| Previous changeset 0:6a6c1b3b186c (2016-03-15) Next changeset 2:ddc092714127 (2016-03-15) |
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Commit message:
Uploaded |
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added:
test_files/EGFR_MQ_bait_ERvWT.txt test_files/MQ_crapome.txt test_files/peptides.txt test_files/scaffold_EGFR.txt test_files/scaffold_bait.txt |
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removed:
test_files/SC_SAINT_list.txt |
| b |
| diff -r 6a6c1b3b186c -r 843ee18d6065 test_files/EGFR_MQ_bait_ERvWT.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test_files/EGFR_MQ_bait_ERvWT.txt Tue Mar 15 15:58:57 2016 -0400 |
| b |
| @@ -0,0 +1,35 @@ +HCC827_EGFR_TAP_1_run1 HCC827_EGFR C +HCC827_EGFR_TAP_1_run2 HCC827_EGFR C +HCC827_EGFR_TAP_2_run1 HCC827_EGFR C +HCC827_EGFR_TAP_2_run2 HCC827_EGFR C +HCC827_ERBB3_TAP_1_run1 HCC827_ERBB3 C +HCC827_ERBB3_TAP_1_run2 HCC827_ERBB3 C +HCC827_ERBB3_TAP_2_run1 HCC827_ERBB3 C +HCC827_ERBB3_TAP_2_run2 HCC827_ERBB3 C +HCC827_GFP_TAP_1_run1 HCC827_GFP C +HCC827_GFP_TAP_1_run2 HCC827_GFP C +HCC827_GFP_TAP_2_run1 HCC827_GFP C +HCC827_GFP_TAP_2_run2 HCC827_GFP C +HCC827_GRB2_TAP_1_run1 HCC827_GRB2 C +HCC827_GRB2_TAP_1_run2 HCC827_GRB2 C +HCC827_GRB2_TAP_2_run1 HCC827_GRB2 C +HCC827_GRB2_TAP_2_run2 HCC827_GRB2 C +HCC827_P85B_TAP_1_run1 HCC827_P85B C +HCC827_P85B_TAP_1_run2 HCC827_P85B C +HCC827_P85B_TAP_2_run1 HCC827_P85B C +HCC827_P85B_TAP_2_run2 HCC827_P85B C +HCC827ER_EGFR_TAP_1_run1 HCC827ER_EGFR T +HCC827ER_EGFR_TAP_1_run2 HCC827ER_EGFR T +HCC827ER_EGFR_TAP_2_run1 HCC827ER_EGFR T +HCC827ER_EGFR_TAP_2_run2 HCC827ER_EGFR T +HCC827ER_ERBB3_TAP_1_run1 HCC827ER_ERBB3 T +HCC827ER_ERBB3_TAP_1_run2 HCC827ER_ERBB3 T +HCC827ER_ERBB3_TAP_2_run1 HCC827ER_ERBB3 T +HCC827ER_ERBB3_TAP_2_run2 HCC827ER_ERBB3 T +HCC827ER_GRB2_TAP_1_run1 HCC827ER_GRB2 T +HCC827ER_GRB2_TAP_1_run2 HCC827ER_GRB2 T +HCC827ER_GRB2_TAP_2_run1 HCC827ER_GRB2 T +HCC827ER_P85B_TAP_1_run1 HCC827ER_P85B T +HCC827ER_P85B_TAP_1_run2 HCC827ER_P85B T +HCC827ER_P85B_TAP_2_run1 HCC827ER_P85B T +HCC827ER_P85B_TAP_2_run2 HCC827ER_P85B T |
| b |
| diff -r 6a6c1b3b186c -r 843ee18d6065 test_files/MQ_crapome.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test_files/MQ_crapome.txt Tue Mar 15 15:58:57 2016 -0400 |
| b |
| b'@@ -0,0 +1,575 @@\n+User Input\tMapped Gene Symbol\tNum of Expt. (found/total)\tAve SC\tMax SC\n+Q8WVM8\tSCFD1\t17 / 411\t1.5\t4\n+Q13049\tTRIM32\t1 / 411\t1\t1\n+P35232\tPHB\t85 / 411\t3.9\t34\n+O00459\tPIK3R2\t6 / 411\t2.2\t7\n+P09382\tLGALS1\t40 / 411\t4.8\t27\n+P07900\tHSP90AA1\t272 / 411\t30\t327\n+P04259\tKRT6B\t319 / 411\t22.1\t320\n+P04264\tKRT1\t386 / 411\t79.5\t1178\n+Q96P48\tARAP1\t1 / 411\t1\t1\n+Q12774\tARHGEF5\t1 / 411\t1\t1\n+P18433\tInvalid identifier / gene not available\t\t\t\n+Q07021\tC1QBP\t223 / 411\t11.4\t381\n+Q07021\tC1QBP\t223 / 411\t11.4\t381\n+P42338\tInvalid identifier / gene not available\t\t\t\n+Q96NH3\tInvalid identifier / gene not available\t\t\t\n+Q12774\tARHGEF5\t1 / 411\t1\t1\n+P33992\tMCM5\t100 / 411\t5\t34\n+P11021\tHSPA5\t360 / 411\t16.9\t112\n+CON__P13645\tInvalid identifier / gene not available\t\t\t\n+O00459\tPIK3R2\t6 / 411\t2.2\t7\n+O95831\tAIFM1\t101 / 411\t7.8\t92\n+O00567\tNOP56\t96 / 411\t5.9\t50\n+P57088\tTMEM33\t34 / 411\t1.9\t6\n+O95782\tAP2A1\t24 / 411\t2.4\t14\n+O15482\tInvalid identifier / gene not available\t\t\t\n+P05109\tS100A8\t57 / 411\t3.1\t17\n+P42338\tInvalid identifier / gene not available\t\t\t\n+O95782\tAP2A1\t24 / 411\t2.4\t14\n+O60716\tCTNND1\t32 / 411\t4.6\t26\n+P07437\tTUBB\t382 / 411\t37.5\t338\n+Q07021\tC1QBP\t223 / 411\t11.4\t381\n+Q12774\tARHGEF5\t1 / 411\t1\t1\n+P42704\tLRPPRC\t130 / 411\t15.5\t112\n+P07900\tHSP90AA1\t272 / 411\t30\t327\n+O00459\tPIK3R2\t6 / 411\t2.2\t7\n+O95831\tAIFM1\t101 / 411\t7.8\t92\n+P38646\tHSPA9\t307 / 411\t19\t160\n+P04264\tKRT1\t386 / 411\t79.5\t1178\n+P35908\tKRT2\t356 / 411\t44.6\t629\n+P11142\tHSPA8\t396 / 411\t39.2\t332\n+Q8TEM1\tNUP210\t25 / 411\t5.9\t24\n+P62993\tGRB2\t7 / 411\t1.4\t3\n+P00533\tEGFR\t16 / 411\t4.3\t15\n+Q12774\tARHGEF5\t1 / 411\t1\t1\n+Q15751\tHERC1\t1 / 411\t1\t1\n+CON__ENSEMBL:ENSBTAP00000016242\tInvalid identifier / gene not available\t\t\t\n+A5A3E0\tPOTEF\t351 / 411\t11.2\t193\n+P68366\tTUBA4A\t377 / 411\t28.6\t242\n+CON__ENSEMBL:ENSBTAP00000016242\tInvalid identifier / gene not available\t\t\t\n+Q99615\tDNAJC7\t59 / 411\t2.9\t10\n+P82930\tMRPS34\t24 / 411\t1.9\t6\n+P35568\tInvalid identifier / gene not available\t\t\t\n+REV__Q8WX94\tInvalid identifier / gene not available\t\t\t\n+P31948\tSTIP1\t120 / 411\t8.6\t58\n+P00533\tEGFR\t16 / 411\t4.3\t15\n+CON__P13645\tInvalid identifier / gene not available\t\t\t\n+CON__P02533\tInvalid identifier / gene not available\t\t\t\n+P11142\tHSPA8\t396 / 411\t39.2\t332\n+P0DMV8\tInvalid identifier / gene not available\t\t\t\n+P42338\tInvalid identifier / gene not available\t\t\t\n+P12236\tSLC25A6\t201 / 411\t7\t119\n+P05141\tSLC25A5\t223 / 411\t7.1\t58\n+O95782\tAP2A1\t24 / 411\t2.4\t14\n+P42336\tPIK3CA\t1 / 411\t1\t1\n+O00459\tPIK3R2\t6 / 411\t2.2\t7\n+Q8WUY1\tTHEM6\t4 / 411\t1.8\t3\n+REV__Q6IE37\tInvalid identifier / gene not available\t\t\t\n+Q9UBL6\tCPNE7\t19 / 411\t1.6\t5\n+P42336\tPIK3CA\t1 / 411\t1\t1\n+P49411\tTUFM\t139 / 411\t8.6\t53\n+P08581\tInvalid identifier / gene not available\t\t\t\n+P11021\tHSPA5\t360 / 411\t16.9\t112\n+P42336\tPIK3CA\t1 / 411\t1\t1\n+O00459\tPIK3R2\t6 / 411\t2.2\t7\n+P43246\tMSH2\t45 / 411\t3\t27\n+P82930\tMRPS34\t24 / 411\t1.9\t6\n+Q8NEG7\tDENND6B\t2 / 411\t1\t1\n+P62258\tYWHAE\t186 / 411\t9.4\t90\n+O00459\tPIK3R2\t6 / 411\t2.2\t7\n+CON__ENSEMBL:ENSBTAP00000016242\tInvalid identifier / gene not available\t\t\t\n+O00459\tPIK3R2\t6 / 411\t2.2\t7\n+Q92552\tMRPS27\t31 / 411\t2.6\t9\n+P42338\tInvalid identifier / gene not available\t\t\t\n+Q14451\tGRB7\t1 / 411\t1\t1\n+O00459\tPIK3R2\t6 / 411\t2.2\t7\n+Q02978\tSLC25A11\t55 / 411\t3.1\t18\n+REV__Q0VFZ6\tInvalid identifier / gene not available\t\t\t\n+Q07889\tSOS1\t1 / 411\t1\t1\n+P22681\tCBL\t2 / 411\t1.5\t2\n+Q05639\tEEF1A2\t343 / 411\t13.4\t175\n+P00533\tEGFR\t16 / 411\t4.3\t15\n+CON__ENSEMBL:ENSBTAP00000016242\tInvalid identifier / gene not available\t\t\t\n+P52735\tVAV2\t1 / 411\t1\t1\n+P00533\tEGFR\t16 / 