| Next changeset 1:528bcf03e561 (2020-07-17) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a" |
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added:
macros.xml pepquery.xml test-data/Uniprot.fasta test-data/iTRAQ_f4.mgf test-data/novel_peptides test-data/novel_proteins.fa |
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| diff -r 000000000000 -r 32d3818fc635 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Jan 22 17:12:37 2020 -0500 |
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| b'@@ -0,0 +1,164 @@\n+ <macros>\n+ <token name="@VERSION@">1.3.0</token>\n+ <xml name="modifications">\n+ <option value="1">HexNAc of T (203.07937251951) modaa</option>\n+ <option value="2">HexNAc of S (203.07937251951) modaa</option>\n+ <option value="3">Propionyl of peptide N-term light (56.02621474784) modn_peptide</option>\n+ <option value="4">iTRAQ 8-plex of K (304.19903946116) modaa</option>\n+ <option value="5">Dimethylation of K 2H(6) 13C(2) (36.075670278260006) modaa</option>\n+ <!--<option value="6">Carbamidomethylation of C (57.02146372057) modaa</option>-->\n+ <option value="7">Dioxidation of M (31.98982923912) modaa</option>\n+ <option value="8">Guanidination of K (42.02179807374) modaa</option>\n+ <option value="9">S-nitrosylation (28.99016359229) modaa</option>\n+ <option value="10">TMT 6-plex of K (229.16293213472) modaa</option>\n+ <option value="11">Propionyl of peptide N-term heavy (59.03627926124) modn_peptide</option>\n+ <option value="12">Formylation of protein N-term (27.99491461956) modn_protein</option>\n+ <option value="13">TMT 10-plex of K+6 (235.18306116152) modaa</option>\n+ <option value="14">TMT 11-plex of K+6 (235.18306116152) modaa</option>\n+ <option value="15">TMT 10-plex of K+8 (237.17713094832) modaa</option>\n+ <option value="16">TMT 11-plex of K+4 (233.18803911764) modaa</option>\n+ <option value="17">Diiodination of Y (251.79329593586) modaa</option>\n+ <option value="18">TMT 10-plex of K+4 (233.18803911764) modaa</option>\n+ <option value="19">ICPL10 of peptide N-term (115.06669973029) modn_peptide</option>\n+ <option value="20">Amidation of the protein C-term (-0.9840155826899988) modc_protein</option>\n+ <option value="21">Acetylation of peptide N-term (42.0105646837) modn_peptide</option>\n+ <option value="22">Palmitoylation of protein N-term (238.22966558166) modn_protein</option>\n+ <option value="23">ICAT-O (227.12699141827) modaa</option>\n+ <option value="24">TMT 2-plex of peptide N-term (225.15583272792) modn_peptide</option>\n+ <option value="25">TMT 11-plex of K+8 (237.17713094832) modaa</option>\n+ <option value="26">Label of K 2H(4) (4.025106982920001) modaa</option>\n+ <option value="27">Isoleucine 13C(6) 15N(1) (7.017163920200005) modaa</option>\n+ <option value="28">Arginine 13C(6) (6.020129026799992) modaa</option>\n+ <option value="29">Acetylation of K (42.0105646837) modaa</option>\n+ <option value="30">Dimethylation of peptide N-term 2H(6) 13C(2) (36.075670278260006) modn_peptide</option>\n+ <option value="31">ICPL0 of K (105.02146372057) modaa</option>\n+ <option value="32">Trimethylation of protein N-term A (42.04695019242) modn_protein</option>\n+ <option value="33">Thioacyl of peptide N-term (87.99828574784) modn_peptide</option>\n+ <option value="34">Trideuterated Methyl Ester of R (17.034480301330003) modaa</option>\n+ <option value="35">ICPL4 of peptide N-term (109.04657070349) modn_peptide</option>\n+ <option value="36">4-Hydroxyproline (83.07349929343) modaa</option>\n+ <option value="37">Hex(5) HexNAc(4) NeuAc(2) of N (2204.77244018348) modaa</option>\n+ <option value="38">Palmitoylation of T (238.22966558166) modaa</option>\n+ <option value="39">Palmitoylation of S (238.22966558166) modaa</option>\n+ <option value="40">Methylation of K (14.01565006414) modaa</option>\n+ <option value="41">Hexose of K (162.0528234185) modaa</option>\n+ <option value="42">Methylation of E (14.01565006414) modaa</option>\n+ <option value="43">Lysine 13C(6) (6.020129026799992) modaa</option>\n+ <option value="44">Palmitoylation of K (238.22966558166) modaa</option>\n+ <option value="45">Methylation of C (14.01565006414) modaa</option>\n+ <option value="46">Sodium adduct to D (21.98194424883) modaa</optio'..b'ide N-term (71.03711378471) modn_peptide</option>\n+ <option value="114">Phosphorylation of Y (79.96633052074999) modaa</option>\n+ <option value="115">Didehydro of T (-2.01565006414) modaa</option>\n+ <option value="116">Oxidation of K (15.99491461956) modaa</option>\n+ <!--<option value="117">Oxidation of M (15.99491461956) modaa</option>-->\n+ <option value="118">Phosphorylation of T (79.96633052074999) modaa</option>\n+ <option value="119">Oxidation of P (15.99491461956) modaa</option>\n+ <option value="120">Trioxidation of C (47.98474385868) modaa</option>\n+ <option value="121">Dimethylation of K 2H(6) (34.068960602660006) modaa</option>\n+ <option value="122">NIPCAM of C (99.06841391299) modaa</option>\n+ <option value="123">Methylthio of N (45.987721064140004) modaa</option>\n+ <option value="124">Trideuterated Methyl Ester of K (17.034480301330003) modaa</option>\n+ <option value="125">Heme B of C (616.17729182368) modaa</option>\n+ <option value="126">Trideuterated Methyl Ester of E (17.034480301330003) modaa</option>\n+ <option value="127">Methylthio of C (45.987721064140004) modaa</option>\n+ <option value="128">Phosphorylation of S (79.96633052074999) modaa</option>\n+ <option value="129">Methylthio of D (45.987721064140004) modaa</option>\n+ <option value="130">Heme B of H (616.17729182368) modaa</option>\n+ <option value="131">Trideuterated Methyl Ester of D (17.034480301330003) modaa</option>\n+ <option value="132">ICPL10 of K (115.06669973029) modaa</option>\n+ <option value="133">Deamidation of N 18O (2.9882619631300003) modaa</option>\n+ <option value="134">Dimethylation of peptide N-term 2H(6) (34.068960602660006) modn_peptide</option>\n+ <option value="135">Pyridylethyl of C (105.05784922929) modaa</option>\n+ <option value="136">Arginine 13C(6) 15N(4) (10.008268600400015) modaa</option>\n+ <option value="137">Trideuterated Methyl Ester of peptide C-term (17.034480301330003) modn_peptide</option>\n+ <option value="138">Hex(1)NAc(1) of S (365.13219593801) modaa</option>\n+ <option value="139">TMT 6-plex of K+8 (237.17713094832) modaa</option>\n+ <option value="140">Hex(1)NAc(1) of T (365.13219593801) modaa</option>\n+ <option value="141">TMT 6-plex of K+6 (235.18306116152) modaa</option>\n+ <option value="142">Propionyl of K heavy (59.03627926124) modaa</option>\n+ <option value="143">Citrullination of R (0.9840155826899988) modaa</option>\n+ <option value="144">TMT 6-plex of K+4 (233.18803911764) modaa</option>\n+ <option value="145">mTRAQ of peptide N-term 13C(3) 15N (144.1020624208) modn_peptide</option>\n+ <option value="146">ICPL0 of peptide N-term (105.02146372057) modn_peptide</option>\n+ <option value="147">Geranyl-geranyl of C (272.25040102624) modaa</option>\n+ <option value="148">Lysine 13C(6) 15N(2) (8.014198813600004) modaa</option>\n+ <option value="149">Homoserine lactone of peptide C-term M (-48.00337112828) modcaa_peptide</option>\n+ <option value="150">Carbamidomethylation of E (57.02146372057) modaa</option>\n+ <option value="151">Dimethylation of K 2H(4) (32.0564071112) modaa</option>\n+ <option value="152">Glutathione of C (305.06815621281) modaa</option>\n+ <option value="153">Carbamidomethylation of K (57.02146372057) modaa</option>\n+ <option value="154">iodoTMT zero of C (324.21614077584) modaa</option>\n+ <option value="155">Lipoyl of K (188.0329570044) modaa</option>\n+ <option value="156">Leucine 13C(6) 15N(1) (7.017163920200005) modaa</option>\n+ <option value="157">iTRAQ 4-plex of peptide N-term (144.1020624208) modn_peptide</option>\n+ <option value="158">Deamidation of Q (0.9840155826899988) modaa</option>\n+ <option value="159">Deamidation of N (0.9840155826899988) modaa</option>\n+ </xml>\n+</macros>\n' |
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| diff -r 000000000000 -r 32d3818fc635 pepquery.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pepquery.xml Wed Jan 22 17:12:37 2020 -0500 |
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| b'@@ -0,0 +1,456 @@\n+<tool id="pepquery" name="PepQuery" version="@VERSION@.0">\n+ <description>Peptide-centric search engine for novel peptide identification and validation.</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <requirements> \n+ <requirement type="package" version="@VERSION@">pepquery</requirement>\n+ </requirements>\n+ <stdio>\n+ <exit_code range="1:" level="fatal" description="Failed" />\n+ <regex match="Exception"\n+ source="stderr"\n+ level="fatal"\n+ description="java Exception" />\n+ </stdio>\n+ <command><![CDATA[\n+ #import re\n+ #set $spectrum_file = $re.sub(\'\\s\',\'_\',$re.sub(\'[.][^.]*$\',\'\',$req_inputs.spectrum_file.display_name.split(\'/\')[-1])) + ".mgf"\n+ #set $db_file = $re.sub(\'\\s\',\'_\',$re.sub(\'[.][^.]*$\',\'\',$req_inputs.db_file.display_name.split(\'/\')[-1])) + ".fa"\n+ ln -s \'$req_inputs.spectrum_file\' \'$spectrum_file\' &&\n+ ln -s \'$req_inputs.db_file\' \'$db_file\' &&\n+ pepquery \n+ -ms \'$spectrum_file\'\n+ -db \'$db_file\'\n+ #if $req_inputs.input_type.input_type_selector == \'peptide\'\n+ -pep \'$req_inputs.input_type.multiple.input\'\n+ #else\n+ -t \'$req_inputs.input_type.input_type_selector\'\n+ #if int(str($req_inputs.input_type.input_type_selector)) == 1\n+ -i \'$req_inputs.input_type.multiple.input\'\n+ #else\n+ -i \'$req_inputs.input_type.input\'\n+ #if int(str($req_inputs.input_type.input_type_selector)) == 2\n+ #if $req_inputs.input_type.frame == \'None\'\n+ -f \'0\'\n+ #else\n+ -f \'$req_inputs.input_type.frame\'\n+ #end if\n+ #else\n+ -anno \'$req_inputs.input_type.anno\'\n+ #end if\n+ #end if\n+ #end if\n+ #if $modifications.fixed_mod\n+ -fixMod \'$modifications.fixed_mod\'\n+ #end if\n+ #if $modifications.var_mod\n+ -varMod \'$modifications.var_mod\'\n+ #end if\n+ -maxVar \'$modifications.max_mods\'\n+ $modifications.unmodified\n+ $modifications.aa\n+ -tol \'$ms_params.tolerance_params.precursor_tolerance\'\n+ -tolu \'$ms_params.tolerance_params.precursor_unit\'\n+ -itol \'$ms_params.tolerance_params.tolerance\'\n+ -e \'$ms_params.digestion.enzyme\'\n+ -fragmentMethod \'$ms_params.search.frag_method\'\n+ -m \'$ms_params.search.scoring_method\'\n+ -maxCharge \'$ms_params.search.max_charge\'\n+ -minCharge \'$ms_params.search.min_charge\'\n+ -minPeaks \'$ms_params.search.min_peaks\'\n+ -minScore \'$ms_params.search.min_score\'\n+ -maxLength \'$ms_params.search.max_length\'\n+ -n \'$ms_params.search.num_random_peptides\'\n+ -o pepquery_output\n+ | sed \'s/No valid peptide/Error: No valid peptide/\' | tee >(cat 1>&2)\n+ #if $report_spectrum_file:\n+ && for f in pepquery_output/psm.txt pepquery_output/psm_annotation.txt pepquery_output/detail.txt pepquery_output/psm_rank.txt; do if [ -e \\${f} ]; then cp \\${f} \\${f}.orig; awk \'BEGIN{FS="\\t"; OFS="\\t"; stc = 0;}; NR==1{for (i = 1; i <= NF; i++) {if (\\$i == "spectrum_title") stc = i;}}; NR==1{if (stc>0){\\$stc = "spectrum_file" FS \\$stc}; print}; NR>1{if (stc>0){\\$stc = "$spectrum_file" FS \\$stc}; print}\' \\${f}.orig > \\${f};fi;done\n+ #end if\n+ ]]>\n+ </command>\n+ <inputs>\n+ <section name="req_inputs" title="Input Data" expanded="true">\n+ <condit'..b'</section> \n+ <section name="modifications">\n+ <param name="fixed_mod" value="6,103,157"/>\n+ <param name="var_mod" value="117"/>\n+ <param name="max_mods" value="3"/>\n+ <param name="unmodified" value="False"/>\n+ <param name="aa" value="True"/>\n+ </section>\n+ <section name="ms_params">\n+ <section name="tolerance_params">\n+ <param name="precursor_tolerance" value="10"/>\n+ <param name="precursor_unit" value="ppm"/>\n+ <param name="tolerance" value="0.6"/>\n+ </section>\n+ <section name="digestion">\n+ <param name="enzyme" value="0"/>\n+ <param name="max_missed_cleavages" value="2"/>\n+ </section>\n+ <section name="search">\n+ <param name="frag_method" value="1"/>\n+ <param name="scoring_method" value="1"/>\n+ <param name="max_charge" value="3"/>\n+ <param name="min_charge" value="2"/>\n+ <param name="min_peaks" value="10"/>\n+ <param name="min_score" value="12"/>\n+ <param name="max_length" value="45"/>\n+ <param name="num_random_peptides" value="1000"/>\n+ </section>\n+ </section>\n+ <param name="report_spectrum_file" value="true"/>\n+ <output name="psm_rank_txt">\n+ <assert_contents>\n+ <has_text text="ELGSSDLTAR" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+\n+ </tests>\n+ <help><![CDATA[\n+PepQuery is a peptide-centric search engine for novel