Example program for retrieving input spectrum data.
#!/usr/local/bin/perl ############################################################################## # file: resfile_input.pl # # 'msparser' toolkit # # Test harness / example code # ############################################################################## # COPYRIGHT NOTICE # # Copyright 1998-2010 Matrix Science Limited All Rights Reserved. # # # ############################################################################## # $Source: parser/examples/test_perl/resfile_input.pl $ # # $Author: villek@matrixscience.com $ # # $Date: 2018-07-30 16:23:53 +0100 $ # # $Revision: 1b450440f9c97e1e41d0fc6016a27d68951d4532 | MSPARSER_REL_2_8_1-0-gea32989045 $ # # $NoKeywords:: $ # ############################################################################## use strict; ############################################################################## use msparser; if (!defined($ARGV[0])) { die "Must specify results filename as parameter"; } my $file = new msparser::ms_mascotresfile($ARGV[0]); if ($file->isValid) { inputData($file); } ############################################################################## # inputData # # - parameter 0 ms_mascotresfile # # Display input data # ############################################################################## sub inputData { my ($resfile) = @_; # display input data via inputquery get functions for my $i (1 .. 1) { # replace 1 .. 1 with 1 .. $resfile->getNumQueries() to get all input # data. print "Input data for query number ", $i , "\n"; print "=========================================", "\n"; my $q = new msparser::ms_inputquery($resfile, $i); my $fmt = " %-16s: %s\n"; printf $fmt, "title" , $q->getStringTitle(1); printf $fmt, "mass_min" , $q->getMassMin(); printf $fmt, "mass_max" , $q->getMassMax(); printf $fmt, "int_min" , $q->getIntMin(); printf $fmt, "int_max" , $q->getIntMax(); printf $fmt, "num_vals" , $q->getNumVals(); printf $fmt, "num_used1" , $q->getNumUsed(); printf $fmt, "ions1" , $q->getStringIons1(); printf $fmt, "ions2" , $q->getStringIons2(); printf $fmt, "ions3" , $q->getStringIons3(); printf $fmt, "peptol" , $q->getPepTol(); printf $fmt, "peptol units", $q->getPepTolUnits(); printf $fmt, "peptol str" , $q->getPepTolString(); printf $fmt, "repeat srch" , $resfile->getRepeatSearchString($i); my $num_peaks = $q->getNumberOfPeaks(1); for my $j (1 .. $num_peaks) { print $q->getPeakMass(1, $j), ", ", $q->getPeakIntensity(1, $j), "\n"; } } print "\n\n"; } =pod Running the program as perl -I../bin resfile_input.pl ../data/F981123.dat will give the following output under Mascot Server 2.3: Input data for query number 1 ========================================= title : mass_min : 72.09 mass_max : 1711.52 int_min : 1.103 int_max : 80.7 num_vals : 425 num_used1 : 0 ions1 : 