411\t4.3\t15\n+P00533\tEGFR\t16 / 411\t4.3\t15\n+Q4G1C9\tInvalid identifier / gene not available\t\t\t\n+P21860\tInvalid identifier / gene not available\t\t\t\n+P11021\tHSPA5\t360 / 411\t16.9\t112\n+P00533\tEGFR\t16 / 411\t4.3\t15\n+Q8NFI3\tENGASE\t2 / 411\t1\t1\n+Q14571\tITPR2\t5 / 411\t4.4\t10\n+P42224\tSTAT1\t23 / 411\t4.7\t19\n+CON__P13645\tInvalid identifier / gene not available\t\t\t\n+P00533\tEGFR\t16 / 411\t4.3\t15\n+P05141\tSLC25A5\t223 / 411\t7.1\t58\n+Q75V66\tInvalid identifier / gene not available\t\t\t\n+O00459\tPIK3R2\t6 / 411\t2.2\t7\n+P00533\tEGFR\t16 / 411\t4.3\t15\n+P62993\tGRB2\t7 / 411\t1.4\t3\n+P0CG4'..b'\n+CON__Q5D862\tInvalid identifier / gene not available\t\t\t\n+P35908\tKRT2\t356 / 411\t44.6\t629\n+O00459\tPIK3R2\t6 / 411\t2.2\t7\n+P46109\tCRKL\t33 / 411\t7.7\t25\n+O00459\tPIK3R2\t6 / 411\t2.2\t7\n+P49368\tCCT3\t165 / 411\t15.1\t114\n+Q14451\tGRB7\t1 / 411\t1\t1\n+P00533\tEGFR\t16 / 411\t4.3\t15\n+O00459\tPIK3R2\t6 / 411\t2.2\t7\n+P11021\tHSPA5\t360 / 411\t16.9\t112\n+Q53GQ0\tHSD17B12\t27 / 411\t1.9\t7\n+P25705\tATP5A1\t210 / 411\t11\t83\n+Q15084\tPDIA6\t129 / 411\t6.7\t52\n+P35568\tInvalid identifier / gene not available\t\t\t\n+O00459\tPIK3R2\t6 / 411\t2.2\t7\n+O00329\tPIK3CD\t1 / 411\t1\t1\n+P42338\tInvalid identifier / gene not available\t\t\t\n+P18433\tInvalid identifier / gene not available\t\t\t\n+O95782\tAP2A1\t24 / 411\t2.4\t14\n+P04264\tKRT1\t386 / 411\t79.5\t1178\n+P04264\tKRT1\t386 / 411\t79.5\t1178\n+CON__ENSEMBL:ENSBTAP00000016242\tInvalid identifier / gene not available\t\t\t\n+P00533\tEGFR\t16 / 411\t4.3\t15\n+Q71U36\tTUBA1A\t389 / 411\t34.9\t299\n+P0CG48\tUBC\t233 / 411\t6.5\t90\n+O00459\tPIK3R2\t6 / 411\t2.2\t7\n+P11021\tHSPA5\t360 / 411\t16.9\t112\n+Q8NF37\tLPCAT1\t7 / 411\t1.4\t4\n+CON__P35527\tInvalid identifier / gene not available\t\t\t\n+P04264\tKRT1\t386 / 411\t79.5\t1178\n+REV__E9PKD4\tInvalid identifier / gene not available\t\t\t\n+CON__P35527\tInvalid identifier / gene not available\t\t\t\n+P04264\tKRT1\t386 / 411\t79.5\t1178\n+P04264\tKRT1\t386 / 411\t79.5\t1178\n+P00533\tEGFR\t16 / 411\t4.3\t15\n+P40763\tSTAT3\t36 / 411\t6\t25\n+Q12774\tARHGEF5\t1 / 411\t1\t1\n+P11142\tHSPA8\t396 / 411\t39.2\t332\n+P11142\tHSPA8\t396 / 411\t39.2\t332\n+Q06124\tPTPN11\t41 / 411\t3.5\t36\n+Q13946\tInvalid identifier / gene not available\t\t\t\n+Q92569\tPIK3R3\t4 / 411\t1.3\t2\n+P11021\tHSPA5\t360 / 411\t16.9\t112\n+P25205\tMCM3\t120 / 411\t6.6\t63\n+Q9Y4H2\tIRS2\t4 / 411\t1.3\t2\n+P62266\tRPS23\t160 / 411\t4.7\t28\n+P00533\tEGFR\t16 / 411\t4.3\t15\n+CON__P00761\tInvalid identifier / gene not available\t\t\t\n+P21860\tInvalid identifier / gene not available\t\t\t\n+P00533\tEGFR\t16 / 411\t4.3\t15\n+CON__P00761\tInvalid identifier / gene not available\t\t\t\n+P35908\tKRT2\t356 / 411\t44.6\t629\n+REV__Q6ZU80\tInvalid identifier / gene not available\t\t\t\n+Q07021\tC1QBP\t223 / 411\t11.4\t381\n+P17066\tHSPA6\t380 / 411\t14.1\t159\n+Q92859\tInvalid identifier / gene not available\t\t\t\n+P42338\tInvalid identifier / gene not available\t\t\t\n+P42338\tInvalid identifier / gene not available\t\t\t\n+P62805\tHIST4H4\t225 / 411\t13.6\t316\n+P13639\tEEF2\t207 / 411\t14.5\t219\n+CON__ENSEMBL:ENSBTAP00000016242\tInvalid identifier / gene not available\t\t\t\n+P43304\tGPD2\t3 / 411\t2\t4\n+P07900\tHSP90AA1\t272 / 411\t30\t327\n+P18433\tInvalid identifier / gene not available\t\t\t\n+REV__Q8WXI4\tInvalid identifier / gene not available\t\t\t\n+CON__P02533\tInvalid identifier / gene not available\t\t\t\n+CON__P13645\tInvalid identifier / gene not available\t\t\t\n+P35030\tPRSS3\t61 / 411\t3.6\t38\n+P00533\tEGFR\t16 / 411\t4.3\t15\n+P21860\tInvalid identifier / gene not available\t\t\t\n+P62993\tGRB2\t7 / 411\t1.4\t3\n+P18433\tInvalid identifier / gene not available\t\t\t\n+P25705\tATP5A1\t210 / 411\t11\t83\n+P11021\tHSPA5\t360 / 411\t16.9\t112\n+P29353\tSHC1\t9 / 411\t1.6\t3\n+P42338\tInvalid identifier / gene not available\t\t\t\n+Q92569\tPIK3R3\t4 / 411\t1.3\t2\n+Q8NF91\tSYNE1\t10 / 411\t1.2\t2\n+Q3BBV2\tInvalid identifier / gene not available\t\t\t\n+P38646\tHSPA9\t307 / 411\t19\t160\n+P14923\tJUP\t109 / 411\t7.7\t46\n+P11021\tHSPA5\t360 / 411\t16.9\t112\n+P11802\tCDK4\t27 / 411\t2.4\t28\n+CON__P13645\tInvalid identifier / gene not available\t\t\t\n+P68871\tHBB\t56 / 411\t2.1\t9\n+Q12774\tARHGEF5\t1 / 411\t1\t1\n+P04264\tKRT1\t386 / 411\t79.5\t1178\n+Q06124\tPTPN11\t41 / 411\t3.5\t36\n+P00533\tEGFR\t16 / 411\t4.3\t15\n+P04259\tKRT6B\t319 / 411\t22.1\t320\n+P04264\tKRT1\t386 / 411\t79.5\t1178\n+P35908\tKRT2\t356 / 411\t44.6\t629\n+P42338\tInvalid identifier / gene not available\t\t\t\n+P42336\tPIK3CA\t1 / 411\t1\t1\n+P62993\tGRB2\t7 / 411\t1.4\t3\n+P05141\tSLC25A5\t223 / 411\t7.1\t58\n+P15924\tDSP\t126 / 411\t19.4\t237\n+P52735\tVAV2\t1 / 411\t1\t1\n+CON__P02662\tInvalid identifier / gene not available\t\t\t\n+Q9Y4H2\tIRS2\t4 / 411\t1.3\t2\n+P07437\tTUBB\t382 / 411\t37.5\t338\n+Q13509\tInvalid identifier / gene not available\t\t\t\n+P00533\tEGFR\t16 / 411\t4.3\t15\n+P63173\tRPL38\t139 / 411\t9\t58\n+Q12774\tARHGEF5\t1 / 411\t1\t1\n+O00459\tPIK3R2\t6 / 411\t2.2\t7\n+P00533\tEGFR\t16 / 411\t4.3\t15\n+P18433\tInvalid identifier / gene not available\t\t\t\n' |
| b |
| diff -r 6a6c1b3b186c -r 843ee18d6065 test_files/SC_SAINT_list.txt --- a/test_files/SC_SAINT_list.txt Tue Mar 15 15:58:41 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,473 +0,0 @@\n-Bait\tPrey\tPreyGene\tSpec\tSpecSum\tAvgSpec\tNumReplicates\tctrlCounts\tAvgP\tMaxP\tTopoAvgP\tTopoMaxP\tSaintScore\tlogOddsScore\tFoldChange\tBFDR\tboosted_by\n-WT_EGFR\tEGFR_HUMAN\tEGFR\t67|52|45|55\t219\t54.75\t4\t0|0|0|0\t1.00\t1.00\t1.00\t1.00\t1.00\t68.87\t547.50\t0.00\t\n-WT_EGFR\tERBB2_HUMAN\tERBB2\t4|5|3|5\t17\t4.25\t4\t0|0|0|0\t1.00\t1.00\t1.00\t1.00\t1.00\t6.28\t42.50\t0.00\t\n-WT_EGFR\tP85B_HUMAN\tPIK3R2\t0|0|0|0\t0\t0.00\t4\t0|0|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.11\t0.00\t0.51\t\n-WT_EGFR\tP55G_HUMAN\tPIK3R3\t0|0|0|0\t0\t0.00\t4\t0|0|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.11\t0.00\t0.51\t\n-WT_EGFR\tP85A_HUMAN\tPIK3R1\t0|0|0|0\t0\t0.00\t4\t0|0|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.11\t0.00\t0.51\t\n-WT_EGFR\tK2C1_HUMAN\tKRT1\t3|4|6|5\t18\t4.50\t4\t10|10|