peptide identification and validation. Cancer genomics studies have identified a large number of genomic alterations that may lead to novel, cancer-specific protein sequences. Proteins resulted from these genomic alterations are attractive candidates for cancer biomarkers and therapeutic targets. The leading approach to proteomic validation of genomic alterations is to analyze tandem mass spectrometry (MS/MS) data using customized proteomics databases created from genomics data. Such analysis is time-consuming and requires thorough training and detailed knowledge in proteomics data analysis, leading to a gap between MS/MS data and the cancer genomics community. PepQuery does not require customized databases and allows quick and easy proteomic validation of genomic alterations.\n+\n+**Inputs**\n+ - A sequence to match, one of the following:\n+\n+ - A peptide string or a history dataset with a list of peptides \n+ - A protein string or a history dataset with a protein fasta \n+ - A DNA string that is at least 60 base pairs in length\n+\n+ - A mass spectrometry MGF file \n+ - A reference protein fasta database, peptides matching a reference sequence will be excluded. \n+\n+**Outputs**\n+ - PSM annotation - tabular with columns: \n+ peptide Query calc_mr observed_mz charge pepSeq m_label m_mz m_intensity mz intensity\n+ - Detail - tabular with columns: \n+ *report_spectrum_file* spectrum_title peptide modification pep_mass score\n+ - PSM - tabular with columns: \n+ peptide modification n *report_spectrum_file* spectrum_title charge exp_mass ppm pep_mass mz score n_db total_db n_random total_random pvalue\n+ - PSM Rank - tabular with columns: \n+ peptide modification n *report_spectrum_file* spectrum_title charge exp_mass ppm pep_mass mz score n_db total_db n_random total_random pvalue rank *n_ptm*\n+ - An MGF with the best matching spectrums\n+\n+ The *report_spectrum_file* is an optional field that can be added. \n+ The *n_ptm* field is added when using unrestricted modification searching (-um).\n+ \n+\n+ ]]></help>\n+ <citations>\n+ <citation type="doi">10.1101/gr.235028.118</citation>\n+ </citations>\n+</tool>\n' |
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| diff -r 000000000000 -r 32d3818fc635 test-data/Uniprot.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Uniprot.fasta Wed Jan 22 17:12:37 2020 -0500 |
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| b'@@ -0,0 +1,20 @@\n+>sp|Q8C4J7|TBL3_MOUSE Transducin beta-like protein 3 OS=Mus musculus GN=Tbl3 PE=2 SV=1\n+MAETAAGLCRFKANYAVERKIEPFYKGGKAQLDQTGHYLFCVCGTKVNILDVASGALLRSLEQEDQEDITSFDLSPDDEVLVTASRALLLAQWAWREGTVTRLWKAIHTAPVASMAFDATSTLLATGGCDGAVRVWDIVQHYGTHHFRGSPGVVHLVAFHPDPTRLLLFSSAVDTSIRVWSLQDRSCLAVLTAHYSAVTSLSFSEGGHTMLSSGRDKICIVWDLQSYQTTRTVPVFESVEASVLLPEQPAPALGVKSSGLHFLTAGDQGILRVWEAASGQCVYTQPQMPGLRQELTHCTLARAADLLLTVTADHNLLLYEAHSLQLQKQFAGYSEEVLDVRFLGPSDSHIVVASNSPCLKVFELQTLACQILHGHTDIVLALDVFRKGWLFASCAKDQSIRIWKMNKAGQVACVAQGSGHTHSVGTICCSRLKESFLVTGSQDCTVKLWPLPEALLAKSTAADSGPVLLQAQTTRRCHDKDINSLAVSPNDKLLATGSQDRTAKLWALPQCQLLGVFTGHRRGLWNVQFSPTDQVLATASADGTIKLWALQDFSCLKTFEGHDASVLKVAFVSRGSQLLSSGSDGLLKLWTIKSNECVRTLDAHEDKVWGLHCSQLDDHAITGGSDSRIILWKDVTEAEQAEEQAKREEQVIKQQELDNLLHEKRYLRALGLAISLDRPHTVLTVIQAIRRDPEACEKLEATVLRLRRDQKEALLRFCVTWNTNSRHCHEAQAVLGVLLRHEAPEELLAYDGVRGSLEALLPYTERHFQRLSRTLQAATFLDFLWHNMKLSPCPAAAPPAL\n+>tr|Q80ZP8|Q80ZP8_MOUSE