157.096962:23.72,185.160000:26.69,286.134951:80.7,385.210000:13.49,480.270000:4.363,129.102412:18.84,187.070000:22.51,354.189124:13.57,399.246727:9.489,482.140542:3.205,130.110251:9.257,258.132661:15.93,357.210000:13.57,443.810000:6.256,481.210000:3.182,136.070000:7.387,213.139215:13.84,371.204929:11.24,459.280000:6.216,489.233770:3.157,147.117662:6.333,229.120000:9.72,326.133204:5.268,423.125582:4.262,483.115000:2.205,159.080000:5.222,240.130000:7.562,298.110000:5.231,444.168974:3.247,474.300000:1.103,158.090000:4.301,270.180000:7.432,324.170000:5.17,411.200000:3.23,475.270000:1.103,86.110000:3.276,175.110000:7.308,312.150879:4.235,463.265712:3.205,476.700000:1.103,102.060000:3.276,241.085275:5.361,293.110000:4.178,445.810000:3.182,478.180000:1.103,115.088725:3.255,243.139772:4.378,353.155308:4.149,401.150000:3.138,486.880000:1.103,72.090000:2.174,76.400000:1.103,84.075000:2.111,87.110000:1.103,88.100000:1.103,98.060000:1.103,103.060000:1.103,105.070000:1.103,116.070000:1.103,117.110000:1.103,118.400000:1.103,120.090000:2.205,126.070000:1.103,127.090000:1.103,128.090000:2.103,131.085000:2.118,132.090000:1.103,135.800000:1.103,137.080000:1.103,138.070000:1.103,139.090000:1.103,140.150000:2.174,141.060000:2.174,143.120000:2.174,146.080000:1.103,152.060000:1.103,155.070000:2.205,156.100000:1.103,159.450000:1.103,165.080000:2.136,166.110000:1.103,167.110000:1.103,169.710000:1.103,170.450000:1.103,171.090000:1.103,173.120000:2.174,177.090000:1.103,178.080000:1.103,181.160000:1.103,182.030000:1.103,183.110000:2.174,183.930000:1.103,186.131024:4.374,188.070000:1.103,188.760000:1.103,189.070000:1.103,190.065000:2.103,191.300000:1.103,197.130000:1.103,199.180000:1.103,200.080000:1.103,201.100000:3.138,202.110000:2.091,203.080000:2.174,203.610000:1.103,211.140000:4.189,212.115000:2.103,212.490000:1.103,214.985000:2.205,216.110000:2.103,217.100000:1.103,218.080000:1.103,219.090000:2.103,223.090000:3.154,224.130000:1.103,225.130000:1.103,227.170000:1.103,227.880000:1.103,228.170000:2.136,229.760000:1.103,231.950000:1.103,233.130000:1.103,234.430000:1.103,235.080000:2.103,236.590000:1.103,238.080000:4.332,239.139997:3.131,242.170000:2.205,244.090000:2.136,244.430000:2.091,245.165685:3.205,246.160000:2.197,247.110000:2.102,248.145000:2.118,249.110000:2.136,250.080000:1.103,251.160000:1.103,253.100000:1.103,254.130000:1.103,255.165000:2.22,256.170000:1.103,257.060000:1.103,259.150000:2.197,260.000000:1.103,260.490000:1.103,262.110000:1.103,265.120000:1.103,266.130000:2.159,266.950000:1.103,267.210000:1.103,268.120000:3.214,269.090000:1.103,271.150000:2.136,272.170000:2.103,274.120000:1.103,275.030000:1.103,276.175000:2.22,278.190000:1.103,279.720000:2.205,281.120000:1.103,283.070000:1.103,284.110000:1.103,285.070000:1.103,287.140000:3.296,287.780000:1.103,288.090000:2.103,290.130000:1.103,294.110000:2.174,295.150000:3.114,295.730000:1.103,297.180000:2.136,300.160000:3.143,302.070000:1.103,303.160000:1.103,303.590000:1.103,304.600000:1.103,305.130000:1.103,306.140000:3.182,307.050000:1.103,308.150000:2.174,308.490000:1.103,312.610000:1.103,312.880000:1.103,314.120000:1.103,316.085000:2.111,317.150000:3.183,318.140000:1.103,320.140000:1.103,322.149731:3.255,323.034482:3.149,327.020000:1.103,328.020000:1.103,331.140000:2.091,332.165000:2.103,333.140000:1.103,335.500000:1.103,336.190000:1.103,337.030000:2.118,338.620000:1.103,338.940000:1.103,339.200000:3.261,341.210000:2.103,342.180000:1.103,342.800000:1.103,343.225000:2.111,343.800000:1.103,344.150000:2.174,346.010000:1.103,347.660000:1.103,348.200000:2.197,349.800000:1.103,350.110000:2.118,351.130000:3.276,352.130000:2.136,353.910000:1.103,354.470000:1.103,355.193955:3