7|7\t0.00\t0.00\t0.00\t0.00\t0.00\t-27.06\t0.53\t0.51\t\n-WT_EGFR\tK1C10_HUMAN\tKRT10\t2|0|3|3\t8\t2.00\t4\t1|2|4|3\t0.01\t0.02\t0.01\t0.02\t0.01\t-9.56\t0.80\t0.49\t\n-WT_EGFR\tK1C16_HUMAN\tKRT16\t0|0|2|1\t3\t0.75\t4\t1|1|2|2\t0.03\t0.12\t0.03\t0.12\t0.03\t-5.35\t0.50\t0.47\t\n-WT_EGFR\tGRB2_HUMAN\tGRB2\t2|0|2|2\t6\t1.50\t4\t0|0|0|0\t0.74\t0.99\t0.74\t0.99\t0.74\t-0.11\t15.00\t0.05\t\n-WT_EGFR\tGRP78_HUMAN\tHSPA5\t16|14|11|12\t53\t13.25\t4\t0|0|0|0\t1.00\t1.00\t1.00\t1.00\t1.00\t19.16\t132.50\t0.00\t\n-WT_EGFR\tK22E_HUMAN\tKRT2\t2|3|6|4\t15\t3.75\t4\t4|4|1|1\t0.15\t0.50\t0.15\t0.50\t0.15\t-5.61\t1.50\t0.44\t\n-WT_EGFR\tK2C8_HUMAN\tKRT8\t1|1|2|2\t6\t1.50\t4\t0|0|0|0\t0.49\t0.99\t0.49\t0.99\t0.49\t2.40\t15.00\t0.19\t\n-WT_EGFR\tK2C5_HUMAN\tKRT5\t1|1|3|2\t7\t1.75\t4\t1|1|2|0\t0.29\t0.74\t0.29\t0.74\t0.29\t-1.74\t1.75\t0.26\t\n-WT_EGFR\tK2C4_HUMAN\tKRT4\t0|0|0|0\t0\t0.00\t4\t0|1|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.65\t0.00\t0.51\t\n-WT_EGFR\tK2C6B_HUMAN\tKRT6B\t1|2|4|4\t11\t2.75\t4\t2|2|2|1\t0.25\t0.47\t0.25\t0.47\t0.25\t-4.44\t1.57\t0.42\t\n-WT_EGFR\tK2C7_HUMAN\tKRT7\t0|0|0|2\t2\t0.50\t4\t0|0|0|0\t0.25\t0.99\t0.25\t0.99\t0.25\t-0.11\t5.00\t0.28\t\n-WT_EGFR\tHSP7C_HUMAN\tHSPA8\t15|10|12|11\t48\t12.00\t4\t0|0|1|1\t1.00\t1.00\t1.00\t1.00\t1.00\t12.83\t24.00\t0.00\t\n-WT_EGFR\tPK3CA_HUMAN\tPIK3CA\t0|0|0|0\t0\t0.00\t4\t0|0|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.11\t0.00\t0.51\t\n-WT_EGFR\tERBB3_HUMAN\tERBB3\t0|0|0|0\t0\t0.00\t4\t0|0|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.11\t0.00\t0.51\t\n-WT_EGFR\tADT2_HUMAN\tSLC25A5\t5|3|5|5\t18\t4.50\t4\t0|0|0|0\t1.00\t1.00\t1.00\t1.00\t1.00\t6.28\t45.00\t0.00\t\n-WT_EGFR\tADT3_HUMAN\tSLC25A6\t5|4|5|5\t19\t4.75\t4\t0|0|0|0\t1.00\t1.00\t1.00\t1.00\t1.00\t8.02\t47.50\t0.00\t\n-WT_EGFR\tK1C9_HUMAN\tKRT9\t1|1|1|0\t3\t0.75\t4\t0|0|1|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.65\t3.00\t0.51\t\n-WT_EGFR\tTBA1A_HUMAN\tTUBA1A\t5|3|5|3\t16\t4.00\t4\t0|0|0|0\t1.00\t1.00\t1.00\t1.00\t1.00\t6.28\t40.00\t0.00\t\n-WT_EGFR\tTBA4A_HUMAN\tTUBA4A\t3|2|3|1\t9\t2.25\t4\t0|0|0|0\t0.75\t1.00\t0.75\t1.00\t0.75\t2.40\t22.50\t0.02\t\n-WT_EGFR\tARHG5_HUMAN\tARHGEF5\t0|0|0|0\t0\t0.00\t4\t0|0|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.11\t0.00\t0.51\t\n-WT_EGFR\tPK3CB_HUMAN\tPIK3CB\t0|0|0|0\t0\t0.00\t4\t0|0|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.11\t0.00\t0.51\t\n-WT_EGFR\tIRS1_HUMAN\tIRS1\t0|0|0|0\t0\t0.00\t4\t0|0|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.11\t0.00\t0.51\t\n-WT_EGFR\tTBB5_HUMAN\tTUBB\t8|6|5|2\t21\t5.25\t4\t0|0|0|0\t1.00\t1.00\t1.00\t1.00\t1.00\t4.43\t52.50\t0.00\t\n-WT_EGFR\tTBB3_HUMAN\tTUBB3\t2|2|3|1\t8\t2.00\t4\t0|0|0|0\t0.74\t1.00\t0.74\t1.00\t0.74\t2.40\t20.00\t0.05\t\n-WT_EGFR\tHS90A_HUMAN\tHSP90AA1\t3|3|1|2\t9\t2.25\t4\t0|0|0|0\t0.75\t1.00\t0.75\t1.00\t0.75\t2.40\t22.50\t0.02\t\n-WT_EGFR\tHS90B_HUMAN\tHSP90AB1\t4|2|1|2\t9\t2.25\t4\t0|0|0|0\t0.74\t1.00\t0.74\t1.00\t0.74\t2.40\t22.50\t0.04\t\n-WT_EGFR\t1433E_HUMAN\tYWHAE\t1|0|0|0\t1\t0.25\t4\t0|0|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.11\t2.50\t0.51\t\n-WT_EGFR\t1