Armet protein OS=Mus musculus GN=Manf PE=1 SV=1\n+METNNYLPSPPSFPVCISYLGRFYQDLKDRDVTFSPATIEEELIKFCREARGKENRLCYYIGATDDAATKIINEVSKPLAHHIPVEKICEKLKKKDSQICELKYDKQIDLSTVDLKKLRVKELKKILDDWGEMCKGCAEKSDYIRKINELMPKYAPKAASARTDL\n+>sp|Q60847|COCA1_MOUSE Collagen alpha-1(XII) chain OS=Mus musculus GN=Col12a1 PE=2 SV=3\n+MQTRLPRALAALGVALLLSSIEAEVDPPSDLNFKIIDENTVHMSWERPVDPIVGYRITVDPTTDGPTKEFTLAASTTETLLSDLIPETQYVVTITSYNEVEESVPVIGQLTIQTGGPTKPGEKKPGKTEIQKCSVSAWTDLVFLVDGSWSVGRNNFKYILDFIVALVSAFDIGEEKTRVGVVQYSSDTRTEFNLNQYYRREDLLAAVKKIPYKGGNTMTGDAIDYLVKNTFTESAGSRAGFPKVAIIITDGKSQDEVEIPARELRNIGVEVFSLGIKAADAKELKQIASTPSLNHVFNVANFDAIVDIQNEIISQVCSGVDEQLGELVSGEEVIEPPSNLVVTELSSKYIRLSWDPSPSAVTGYKILLTPMAAGSRHHALSVGPQTTTLNVRDLTADTEYQISVFAMKGLTSSEPTSVMEKTQPMKVQVECSRGVDIKADIVFLVDGSYSIGIANFVKVRAFLEVLAKSFEISPNRVQISLVQYSRDPHTEFTLKEFNRVEDIIKAINTFPYRGGSTNTGKAMTYVREKIFVPNKGSRSNVPKVMILITDGKSSDAFRDPAIKLRNSDVEIFAVGVKDAVRSELEAIASPPAETHVFTVEDFDAFQRISFELTQSICLRIEQELAAIKKKAYVPPKDLRFTQVTANSFKAEWSPPGDNVFSYHVTYKDANGDDEVTVVEPASSTSVVLNNLRPETLYLVNVTAEYEDGFSVPITGEETTAEVKGVPRNLKVTDETTDSFKLTWSQAPGRVLRYRIRYRPVSGGESKEVSTPANQRRKTLENLTPDTKYEISVIAEYSSGPGSPLTGNAATEEVRGNPRDLRVSDATTSTLKLSWSRAPGKVKQYLVTYTPAAGGETQEVTVRGDTTTTMLRKLKEGTQYDLSVTALYASGAGEALSGKGSTLEERGSPQNLVTKDITDTSIGAYWTSAPGMVRGYRVSWKSLYDDIEAGETTLPGDAIHTMIENLQPETKYKISVFATYSSGEGEPVTGDATTELSQDSKILRVDEETEHTMRVTWKAAPGKVVNYRVVYRPQGGGRQMVAKVPPTVTSTVLKRLQPQTTYDITVLPMYKTGEGKLRQGSGTTASRFKSPRNLKTSDPTMSSFRVTWEPAPGEVKGYKVTFHPTGDDRRLGELVLGPYDNTVVLEELRAGTTYRVNVFGMFDGGESLPLVGQEMTTLSDTTVTPFLSSGMDCLTRAEADIVLLVDGSWSIGRANFRTVRSFISRIVEVFEIGPKRVQIALAQYSGDPRTEWQLNAHRDKKSLLQAVANLPYKGGNTLTGMALNFIRQQSFKTQAGMRPRARKIGVLITDGKSQDDVEAPSKKLKDEGVELFAIGIKNADEVELKMIATDPDDTHAYNVADFESLSKIVDDLTINLCNSVKGPGDLEAPTNLVISERTHRSFRVSWTPPSDSVDRYKVEYYPVSGGKRQEFYVSRLDTSTVLKDLKPETDYVVNVYSVVEDEYSEPLKGTEKTLPVPVVSLNIYDVGPTTMHVQWQPVGGATGYTVSYQPTRSPEGTKPKEMRVGPTVNDVQLTGLLPNTEYEVTVQAVLYDLTSEPAKAREVTLPLPRPQDVKLRDVTHSTMNVVWEPVLGKVRKYIVRYKTPDEEFKEVEVDRSRASTILKDLSSQTQYTVSVSAVYDEGTSPPATAYDTTRRVPAPTNLQFTEVTPESFRGTWDHGASDVSLYRITWAPVGNPDKMETILNGDENTLVFENLNPNTPYEVSITAIYPDESESEDLSGTERTLRLIPLTTQAPKSGPRNLQVYNATSNSLTVKWDPASGRVQKYRITYQPSTGEGNEQTITVGGRQNSVLLQKLKPDTPYTITVYSQYPDGEGGRMTGRGKTKPLNTVRNLRVYDPSTSSLSVRWDHAEGNPRQYKLFYAPTSGGPEELVPIPGNTNYAILRNLQPDTPYTITVVPVYTEGDGGRTSDTGRTLVRGLARNIQVYNPTPNSLDVRWDPAPGPVQQYRIVYSPVAGTRPSESIVVPGNTRTVHLERLIPDTPYSVNIVALYSDGEGNPSPSQGRTLPRSGPRNIRVFGETTNSLSVAWDHADGPVQQYRIIYSPTVGDPIDEYTTVPGRRNNVILQPLQPDTPYKITVIAIYEDGDGGHLTGNGRTVGLLPPQNIHIFDEWYTRFRVSWDPSPSPVLGYKIVYKPVGSNEPMEAFVGEVTSYTLHNLNPSTTYDVSVYAQYDSGLSVPLTDQGTTLYLNVTDLKTYQVGWDTFCVKWSPHRAATSYRLKLSPADGTRGQEITVRGSETSHCFTGLSPEAEYGVTVFVQTPNLEGPGVPIKEQTTVKPTEAPTEPPTPSPPPTIPPARDVCKGAKADIVFLTDASWSIGDDNFNKVVKFIFNTVGAFDEVNPAGIQVSFVQYSDEVKSEFKLNTYNDKALALGALQNIRYRGGNTRTGKALTFIKEKVLTWESGMRKNVPKVLVVVTDGRSQDEVKKAAFVIQQSGFSVFVVGVADVDYNELANIASKPSERHVFIVDDFESFEKIEDNLITFVCETATSSCPLIYLDGYTSPGFKMLEAYNLTEKNFASVQGVSLESGSFPSYSAYRLQKNAFINQPTAELHPNGLPPSYTIILLFRLLPETPSDPFAIWQITDRDYRPQVGVIADPSSKTLSFFNKDTRGEVQTVTFDTDEVKTLFYGSFHKVHIVVTSKSVKIYIDCYEIIEKDIKEAGNITTDGYEILGKLLKGERKSATFQIQSFDIVCSPVWTSRDRCCDIPSRRDEAKCPALPNACTCTQDSVGPPGPPGPAGGPG'..b'GPPGPRGDTGPPGPQGPPGPQGPNGLSIPGEQGRQGMKGDAGEPGLPGRTGTPGLPGPPGPMGPPGDRGFTGKDGAMGPRGPPGPPGSPGSPGVTGPSGKPGKPGDHGRPGQSGLKGEKGDRGDIASQNMMRAVARQVCEQLISGQMSRFNQMLNQIPNDYHSSRNQPGPPGPPGPPGSAGARGEPGPGGRPGFPGTPGMQGPPGERGLPGEKGERGTGSQGPRGPPGPPGPQGESRTGPPGSTGSRGPPGPPGRPGNSGIRGPPGPPGYCDSSQCASIPYNGQGYPEPYVPEGGAYLPEREPFIVPVEPERTAEYEDDYGADEPDQQHPDHMRWRRALRPGPAE\n+>tr|D6RFR8|D6RFR8_MOUSE Choline/ethanolaminephosphotransferase 1 OS=Mus musculus GN=Cept1 PE=4 SV=1\n+MSGHRSTRKRCGDSHPESPVGFGHMSTTGHLCGLILPVLVAFSFTSLWMP\n+>tr|Q91VK2|Q91VK2_MOUSE Eef1d protein OS=Mus musculus GN=Eef1d PE=1 SV=1\n+MATNFLAHEKIWFDKFKYDDAERRFYEQMNGPVTSGSRQLKVMLPNSPEALGQATPGTSSGPGASSGPGGDHSELIVRITSLEVENQNLRGVVQDLQQAISKLEARLSSLEKSSPTPRATAPQTQHVSPMRQVEPPTKKGATPAEDDEDKDIDLFGSDEEEEDKEAARLREERLRQYAEKKAKKPTLVAKSSILLDVKPWDDETDMAQLETCVRSIQLDGLVWGASKLVPVGYGIRKLQIQCVVEDDKVGTDLLEEEITKFEEHVQSVDIAAFNKI\n+>tr|F6WN43|F6WN43_MOUSE Iron-sulfur cluster co-chaperone protein HscB, mitochondrial (Fragment) OS=Mus musculus GN=Hscb PE=1 SV=1\n+XQKSQTEKHFSDKHSTLVNDAYKTLQAPLTRGLYLVS\n+>sp|Q6NXK2|ZN532_MOUSE Zinc finger protein 532 OS=Mus musculus GN=Znf532 PE=1 SV=1\n+MTMGDMKTPDFDDLLAAFDIPDMVDPKAAIESGHDDHESHIKQNAHVDDDSHTPSSSDVGVSVIVKNVRNIDSSEGVEKDGHNPTGNGLHNGFLTASSLDSYGKDGAKSLKGDTPASEVTLKDPAFSQFSPISSAEEFEDDEKIEVDDPPDKEEARAGFRSNVLTGSAPQQDFDKLKALGGENSSKTGVSTSGHTDKNKVKREAESNSITLSVYEPFKVRKAEDKLKENSEKMLESRVLDGKPSSEKSDSGIAAAASSKTKPSSKLSSCIAAIAALSAKKAASDSCKEPVANSREASPLPKEVNDSPKAADKSPESQNLIDGTKKASLKPSDSPRSVSSENSSKGSPSSPVGSTPAIPKVRIKTIKTSSGEIKRTVTRVLPEVDLDSGKKPSEQAASVMASVTSLLSSSASATVLSSPPRAPLQTAMVTSAVSSAELTPKQVTIKPVATAFLPVSAVKTAGSQVINLKLANNTTVKATVISAASVQSASSAIIKAANAIQQQTVVVPASSLANAKLVPKTVHLANLNLLPQGAQATSELRQVLTKPQQQIKQAIINAAASQPPKKVSRVQVVSSLQSSVVEAFNKVLSSVNPVPVYTPNLSPPANAGITLPMRGYKCLECGDAFALEKSLSQHYDRRSVRIEVTCNHCTKNLVFYNKCSLLSHARGHKEKGVVMQCSHLILKPVPADQMIVPPSSNTAASTLQSSVGAATHTVPKVQPGIAGAVISAPASTPMSPAMPLDEDPSKLCRHSLKCLECNEVFQDEPSLATHFQHAADTSGQQMKKHPCRQCDKSFSSSHSLCRHNRIKHKGIRKVYACSHCPDSRRTFTKRLMLERHIQLMHGIKDPDVKELSDDAGDVTNDEEEEAEIKEDAKVPSPKRKLEEPVLEFRPPRGAITQPLKKLKINVFKVHKCAVCGFTTENLLQFHEHIPQHRSDGSSHQCRECGLCYTSHGSLARHLFIVHKLKEPQPVSKQNGAGEDSQQENKPSPEDEAAEGAASDRKCKVCAKTFETEAALNTHMRTHGMAFIKSKRMSSAEK\n+>sp|P58006|SESN1_MOUSE Sestrin-1 OS=Mus musculus GN=Sesn1 PE=1 SV=3\n+MRLAAASNEAYAASLAVSELLSCHQCGGDRGQDEELGIRIPRPLGHGPSRFIPEKEMLQVGSEDAQMHALFADSFAALGRLDNITLVMVFHPQYLESFLKTQHYLLQMDGPLPLHYRHYIGIMAAARHQCSYLVNLHVSDFLHVGGDPKWLNGLENAPQKLQNLGELNKVLAHRPWLITKEHIEGLLKAEEHSWSLAELVHAVVLLTHYHSLASFTFGCGISPEIHCDGGHTFRPPSVSNYCICDITNGNHSVDEMQVNSAGNASVSDSFFEVEALMEKMRQLQECREEEEASQEEMASRFEMEKRESMFVFSSDDDEVTPARDVSRHFEDTSYGYKDFSRHGMHVPTFRVQDYCWEDHGYSLVNRLYPDVGQLIDEKFHIAYNLTYNTMAMHKDVDTSMLRRAIWNYIHCMFGIRYDDYDYGEINQLLDRSFKVYIKTVVCTPEKVTKRMYDSFWRQFKHSEKVHVNLLLIEARMQAELLYALRAITRYMT\n+>tr|A0A1B0GSE5|A0A1B0GSE5_MOUSE Ubiquitin carboxyl-terminal hydrolase CYLD OS=Mus musculus GN=Cyld PE=1 