.376,358.200000:1.103,359.210000:2.174,359.910000:1.103,360.470000:1.103,361.080000:1.103,362.190000:1.103,363.040000:1.103,364.080000:1.103,366.120000:1.103,367.150000:1.103,368.330000:1.103,368.730000:1.103,369.230000:3.15,369.820000:1.103,370.177065:3.279,373.130000:2.197,374.055000:2.217,374.510000:2.205,376.040000:1.103,377.040000:1.103,380.160000:2.103,382.180000:3.102,383.115000:2.209,385.890000:2.205,386.370000:1.103,387.170000:3.114,387.680000:2.217,388.050000:1.103,389.620000:1.103,390.190000:1.103,390.610000:1.103,394.260000:1.103,395.180000:1.103,396.140000:2.205,397.980000:1.103,400.165000:2.209,403.210000:1.103,404.150000:1.103,404.470000:1.103,410.165000:2.111,411.550000:1.103,413.240000:1.103,414.080000:1.103,415.000000:1.103,416.190000:1.103,416.830000:1.103,417.230000:1.103,417.760000:1.103,418.285000:2.111,418.680000:1.103,420.650000:1.103,421.170000:2.136,422.580000:1.103,425.215000:2.103,425.690000:1.103,426.220000:3.125,428.140000:2.155,428.650000:1.103,430.260000:1.103,430.995000:2.205,433.200000:1.103,433.690000:1.103,435.000000:1.103,435.260000:1.103,437.180000:1.103,438.710000:2.174,439.230000:1.103,440.210000:1.103,442.190000:1.103,443.120000:1.103,444.680000:1.103,445.120000:1.103,449.110000:1.103,450.710000:1.103,452.150000:2.209,453.240000:3.12,454.200000:1.103,454.700000:1.103,458.310000:1.103,460.290000:1.103,461.250000:1.103,461.830000:1.103,462.195000:2.103,463.850000:1.103,464.250000:1.103,467.180000:2.174,470.210000:1.103,471.120000:1.103,489.700000:1.103,493.200000:1.103,494.200000:1.103,505.200000:1.103,508.170000:2.197,508.840000:1.103,509.200000:2.103,511.450000:1.103,522.170000:2.197,523.190000:1.103,524.150000:2.174,527.160000:1.103,528.410000:2.19,529.280000:1.103,530.230000:1.103,531.250000:1.103,533.130000:1.103,533.670000:1.103,536.720000:1.103,537.240000:1.103,538.080000:1.103,538.450000:1.103,540.220000:1.103,545.210000:2.174,545.490000:1.103,546.250000:1.103,547.350000:1.103,550.750000:2.205,558.070000:1.103,561.360000:1.103,562.200000:1.103,563.330000:1.103,568.230000:1.103,571.290000:3.136,573.010000:1.103,575.410000:1.103,580.240000:1.103,581.260000:1.103,585.160000:1.103,588.380000:1.103,590.120000:1.103,599.450000:1.103,605.210000:2.197,607.285000:4.499,608.270000:3.143,613.330000:2.103,614.330000:1.103,617.320000:1.103,621.230000:1.103,622.310000:1.103,625.320000:3.23,626.210000:1.103,633.275000:2.205,640.350000:1.103,642.220000:1.103,644.280000:1.103,646.250000:1.103,648.390000:1.103,651.335000:2.103,653.360000:2.136,658.300000:1.103,662.320000:1.103,663.800000:1.103,668.275000:2.209,674.370000:1.103,676.090000:1.103,677.350000:1.103,678.070000:1.103,683.370000:1.103,684.920000:1.103,685.380000:2.091,686.390000:1.103,701.410000:1.103,702.380000:7.387,703.420000:3.12,707.360000:1.103,713.340000:1.103,718.370000:2.197,720.400000:1.103,724.180000:1.103,728.390000:1.103,734.380000:1.103,735.430000:1.103,736.360000:1.103,737.310000:1.103,741.070000:1.103,745.480000:1.103,747.290000:1.103,748.320000:1.103,754.358237:6.383,755.370000:2.136,760.490000:1.103,765.360000:1.103,767.500000:1.103,770.370000:1.103,775.230000:1.103,778.490000:1.103,792.360000:1.103,796.420000:1.103,801.380000:1.103,814.390000:2.118,815.390000:1.103,816.410000:1.103,820.470000:1.103,825.350000:1.103,841.510000:1.103,848.450000:1.103,883.450000:1.103,884.470000:1.103,896.410000:1.103,907.420000:1.103,908.430000:1.103,916.380000:1.103,1074.300000:1.103,1092.600000:1.103,1164.300000:1.103,1231.540000:1.103,1397.690000:1.103,1660.400000:1.103,1711.520000:1.103 