDKDKKKKNPAPTIDIRPRSATIQMNNATHLQER
+DEEYGYECLDGKDCASFFCCFEDCRTGAWRHGRIHIRIAKMDSYARIFFPTAFCLFNLVY
+WVSYLYL

micronota/bfillings/tests/data/signalp/euk10.fsa

@@ -0,0 +1,69 @@
+>IPI:IPI00000001.2 SWISS-PROT:O95793-1 TREMBL:A8K622;Q59F99 ENSEMBL:ENSP00000360922;ENSP00000379466 REFSEQ:NP_059347 H-INV:HIT000329496 VEGA:OTTHUMP00000031233  Tax_Id=9606 Gene_Symbol=STAU1 Isoform Long of Double-stranded RNA-binding protein Staufen homolog 1
+MSQVQVQVQNPSAALSGSQILNKNQSLLSQPLMSIPSTTSSLPSENAGRPIQNSALPSAS
+ITSTSAAAESITPTVELNALCMKLGKKPMYKPVDPYSRMQSTYNYNMRGGAYPPRYFYPF
+PVPPLLYQVELSVGGQQFNGKGKTRQAAKHDAAAKALRILQNEPLPERLEVNGRESEEEN
+LNKSEISQVFEIALKRNLPVNFEVARESGPPHMKNFVTKVSVGEFVGEGEGKSKKISKKN
+AAIAVLEELKKLPPLPAVERVKPRIKKKTKPIVKPQTSPEYGQGINPISRLAQIQQAKKE
+KEPEYTLLTERGLPRRREFVMQVKVGNHTAEGTGTNKKVAKRNAAENMLEILGFKVPQAQ
+PTKPALKSEEKTPIKKPGDGRKVTFFEPGSGDENGTSNKEDEFRMPYLSHQQLPAGILPM
+VPEVAQAVGVSQGHHTKDFTRAAPNPAKATVTAMIARELLYGGTSPTAETILKNNISSGH
+VPHGPLTRPSEQLDYLSRVQGFQVEYKDFPKNNKNEFVSLINCSSQPPLISHGIGKDVES
+CHDMAALNILKLLSELDQQSTEMPRTGNGPMSVCGRC
+>IPI:IPI00000005.1 SWISS-PROT:P01111 TREMBL:Q5U091 ENSEMBL:ENSP00000358548 REFSEQ:NP_002515 VEGA:OTTHUMP00000013879  Tax_Id=9606 Gene_Symbol=NRAS GTPase NRas
+MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAG
+QEEYSAMRDQYMRTGEGFLCVFAINNSKSFADINLYREQIKRVKDSDDVPMVLVGNKCDL
+PTRTVDTKQAHELAKSYGIPFIETSAKTRQGVEDAFYTLVREIRQYRMKKLNSSDDGTQG
+CMGLPCVVM
+>IPI:IPI00000006.1 SWISS-PROT:P01112 ENSEMBL:ENSP00000309845;ENSP00000373382;ENSP00000380723;ENSP00000407586 REFSEQ:NP_001123914;NP_005334 H-INV:HIT000080764 VEGA:OTTHUMP00000162769;OTTHUMP00000166055  Tax_Id=9606 Gene_Symbol=HRAS GTPase HRas
+MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAG
+QEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDL
+AARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQHKLRKLNPPDESGPG
+CMSCKCVLS
+>IPI:IPI00000012.4 SWISS-PROT:Q6XR72-4 TREMBL:B3KR19;B3KUL2 ENSEMBL:ENSP00000355893 REFSEQ:NP_061183 H-INV:HIT000251072 VEGA:OTTHUMP00000035563  Tax_Id=9606 Gene_Symbol=SLC30A10 Cation efflux protein family protein
+MGRYSGKTCRLLFMLVLTVAFFVAELVSGYLGNSIALLSDSFNMFSDLISLCVGLSAGYI
+ARRPTRGFSATYGYARAEVVGALSNAVFLTALCFTIFVEAVLRLARPERIDDPELVLIVG
+VLGLLVNVVGLLIFQDCAAWFACCLRGRSRRLQQRQQLAEGCVPGAFGGPQGAEDPRRAA
+DPTAPGSDSAVTLRGTSVERKREKGATVFANVAGDSFNTQNEPEDMMKKEKKSEALNIRG
+VLLHVMGDALGSVVVVITAIIFYVLPLKSEDPCNWQCYIDPSLTVLMVIIILSSAFPLIK
+ETAAILLQMVPKGVNMEELMSKLSAVPGISSVHEVHIWELVSGKIIATLHIKYPKDRGYQ
+DASTKIREIFHHAGIHNVTIQFENVDLKEPLEQKDLLLLCNSPCISKGCAKQLCCPPGAL
+PLAHVNGCAEHFLCHVNGCAEHNGGPSLDTYGSDGLSRRDAREVAIEVSLDSCLSDHGQS
+LNKTQEDQCYVNRTHF
+>IPI:IPI00000013.1 SWISS-PROT:O60911 TREMBL:B2R717 ENSEMBL:ENSP00000259470 REFSEQ:NP_001324 H-INV:HIT000252685 VEGA:OTTHUMP00000021738  Tax_Id=9606 Gene_Symbol=CTSL2 Cathepsin L2
+MNLSLVLAAFCLGIASAVPKFDQNLDTKWYQWKATHRRLYGANEEGWRRAVWEKNMKMIE