SV=1\n+MSSGLWSQEKVTSPYWEERIFYLLLQECSVTDKQTQKLLKVPKGSIGQYIQDRSVGHSRVPSTKGKKNQIGLKILEQPHAVLFVDEKDVVEINEKFTELLLAITNCEERLSLFRNRLRLSKGLQVDVGSPVKVQLRSGEEKFPGVVRFRGPLLAERTVSGIFFGVELLEEGRGQGFTDGVYQGKQLFQCDEDCGVFVALDKLELIEDDDNGLESDFAGPGDTMQVEPPPLEINSRVSLKVGESTESGTVIFCDVLPGKESLGYFVGVDMDNPIGNWDGRFDGVQLCSFASVESTILLHINDIIPDSVTQERRPPKLAFMSRGVGDKGSSSHNKPKVTGSTSDPGSRNRSELFYTLNGSSVDSQQSKSKNPWYIDEAFGGYLSEVVEENTPPKMEKEGLEIMIGKKKGIQGHYNSCYLDSTLFCLFAFSSALDTVLLRPKEKNDIEYYSETQELLRTEIVNPLRIYGYVCATKIMKLRKILEKVEAASGFTSEEKDPEEFLNILFHDILRVEPLLKIRSAGQKVQDCNFYQIFMEKNEKVGVPTIQQLLEWSFINSNLKFAEAPSCLIIQMPRFGKDFKLFKKIFPSLELNITDLLEDTPRQCRICGGLAMYECRECYDDPDISAGKIKQFCKTCSTQVHLHPRRLNHSYHPVSLPKDLPDWDWRHGCIPCQKMELFAVLCIETSHYVAFVKYGKDDSAWLFFDSMADRDGGQNGFNIPQVTPCPEVGEYLKMSLEDLHSLDSRRIQGCARRLLCDAYMCMYQSPTMSLYK\n+>sp|Q60880|OL141_MOUSE Olfactory receptor 141 OS=Mus musculus GN=Olfr141 PE=3 SV=2\n+MRNITEATFFVLKGLTDNNELQIILFLLFLAIYIFTLIGNVGLIILVVGDSQLHNPMYCFLSVLSSVDACYSTDITPNMLVGFMSKSKIISFYGCATQMFLAVTFGTTECFLLAAMAYDRYVAIHDPLLYAVSMSPRVYIPLIIASYAGGIVHAIIHTVATFSLSFCRSNEVKHIFCDIPPLLAISCSETYVNELLLFFFVSFIELVTILIVLVSYAFILLSILKMNSSEGRRKVFSTCGAHLTAVSIYYGTILFMYVRPSSNYSLEHDMIVSTFYTIGIPMLNPIIYSLRNKDVKEAMKRVLRKKINIKHRIKKLNDFSVFLMP\n' |
| b |
| diff -r 000000000000 -r 32d3818fc635 test-data/iTRAQ_f4.mgf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/iTRAQ_f4.mgf Wed Jan 22 17:12:37 2020 -0500 |
| b |
| b'@@ -0,0 +1,753 @@\n+COM=Conversion to mascot generic\n+CHARGE=2+ and 3+\n+BEGIN IONS\n+PEPMASS=740.462952\n+CHARGE=3+\n+SCANS=277\n+TITLE=Mo_Tai_iTRAQ_f4.00277.00277.3\n+111.017494 85.198502\n+112.240982 97.204994\n+114.110542 168.274780\n+115.107582 369.265503\n+115.650398 84.005325\n+117.296082 86.641182\n+117.595589 82.974037\n+120.657990 81.247025\n+123.208023 88.939392\n+126.714996 76.470490\n+126.995316 81.651260\n+129.369080 82.580246\n+129.410400 90.817963\n+132.734039 124.614685\n+143.307465 87.847046\n+178.966888 94.961578\n+179.972855 89.878273\n+183.256714 104.533241\n+188.080093 123.015953\n+212.102753 442.314178\n+213.104324 84.621696\n+233.001801 107.842552\n+244.242355 102.163200\n+281.079132 97.696259\n+291.216034 243.588058\n+309.183807 104.681831\n+325.188324 282.187622\n+345.226288 167.099777\n+347.629883 88.744476\n+357.377533 105.747673\n+388.266266 1321.324341\n+430.317047 94.113419\n+458.310547 310.033203\n+489.807434 100.114334\n+490.700165 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1886.298706\n+930.495483 1311.800903\n+952.429504 625.323181\n+965.766296 606.633911\n+972.546692 2437.769531\n+999.546753 632.162537\n+1026.609131 980.280151\n+1040.573853 1742.042114\n+1041.564087 3165.200439\n+1042.581787 3063.955566\n+1043.577515 6683.765625\n+1045.518311 945.700500\n+1147.621704 832.881104\n+1148.635742 1159.247681\n+1467.104980 653.335815\n+1533.474243 661.718018\n+1620.307251 616.238525\n+1664.717529 648.275024\n+END IONS\n' |
| b |
| diff -r 000000000000 -r 32d3818fc635 test-data/novel_peptides --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/novel_peptides Wed Jan 22 17:12:37 2020 -0500 |
| b |
| @@ -0,0 +1,3 @@ +DSGASGSILEASAAR +ELGSSDLTAR +SPYREFTDHLVK |
| b |
| diff -r 000000000000 -r 32d3818fc635 test-data/novel_proteins.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/novel_proteins.fa Wed Jan 22 17:12:37 2020 -0500 |
| b |
| @@ -0,0 +1,6 @@ +>DSGASGSILEASAAR +DSGASGSILEASAAR +>ELGSSDLTAR +ELGSSDLTAR +>SPYREFTDHLVK +SPYREFTDHLVK |