ions2 : ions3 : peptol : 0 peptol units : peptol str : repeat srch : 497.265612 from(498.272888,1+) query(1) 157.096962, 23.72 185.16, 26.69 286.134951, 80.7 385.21, 13.49 480.27, 4.363 129.102412, 18.84 187.07, 22.51 354.189124, 13.57 399.246727, 9.489 482.140542, 3.205 130.110251, 9.257 258.132661, 15.93 357.21, 13.57 443.81, 6.256 481.21, 3.182 136.07, 7.387 213.139215, 13.84 371.204929, 11.24 459.28, 6.216 489.23377, 3.157 147.117662, 6.333 229.12, 9.72 326.133204, 5.268 423.125582, 4.262 483.115, 2.205 159.08, 5.222 240.13, 7.562 298.11, 5.231 444.168974, 3.247 474.3, 1.103 158.09, 4.301 270.18, 7.432 324.17, 5.17 411.2, 3.23 475.27, 1.103 86.11, 3.276 175.11, 7.308 312.150879, 4.235 463.265712, 3.205 476.7, 1.103 102.06, 3.276 241.085275, 5.361 293.11, 4.178 445.81, 3.182 478.18, 1.103 115.088725, 3.255 243.139772, 4.378 353.155308, 4.149 401.15, 3.138 486.88, 1.103 72.09, 2.174 76.4, 1.103 84.075, 2.111 87.11, 1.103 88.1, 1.103 98.06, 1.103 103.06, 1.103 105.07, 1.103 116.07, 1.103 117.11, 1.103 118.4, 1.103 120.09, 2.205 126.07, 1.103 127.09, 1.103 128.09, 2.103 131.085, 2.118 132.09, 1.103 135.8, 1.103 137.08, 1.103 138.07, 1.103 139.09, 1.103 140.15, 2.174 141.06, 2.174 143.12, 2.174 146.08, 1.103 152.06, 1.103 155.07, 2.205 156.1, 1.103 159.45, 1.103 165.08, 2.136 166.11, 1.103 167.11, 1.103 169.71, 1.103 170.45, 1.103 171.09, 1.103 173.12, 2.174 177.09, 1.103 178.08, 1.103 181.16, 1.103 182.03, 1.103 183.11, 2.174 183.93, 1.103 186.131024, 4.374 188.07, 1.103 188.76, 1.103 189.07, 1.103 190.065, 2.103 191.3, 1.103 197.13, 1.103 199.18, 1.103 200.08, 1.103 201.1, 3.138 202.11, 2.091 203.08, 2.174 203.61, 1.103 211.14, 4.189 212.115, 2.103 212.49, 1.103 214.985, 2.205 216.11, 2.103 217.1, 1.103 218.08, 1.103 219.09, 2.103 223.09, 3.154 224.13, 1.103 225.13, 1.103 227.17, 1.103 227.88, 1.103 228.17, 2.136 229.76, 1.103 231.95, 1.103 233.13, 1.103 234.43, 1.103 235.08, 2.103 236.59, 1.103 238.08, 4.332 239.139997, 3.131 242.17, 2.205 244.09, 2.136 244.43, 2.091 245.165685, 3.205 246.16, 2.197 247.11, 2.102 248.145, 2.118 249.11, 2.136 250.08, 1.103 251.16, 1.103 253.1, 1.103 254.13, 1.103 255.165, 2.22 256.17, 1.103 257.06, 1.103 259.15, 2.197 260, 1.103 260.49, 1.103 262.11, 1.103 265.12, 1.103 266.13, 2.159 266.95, 1.103 267.21, 1.103 268.12, 3.214 269.09, 1.103 271.15, 2.136 272.17, 2.103 274.12, 1.103 275.03, 1.103 276.175, 2.22 278.19, 1.103 279.72, 2.205 281.12, 1.103 283.07, 1.103 284.11, 1.103 285.07, 1.103 287.14, 3.296 287.78, 1.103 288.09, 2.103 290.13, 1.103 294.11, 2.174 295.15, 3.114 295.73, 1.103 297.18, 2.136 300.16, 3.143 302.07, 1.103 303.16, 1.103 303.59, 1.103 304.6, 1.103 305.13, 1.103 306.14, 3.182 307.05, 1.103 308.15, 2.174 308.49, 1.103 312.61, 1.103 312.88, 1.103 314.12, 1.103 316.085, 2.111 317.15, 3.183 318.14, 1.103 320.14, 1.103 322.149731, 3.255 323.034482, 3.149 327.02, 1.103 328.02, 1.103 331.14, 2.091 332.165, 2.103 333.14, 1.103 335.5, 1.103 336.19, 1.103 