433T_HUMAN\tYWHAQ\t1|0|0|0\t1\t0.25\t4\t0|0|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.11\t2.50\t0.51\t\n-WT_EGFR\tLPPRC_HUMAN\tLRPPRC\t1|3|3|3\t10\t2.50\t4\t0|0|0|0\t0.75\t1.00\t0.75\t1.00\t0.75\t2.40\t25.00\t0.00\t\n-WT_EGFR\tERRFI_HUMAN\tERRFI1\t1|2|1|1\t5\t1.25\t4\t0|0|0|0\t0.25\t0.99\t0.25\t0.99\t0.25\t2.40\t12.50\t0.28\t\n-WT_EGFR\tAP2A1_HUMAN\tAP2A1\t1|1|1|1\t4\t1.00\t4\t0|0|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t2.40\t10.00\t0.51\t\n-WT_EGFR\tGRB7_HUMAN\tGRB7\t0|0|0|0\t0\t0.00\t4\t0|0|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.11\t0.00\t0.51\t\n-WT_EGFR\tSTAT3_HUMAN\tSTAT3\t4|5|3|3\t15\t3.75\t4\t0|0|0|0\t1.00\t1.00\t1.00\t1.00\t1.00\t6.28\t37.50\t0.00\t\n-WT_EGFR\tANXA2_HUMAN\tANXA2\t3|4|0|1\t8\t2.00\t4\t0|0|0|0\t0.50\t1.00\t0.50\t1.00\t0.50\t-0.11\t20.00\t0.10\t\n-WT_EGFR\tPTPRA_HUMAN\tPTPRA\t0|0|0|0\t0\t0.00\t4\t0|0|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.11\t0.00\t0.51\t\n-WT_EGFR\tC1QBP_HUMAN\tC1QBP\t0|0|0|0\t0\t0.00\t4\t7|'..b'\t0|0|1|1\t0.00\t0.00\t0.00\t0.00\t0.00\t-1.55\t1.00\t0.51\t\n-ER_P85B\tPK3CA_HUMAN\tPIK3CA\t3|3|6|6\t18\t4.50\t4\t0|0|0|0\t1.00\t1.00\t1.00\t1.00\t1.00\t6.28\t45.00\t0.00\t\n-ER_P85B\tERBB3_HUMAN\tERBB3\t1|0|2|1\t4\t1.00\t4\t0|0|0|0\t0.25\t0.99\t0.25\t0.99\t0.25\t-0.11\t10.00\t0.28\t\n-ER_P85B\tADT2_HUMAN\tSLC25A5\t0|0|0|0\t0\t0.00\t4\t0|0|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.11\t0.00\t0.51\t\n-ER_P85B\tADT3_HUMAN\tSLC25A6\t0|0|0|0\t0\t0.00\t4\t0|0|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.11\t0.00\t0.51\t\n-ER_P85B\tK1C9_HUMAN\tKRT9\t1|0|1|0\t2\t0.50\t4\t0|0|1|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.65\t2.00\t0.51\t\n-ER_P85B\tTBA1A_HUMAN\tTUBA1A\t0|0|0|0\t0\t0.00\t4\t0|0|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.11\t0.00\t0.51\t\n-ER_P85B\tTBA4A_HUMAN\tTUBA4A\t0|0|0|0\t0\t0.00\t4\t0|0|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.11\t0.00\t0.51\t\n-ER_P85B\tARHG5_HUMAN\tARHGEF5\t0|0|0|0\t0\t0.00\t4\t0|0|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.11\t0.00\t0.51\t\n-ER_P85B\tPK3CB_HUMAN\tPIK3CB\t1|1|4|2\t8\t2.00\t4\t0|0|0|0\t0.50\t1.00\t0.50\t1.00\t0.50\t2.40\t20.00\t0.14\t\n-ER_P85B\tIRS1_HUMAN\tIRS1\t2|3|3|4\t12\t3.00\t4\t0|0|0|0\t1.00\t1.00\t1.00\t1.00\t1.00\t4.43\t30.00\t0.00\t\n-ER_P85B\tTBB5_HUMAN\tTUBB\t0|0|0|0\t0\t0.00\t4\t0|0|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.11\t0.00\t0.51\t\n-ER_P85B\tTBB3_HUMAN\tTUBB3\t0|0|0|0\t0\t0.00\t4\t0|0|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.11\t0.00\t0.51\t\n-ER_P85B\tHS90A_HUMAN\tHSP90AA1\t0|0|0|0\t0\t0.00\t4\t0|0|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.11\t0.00\t0.51\t\n-ER_P85B\tHS90B_HUMAN\tHSP90AB1\t0|0|0|0\t0\t0.00\t4\t0|0|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.11\t0.00\t0.51\t\n-ER_P85B\t1433E_HUMAN\tYWHAE\t0|0|1|1\t2\t0.50\t4\t0|0|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.11\t5.00\t0.51\t\n-ER_P85B\t1433T_HUMAN\tYWHAQ\t0|0|1|1\t2\t0.50\t4\t0|0|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.11\t5.00\t0.51\t\n-ER_P85B\tLPPRC_HUMAN\tLRPPRC\t0|0|0|0\t0\t0.00\t4\t0|