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Show the list of peptides in a table - for use as a CGI application.
/* ############################################################################## # file: peptide_list.cpp # # 'msparser' toolkit # # Test harness / example code # ############################################################################## # COPYRIGHT NOTICE # # Copyright 1998-2005 Matrix Science Limited All Rights Reserved. # # # ############################################################################## # $Source: parser/examples/test_cxx/peptide_list.cpp $ # # $Author: villek@matrixscience.com $ # # $Date: 2018-07-30 16:23:53 +0100 $ # # $Revision: 1b450440f9c97e1e41d0fc6016a27d68951d4532 | MSPARSER_REL_2_8_1-0-gea32989045 $ # # $NoKeywords:: $ # ############################################################################## */ /* ############################################################################## # Print out a table of results - peptide based list for QA # Table should contain a list of unique peptides - every significant match # Copy the executable to the mascot/cgi directory, and then, when looking # at a report replace the master_results.pl in the URL with peptide_list.exe ############################################################################## */ #include "msparser.hpp" #include <set> #include <iostream> #include <time.h> #include <iomanip> // All the classes are part of the matrix_science namespace using namespace matrix_science; /*****************************************************************************/ /* main */ /* Call this program with a single argument - file=[name of the .dat file] */ /*****************************************************************************/ int main(int argc, char * argv[]) { #ifdef _DEBUG putenv("QUERY_STRING=file=../data/20021123/F018521.dat"); #endif std::cout << "Content-type: text/html" << std::endl << std::endl; std::cout << "<HTML>" << std::endl; std::cout << "<HEAD>" << std::endl; std::cout << " <TITLE>Mascot summary</TITLE>" << std::endl; std::cout << "</HEAD>" << std::endl; std::cout << "<BODY BGCOLOR=\"#ffffff\">" << std::endl;; if (getenv("QUERY_STRING") && strncmp(getenv("QUERY_STRING"), "file=", 5) == 0) { ms_mascotresfile file(getenv("QUERY_STRING")+strlen("file=")); if (file.isValid()) { if (file.isMSMS()) { ms_mascotresults * results; results = new ms_peptidesummary(file, ms_mascotresults::MSRES_GROUP_PROTEINS | ms_mascotresults::MSRES_SHOW_SUBSETS, 0, // minProbability 1000, // number of hits 0, // ignoreIonsScoreBelow 0); // minimum peptide length ms_protein * prot = results->getHit(1); if (!prot) std::cout << "No significant matches" << std::endl; else { std::set<std::string> pep_strings; std::cout << "<TABLE BORDER=1>" << std::endl; std::cout << " <TR>" << std::endl; std::cout << " <TD><B>Peptide</B></TD>" << std::endl << " <TD><B>Score</B></TD>" << std::endl << " <TD><B>Query</B></TD>" << std::endl << " <TD><B>Rank</B></TD>" << std::endl << " <TD><B>Proteins</B></TD>" << std::endl; std::cout << " </TR>" << std::endl; for (int query=1; query <= file.getNumQueries(); query++) { for (int p=1; p <= 10; p++) { double threshold = results->getPeptideIdentityThreshold(query, 20); ms_peptide * pep; if ( results->getPeptide(query, p, pep) && (pep->getIonsScore() >= threshold)) { if (pep_strings.insert(pep->getPeptideStr()).second) { std::cout << " <TR>" << std::endl; std::cout << " <TD>" << pep->getPeptideStr().c_str() << " </TD>" << std::endl; std::cout << " <TD>" << pep->getIonsScore() << " </TD>" << std::endl; std::cout << " <TD>" << query << " </TD>" << std::endl; std::cout << " <TD>" << p << " </TD>" << std::endl; std::cout << " <TD>" << results->getProteinsWithThisPepMatch(query, p).c_str() << " </TD>" << std::endl; std::cout << " </TR>" << std::endl; } } } } std::cout << "</TABLE>" << std::endl; } if (file.getLastError()) { std::cout << "There was an error..." << std::endl; std::cout << "Error: " << file.getLastErrorString() << std::endl; } } } else std::cout << "Error: " << file.getLastErrorString() << std::endl; } else std::cout << "Must supply 'file=[name of a .dat file]'" << "Number of args = " << argc << "QS=" << getenv("QUERY_STRING") <<std::endl; std::cout << "</BODY>" << std::endl;; std::cout << "</HTML>" << std::endl;; return 0; } /* Will give for example the following output: <TABLE BORDER=1> <TR> <TD><B>Peptide</B></TD> <TD><B>Score</B></TD> <TD><B>Query</B></TD> <TD><B>Rank</B></TD> <TD><B>Proteins</B></TD> </TR> <TR> <TD>GPSSVEDIK </TD> <TD>68.06 </TD> <TD>17 </TD> <TD>1 </TD> <TD>9:Q96AT6 </TD> </TR> <TR> <TD>SGEVLVNVK </TD> <TD>79.37 </TD> <TD>18 </TD> <TD>1 </TD> <TD>13:S60335 15:Q9QZD9 </TD> </TR> <TR> <TD>MSDGLFLQK </TD> <TD>54.93 </TD> <TD>29 </TD> <TD>1 </TD> <TD>16:S55282 </TD> </TR> <TR> <TD>LGGSQEDQIK </TD> <TD>67.93 </TD> <TD>31 </TD> <TD>1 </TD> <TD>2:AAH10103 </TD> </TR> <TR> <TD>AGLGHPAAFGR </TD> <TD>57.48 </TD> <TD>34 </TD> <TD>1 </TD> <TD>19:DDH1_HUMAN </TD> </TR> <TR> <TD>TPEEYPESAK </TD> <TD>54.88 </TD> <TD>37 </TD> <TD>1 </TD> <TD>19:DDH1_HUMAN </TD> </TR> <TR> <TD>SSGTSYPDVLK </TD> <TD>63.42 </TD> <TD>38 </TD> <TD>1 </TD> <TD>4:TRBOTR 6:1NTP </TD> </TR> <TR> <TD>VCNYVSWIK </TD> <TD>55.78 </TD> <TD>41 </TD> <TD>1 </TD> <TD>4:TRBOTR 6:1NTP </TD> </TR> <TR> <TD>IDTIEIITDR </TD> <TD>69.04 </TD> <TD>43 </TD> <TD>1 </TD> <TD>8:AAC26867 11:Q9TTV2 </TD> </TR> <TR> <TD>DITSDTSGDFR </TD> <TD>69.53 </TD> <TD>45 </TD> <TD>1 </TD> <TD>1:LUHU 3:AAB19866 7:ANX1_MOUSE </TD> </TR> <TR> <TD>LLGELLQDNAK </TD> <TD>64.14 </TD> <TD>46 </TD> <TD>1 </TD> <TD>2:AAH10103 </TD> </TR> <TR> <TD>VGMIPVPYVEK </TD> <TD>54.23 </TD> <TD>52 </TD> <TD>1 </TD> <TD>18:S41754 </TD> </TR> <TR> <TD>TPAQFDADELR </TD> <TD>66.27 </TD> <TD>53 </TD> <TD>1 </TD> <TD>1:LUHU 3:AAB19866 5:AAC78495 7:ANX1_MOUSE 27:CAA64477 </TD> </TR> <TR> <TD>LSSTWEGIQAGK </TD> <TD>77.53 </TD> <TD>54 </TD> <TD>1 </TD> <TD>2:AAH10103 </TD> </TR> <TR> <TD>SLDLDSIIAEVK </TD> <TD>80.49 </TD> <TD>56 </TD> <TD>1 </TD> <TD>17:AAG41947 </TD> </TR> <TR> <TD>AVLENNLGAAVLR </TD> <TD>57.63 </TD> <TD>63 </TD> <TD>1 </TD> <TD>36:Q9BS89 </TD> </TR> <TR> <TD>ALEESNYELEGK </TD> <TD>59.06 </TD> <TD>67 </TD> <TD>1 </TD> <TD>22:KRMSE1 </TD> </TR> <TR> <TD>VLGTEELYGYLK </TD> <TD>65.31 </TD> <TD>68 </TD> <TD>1 </TD> <TD>14:B35838 </TD> </TR> <TR> <TD>VLGTDELYGYLK </TD> <TD>65.31 </TD> <TD>68 </TD> <TD>2 </TD> <TD>12:B38611 </TD> </TR> <TR> <TD>GVDEATIIDILTK </TD> <TD>73.44 </TD> <TD>69 </TD> <TD>1 </TD> <TD>1:LUHU 3:AAB19866 5:AAC78495 