337.03, 2.118 338.62, 1.103 338.94, 1.103 339.2, 3.261 341.21, 2.103 342.18, 1.103 342.8, 1.103 343.225, 2.111 343.8, 1.103 344.15, 2.174 346.01, 1.103 347.66, 1.103 348.2, 2.197 349.8, 1.103 350.11, 2.118 351.13, 3.276 352.13, 2.136 353.91, 1.103 354.47, 1.103 355.193955, 3.376 358.2, 1.103 359.21, 2.174 359.91, 1.103 360.47, 1.103 361.08, 1.103 362.19, 1.103 363.04, 1.103 364.08, 1.103 366.12, 1.103 367.15, 1.103 368.33, 1.103 368.73, 1.103 369.23, 3.15 369.82, 1.103 370.177065, 3.279 373.13, 2.197 374.055, 2.217 374.51, 2.205 376.04, 1.103 377.04, 1.103 380.16, 2.103 382.18, 3.102 383.115, 2.209 385.89, 2.205 386.37, 1.103 387.17, 3.114 387.68, 2.217 388.05, 1.103 389.62, 1.103 390.19, 1.103 390.61, 1.103 394.26, 1.103 395.18, 1.103 396.14, 2.205 397.98, 1.103 400.165, 2.209 403.21, 1.103 404.15, 1.103 404.47, 1.103 410.165, 2.111 411.55, 1.103 413.24, 1.103 414.08, 1.103 415, 1.103 416.19, 1.103 416.83, 1.103 417.23, 1.103 417.76, 1.103 418.285, 2.111 418.68, 1.103 420.65, 1.103 421.17, 2.136 422.58, 1.103 425.215, 2.103 425.69, 1.103 426.22, 3.125 428.14, 2.155 428.65, 1.103 430.26, 1.103 430.995, 2.205 433.2, 1.103 433.69, 1.103 435, 1.103 435.26, 1.103 437.18, 1.103 438.71, 2.174 439.23, 1.103 440.21, 1.103 442.19, 1.103 443.12, 1.103 444.68, 1.103 445.12, 1.103 449.11, 1.103 450.71, 1.103 452.15, 2.209 453.24, 3.12 454.2, 1.103 454.7, 1.103 458.31, 1.103 460.29, 1.103 461.25, 1.103 461.83, 1.103 462.195, 2.103 463.85, 1.103 464.25, 1.103 467.18, 2.174 470.21, 1.103 471.12, 1.103 489.7, 1.103 493.2, 1.103 494.2, 1.103 505.2, 1.103 508.17, 2.197 508.84, 1.103 509.2, 2.103 511.45, 1.103 522.17, 2.197 523.19, 1.103 524.15, 2.174 527.16, 1.103 528.41, 2.19 529.28, 1.103 530.23, 1.103 531.25, 1.103 533.13, 1.103 533.67, 1.103 536.72, 1.103 537.24, 1.103 538.08, 1.103 538.45, 1.103 540.22, 1.103 545.21, 2.174 545.49, 1.103 546.25, 1.103 547.35, 1.103 550.75, 2.205 558.07, 1.103 561.36, 1.103 562.2, 1.103 563.33, 1.103 568.23, 1.103 571.29, 3.136 573.01, 1.103 575.41, 1.103 580.24, 1.103 581.26, 1.103 585.16, 1.103 588.38, 1.103 590.12, 1.103 599.45, 1.103 605.21, 2.197 607.285, 4.499 608.27, 3.143 613.33, 2.103 614.33, 1.103 617.32, 1.103 621.23, 1.103 622.31, 1.103 625.32, 3.23 626.21, 1.103 633.275, 2.205 640.35, 1.103 642.22, 1.103 644.28, 1.103 646.25, 1.103 648.39, 1.103 651.335, 2.103 653.36, 2.136 658.3, 1.103 662.32, 1.103 663.8, 1.103 668.275, 2.209 674.37, 1.103 676.09, 1.103 677.35, 1.103 678.07, 1.103 683.37, 1.103 684.92, 1.103 685.38, 2.091 686.39, 1.103 701.41, 1.103 702.38, 7.387 703.42, 3.12 707.36, 1.103 713.34, 1.103 718.37, 2.197 720.4, 1.103 724.18, 1.103 728.39, 1.103 734.38, 1.103 735.43, 1.103 736.36, 1.103 737.31, 1.103 741.07, 1.103 745.48, 1.103 747.29, 1.103 748.32, 1.103 754.358237, 6.383 755.37, 2.136 760.49, 1.103 765.36, 1.103 767.5, 1.103 770.37, 1.103 775.23, 1.103 778.49, 1.103 792.36, 1.103 796.42, 1.103 801.38, 1.103 814.39, 2.118 815.39, 1.103 816.41, 1.103 820.47, 1.103 825.35, 1.103 841.51, 1.103 848.45, 1.103 883.45, 1.103 884.47, 1.103 896.41, 1.103 907.42, 1.103 908.43, 1.103 916.38, 1.103 1074.3, 1.103 1092.6, 1.103 1164.3, 1.103 1231.54, 1.103 1397.69, 1.103 1660.4, 1.103 1711.52, 1.103 =cut
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