0|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.11\t0.00\t0.51\t\n-ER_P85B\tERRFI_HUMAN\tERRFI1\t0|0|0|0\t0\t0.00\t4\t0|0|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.11\t0.00\t0.51\t\n-ER_P85B\tAP2A1_HUMAN\tAP2A1\t0|0|0|0\t0\t0.00\t4\t0|0|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.11\t0.00\t0.51\t\n-ER_P85B\tGRB7_HUMAN\tGRB7\t1|1|1|0\t3\t0.75\t4\t0|0|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.11\t7.50\t0.51\t\n-ER_P85B\tSTAT3_HUMAN\tSTAT3\t0|0|0|0\t0\t0.00\t4\t0|0|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.11\t0.00\t0.51\t\n-ER_P85B\tANXA2_HUMAN\tANXA2\t0|0|0|0\t0\t0.00\t4\t0|0|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.11\t0.00\t0.51\t\n-ER_P85B\tPTPRA_HUMAN\tPTPRA\t0|0|0|0\t0\t0.00\t4\t0|0|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.11\t0.00\t0.51\t\n-ER_P85B\tC1QBP_HUMAN\tC1QBP\t0|0|0|0\t0\t0.00\t4\t7|5|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-11.03\t0.00\t0.51\t\n-ER_P85B\tSHC1_HUMAN\tSHC1\t0|0|0|0\t0\t0.00\t4\t0|0|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.11\t0.00\t0.51\t\n-ER_P85B\tPTN11_HUMAN\tPTPN11\t0|0|0|0\t0\t0.00\t4\t0|0|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.11\t0.00\t0.51\t\n-ER_P85B\tPON2_HUMAN\tPON2\t0|0|0|0\t0\t0.00\t4\t0|0|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.11\t0.00\t0.51\t\n-ER_P85B\tMET_HUMAN\tMET\t0|0|1|1\t2\t0.50\t4\t0|0|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.11\t5.00\t0.51\t\n-ER_P85B\tCRKL_HUMAN\tCRKL\t0|0|0|0\t0\t0.00\t4\t0|0|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.11\t0.00\t0.51\t\n-ER_P85B\tCBL_HUMAN\tCBL\t0|0|0|0\t0\t0.00\t4\t0|0|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.11\t0.00\t0.51\t\n-ER_P85B\tPHLA2_HUMAN\tPHLDA2\t0|0|0|0\t0\t0.00\t4\t0|0|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.11\t0.00\t0.51\t\n-ER_P85B\tRT27_HUMAN\tMRPS27\t0|0|0|0\t0\t0.00\t4\t0|0|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.11\t0.00\t0.51\t\n-ER_P85B\tM2OM_HUMAN\tSLC25A11\t0|0|0|0\t0\t0.00\t4\t0|0|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.11\t0.00\t0.51\t\n-ER_P85B\tSTAT1_HUMAN\tSTAT1\t0|0|0|0\t0\t0.00\t4\t0|0|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.11\t0.00\t0.51\t\n-ER_P85B\tSLIRP_HUMAN\tSLIRP\t0|0|0|0\t0\t0.00\t4\t0|0|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.11\t0.00\t0.51\t\n-ER_P85B\tPK3CD_HUMAN\tPIK3CD\t0|0|0|0\t0\t0.00\t4\t0|0|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.11\t0.00\t0.51\t\n-ER_P85B\tGRP75_HUMAN\tHSPA9\t0|0|0|0\t0\t0.00\t4\t0|0|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.11\t0.00\t0.51\t\n-ER_P85B\tAIFM1_HUMAN\tAIFM1\t0|0|0|0\t0\t0.00\t4\t0|0|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.11\t0.00\t0.51\t\n-ER_P85B\tPHB_HUMAN\tPHB\t0|0|0|0\t0\t0.00\t4\t0|0|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.11\t0.00\t0.51\t\n-ER_P85B\tHNRPK_HUMAN\tHNRNPK\t0|0|0|0\t0\t0.00\t4\t0|0|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.11\t0.00\t0.51\t\n-ER_P85B\tTMM33_HUMAN\tTMEM33\t0|0|0|0\t0\t0.00\t4\t0|0|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.11\t0.00\t0.51\t\n-ER_P85B\tRT34_HUMAN\tMRPS34\t0|0|0|0\t0\t0.00\t4\t0|0|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.11\t0.00\t0.51\t\n' |