7:ANX1_MOUSE 20:LUGP1 </TD> </TR> <TR> <TD>QSLEASLAETEGR </TD> <TD>60.48 </TD> <TD>70 </TD> <TD>1 </TD> <TD>22:KRMSE1 </TD> </TR> <TR> <TD>TPYTDVNIVTIR </TD> <TD>73.23 </TD> <TD>71 </TD> <TD>1 </TD> <TD>16:S55282 </TD> </TR> <TR> <TD>ALAGCDFLTISPK </TD> <TD>58.07 </TD> <TD>72 </TD> <TD>1 </TD> <TD>2:AAH10103 </TD> </TR> <TR> <TD>WELLQQVDTSTR </TD> <TD>64.49 </TD> <TD>80 </TD> <TD>1 </TD> <TD>17:AAG41947 </TD> </TR> <TR> <TD>EVYQQQQYGSGGR </TD> <TD>66.95 </TD> <TD>83 </TD> <TD>1 </TD> <TD>10:Q9BQ99 </TD> </TR> <TR> <TD>IFVGGLNPEATEEK </TD> <TD>62.15 </TD> <TD>84 </TD> <TD>1 </TD> <TD>10:Q9BQ99 </TD> </TR> <TR> <TD>IFVGGINPEATEEK </TD> <TD>62.15 </TD> <TD>84 </TD> <TD>2 </TD> <TD>23:PC4375 </TD> </TR> <TR> <TD>QLYQILTDFDIR </TD> <TD>63.62 </TD> <TD>87 </TD> <TD>1 </TD> <TD>12:B38611 14:B35838 </TD> </TR> <TR> <TD>GTDVNVFNTILTTR </TD> <TD>71.62 </TD> <TD>93 </TD> <TD>1 </TD> <TD>1:LUHU 3:AAB19866 </TD> </TR> <TR> <TD>SDSEKLNLDSIIGR </TD> <TD>58.2 </TD> <TD>96 </TD> <TD>1 </TD> <TD>39:Q9Z1G2 </TD> </TR> <TR> <TD>DSCQGDSGGPVVCSGK </TD> <TD>71.13 </TD> <TD>97 </TD> <TD>1 </TD> <TD>4:TRBOTR 6:1NTP </TD> </TR> <TR> <TD>DLAKDITSDTSGDFR </TD> <TD>57.65 </TD> <TD>99 </TD> <TD>1 </TD> <TD>1:LUHU 3:AAB19866 7:ANX1_MOUSE </TD> </TR> <TR> <TD>GLGTDEDTLIEILASR </TD> <TD>87.32 </TD> <TD>103 </TD> <TD>1 </TD> <TD>1:LUHU 5:AAC78495 </TD> </TR> <TR> <TD>GAGTEEACLIDILASR </TD> <TD>54.48 </TD> <TD>103 </TD> <TD>2 </TD> <TD>33:O93444 </TD> </TR> <TR> <TD>SEDFGVNEDLADSDAR </TD> <TD>103.46 </TD> <TD>105 </TD> <TD>1 </TD> <TD>1:LUHU </TD> </TR> <TR> <TD>LISWYDNEFGYSNR </TD> <TD>58.42 </TD> <TD>107 </TD> <TD>1 </TD> <TD>28:DEHUG3 30:AAC16069 </TD> </TR> <TR> <TD>LVTWYDNEFGYSNR </TD> <TD>57.61 </TD> <TD>107 </TD> <TD>2 </TD> <TD>37:Q90Z48 </TD> </TR> <TR> <TD>TPALVFEYINNTDFK </TD> <TD>69.27 </TD> <TD>108 </TD> <TD>1 </TD> <TD>12:B38611 14:B35838 </TD> </TR> <TR> <TD>IFVGGLNPEATEEKIR </TD> <TD>54.63 </TD> <TD>109 </TD> <TD>1 </TD> <TD>10:Q9BQ99 </TD> </TR> <TR> <TD>IFVGGINPEATEEKIR </TD> <TD>54.63 </TD> <TD>109 </TD> <TD>2 </TD> <TD>23:PC4375 </TD> </TR> <TR> <TD>VGAVAGNDWLIWDITR </TD> <TD>63.06 </TD> <TD>113 </TD> <TD>1 </TD> <TD>35:Q9H644 </TD> </TR> <TR> <TD>VGAVAGNDWIIWDITR </TD> <TD>63.06 </TD> <TD>113 </TD> <TD>2 </TD> <TD>32:Q9CWU9 </TD> </TR> <TR> <TD>LFIGGLSFETTDESLR </TD> <TD>61.89 </TD> <TD>117 </TD> <TD>1 </TD> <TD>25:1HA11 </TD> </TR> <TR> <TD>LFIGGLSFETTEESLR </TD> <TD>61.89 </TD> <TD>117 </TD> <TD>2 </TD> <TD>8:AAC26867 21:S40776 </TD> </TR> <TR> <TD>LFIGGLSFETTDDSLR </TD> <TD>61.89 </TD> <TD>117 </TD> <TD>3 </TD> <TD>26:Q9CRI0 </TD> </TR> <TR> <TD>MTDQEAIQDLWQWR </TD> <TD>58.31 </TD> <TD>118 </TD> <TD>1 </TD> <TD>9:Q96AT6 </TD> </TR> <TR> <TD>GFSEGLWEIENNPTVK </TD> <TD>54.12 </TD> <TD>119 </TD> <TD>1 </TD> <TD>24:Q9XSK7 </TD> </TR> <TR> <TD>QAWFIENEEQEYVQTVK </TD> <TD>71.47 </TD> <TD>132 </TD> <TD>1 </TD> <TD>1:LUHU </TD> </TR> <TR> <TD>LGEDNINVVEGNEQFISASK </TD> <TD>83.36 </TD> <TD>134 </TD> <TD>1 </TD> <TD>4:TRBOTR 6:1NTP </TD> </TR> <TR> <TD>MSVQPTVSLGGFEITPPVVLR </TD> <TD>81.19 </TD> <TD>140 </TD> <TD>1 </TD> <TD>9:Q96AT6 </TD> </TR> <TR> <TD>GGPGSAVSPYPTFNPSSDVAALHK </TD> <TD>64.58 </TD> <TD>149 </TD> <TD>1 </TD> <TD>1:LUHU </TD> </TR> </TABLE> */
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