+LHNGEYSQGKHGFTMAMNAFGDMTNEEFRQMMGCFRNQKFRKGKVFREPLFLDLPKSVDW
+RKKGYVTPVKNQKQCGSCWAFSATGALEGQMFRKTGKLVSLSEQNLVDCSRPQGNQGCNG
+GFMARAFQYVKENGGLDSEESYPYVAVDEICKYRPENSVANDTGFTVVAPGKEKALMKAV
+ATVGPISVAMDAGHSSFQFYKSGIYFEPDCSSKNLDHGVLVVGYGFEGANSNNSKYWLVK
+NSWGPEWGSNGYVKIAKDKNNHCGIATAASYPNV
+>IPI:IPI00000015.2 SWISS-PROT:Q08170 TREMBL:A8K644;Q53F45;Q59EF5 ENSEMBL:ENSP00000362900 REFSEQ:NP_005617 H-INV:HIT000275139 VEGA:OTTHUMP00000003790  Tax_Id=9606 Gene_Symbol=SRSF4 Serine/arginine-rich splicing factor 4
+MPRVYIGRLSYQARERDVERFFKGYGKILEVDLKNGYGFVEFDDLRDADDAVYELNGKDL
+CGERVIVEHARGPRRDGSYGSGRSGYGYRRSGRDKYGPPTRTEYRLIVENLSSRCSWQDL
+KDYMRQAGEVTYADAHKGRKNEGVIEFVSYSDMKRALEKLDGTEVNGRKIRLVEDKPGSR
+RRRSYSRSRSHSRSRSRSRHSRKSRSRSGSSKSSHSKSRSRSRSGSRSRSKSRSRSQSRS
+RSKKEKSRSPSKEKSRSRSHSAGKSRSKSKDQAEEKIQNNDNVGKPKSRSPSRHKSKSKS
+RSRSQERRVEEEKRGSVSRGRSQEKSLRQSRSRSRSKGGSRSRSRSRSKSKDKRKGRKRS
+REESRSRSRSRSKSERSRKRGSKRDSKAGSSKKKKKEDTDRSQSRSPSRSVSKEREHAKS
+ESSQREGRGESENAGTNQETRSRSRSNSKSKPNLPSESRSRSKSASKTRSRSKSRSRSAS
+RSPSRSRSRSHSRS
+>IPI:IPI00000017.1 TREMBL:Q16191  Tax_Id=9606 Gene_Symbol=- Orf1 5' to PD-ECGF/TP protein
+MGLGAGRPDANSDAPRLRLGHDPCGRAPPPSPSARASPRSRRRAAPGQATWCPLA
+>IPI:IPI00000020.1 TREMBL:Q16192  Tax_Id=9606 Gene_Symbol=ODF3B Orf3 5' of PD-ECGF/TP protein
+MLPGYALAMTRAAARPRLHLRRALPHAADDVRPRARPPGARSHDRARHRRRPRLLHLRPP
+TPLSALPHSGTWSGPPGPWPPQRRTASREAHLGTPDLNPESPSDTLTRYSVPPYPDLKSQ
+TPNPRGFDKSWLRLPTSPRTPSRVPTRLPRSSSPPHP
+>IPI:IPI00000021.5 TREMBL:A1L1A8  Tax_Id=9606 Gene_Symbol=- ODF3B protein (Fragment)
+GAASRKRPPPALWARTPGWAFGGHTGPAAPSRRTTEAPGPNTSCRPTPQTTCGPGPGHLV
+PARMTVRGTDGAPAYSIYGRPRRSAPFLTPGPGRYFPERAGNATYPSAPRHTIAPRNWGV
+QAEQQSPGPAAYTVPSLLGPRVIGKVSAPTCSIYGRRAAGSFFEDLSKTPGPCAYQVVSP
+GVYKSRAPQFTILARTSLPQDNTRKPGPAAYNVDQHRKPRGWSFGIRHSDYLAPLVTDAD
+N
+>IPI:IPI00000023.4 SWISS-PROT:P18507 TREMBL:B4DSA1 ENSEMBL:ENSP00000354651 REFSEQ:NP_000807 H-INV:HIT000263500 VEGA:OTTHUMP00000160874  Tax_Id=9606 Gene_Symbol=GABRG2 Gamma-aminobutyric acid receptor subunit gamma-2
+MSSPNIWSTGSSVYSTPVFSQKMTVWILLLLSLYPGFTSQKSDDDYEDYASNKTWVLTPK
+VPEGDVTVILNNLLEGYDNKLRPDIGVKPTLIHTDMYVNSIGPVNAINMEYTIDIFFAQT
+WYDRRLKFNSTIKVLRLNSNMVGKIWIPDTFFRNSKKADAHWITTPNRMLRIWNDGRVLY
+TLRLTIDAECQLQLHNFPMDEHSCPLEFSSYGYPREEIVYQWKRSSVEVGDTRSWRLYQF
+SFVGLRNTTEVVKTTSGDYVVMSVYFDLSRRMGYFTIQTYIPCTLIVVLSWVSFWINKDA
+VPARTSLGITTVLTMTTLSTIARKSLPKVSYVTAMDLFVSVCFIFVFSALVEYGTLHYFV
+SNRKPSKDKDKKKKNPAPTIDIRPRSATIQMNNATHLQERDEEYGYECLDGKDCASFFCC
+FEDCRTGAWRHGRIHIRIAKMDSYARIFFPTAFCLFNLVYWVSYLYL

micronota/bfillings/tests/data/signalp/euk10.gff

@@ -0,0 +1,5 @@
+##gff-version 2
+##sequence-name	source	feature	start	end	score	N/A ?
+## -----------------------------------------------------------
+IPI:IPI00000013.1	SignalP-4.1	SIGNAL	1	17	0.834	.	.	YES
+IPI:IPI00000023.4	SignalP-4.1	SIGNAL	1	40	0.533	.	.	YES