| b |
| diff -r 6a6c1b3b186c -r 843ee18d6065 test_files/peptides.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test_files/peptides.txt Tue Mar 15 15:58:57 2016 -0400 |
| b |
| b'@@ -0,0 +1,575 @@\n+id\tProtein Group IDs\tMod. Peptide IDs\tEvidence IDs\tMS/MS IDs\tBest MS/MS\tOxidation (M) Site IDs\tSequence\tA Count\tR Count\tN Count\tD Count\tC Count\tQ Count\tE Count\tG Count\tH Count\tI Count\tL Count\tK Count\tM Count\tF Count\tP Count\tS Count\tT Count\tW Count\tY Count\tV Count\tU Count\tLength\tMissed Cleavages\tMass\tProteins\tLeading Razor Protein\tGene Names\tProtein Names\tUnique (Groups)\tUnique (Proteins)\tCharges\tPEP\tScore\tSlice Average\tSlice Std. Dev.\tSlice 1\tUnique Slice Average\tUnique Slice Std. Dev.\tUnique Slice 1\tExperiment HCC827_EGFR_TAP_1_run1\tExperiment HCC827_EGFR_TAP_1_run2\tExperiment HCC827_EGFR_TAP_2_run1\tExperiment HCC827_EGFR_TAP_2_run2\tExperiment HCC827_ERBB3_TAP_1_run1\tExperiment HCC827_ERBB3_TAP_1_run2\tExperiment HCC827_ERBB3_TAP_2_run1\tExperiment HCC827_ERBB3_TAP_2_run2\tExperiment HCC827_GFP_TAP_1_run1\tExperiment HCC827_GFP_TAP_1_run2\tExperiment HCC827_GFP_TAP_2_run1\tExperiment HCC827_GFP_TAP_2_run2\tExperiment HCC827_GRB2_TAP_1_run1\tExperiment HCC827_GRB2_TAP_1_run2\tExperiment HCC827_GRB2_TAP_2_run1\tExperiment HCC827_GRB2_TAP_2_run2\tExperiment HCC827_P85B_TAP_1_run1\tExperiment HCC827_P85B_TAP_1_run2\tExperiment HCC827_P85B_TAP_2_run1\tExperiment HCC827_P85B_TAP_2_run2\tExperiment HCC827ER_EGFR_TAP_1_run1\tExperiment HCC827ER_EGFR_TAP_1_run2\tExperiment HCC827ER_EGFR_TAP_2_run1\tExperiment HCC827ER_EGFR_TAP_2_run2\tExperiment HCC827ER_ERBB3_TAP_1_run1\tExperiment HCC827ER_ERBB3_TAP_1_run2\tExperiment HCC827ER_ERBB3_TAP_2_run1\tExperiment HCC827ER_ERBB3_TAP_2_run2\tExperiment HCC827ER_GRB2_TAP_1_run1\tExperiment HCC827ER_GRB2_TAP_1_run2\tExperiment HCC827ER_GRB2_TAP_2_run1\tExperiment HCC827ER_P85B_TAP_1_run1\tExperiment HCC827ER_P85B_TAP_1_run2\tExperiment HCC827ER_P85B_TAP_2_run1\tExperiment HCC827ER_P85B_TAP_2_run2\tUnique Experiment HCC827_EGFR_TAP_1_run1\tUnique Experiment HCC827_EGFR_TAP_1_run2\tUnique Experiment HCC827_EGFR_TAP_2_run1\tUnique Experiment HCC827_EGFR_TAP_2_run2\tUnique Experiment HCC827_ERBB3_TAP_1_run1\tUnique Experiment HCC827_ERBB3_TAP_1_run2\tUnique Experiment HCC827_ERBB3_TAP_2_run1\tUnique Experiment HCC827_ERBB3_TAP_2_run2\tUnique Experiment HCC827_GFP_TAP_1_run1\tUnique Experiment HCC827_GFP_TAP_1_run2\tUnique Experiment HCC827_GFP_TAP_2_run1\tUnique Experiment HCC827_GFP_TAP_2_run2\tUnique Experiment HCC827_GRB2_TAP_1_run1\tUnique Experiment HCC827_GRB2_TAP_1_run2\tUnique Experiment HCC827_GRB2_TAP_2_run1\tUnique Experiment HCC827_GRB2_TAP_2_run2\tUnique Experiment HCC827_P85B_TAP_1_run1\tUnique Experiment HCC827_P85B_TAP_1_run2\tUnique Experiment HCC827_P85B_TAP_2_run1\tUnique Experiment HCC827_P85B_TAP_2_run2\tUnique Experiment HCC827ER_EGFR_TAP_1_run1\tUnique Experiment HCC827ER_EGFR_TAP_1_run2\tUnique Experiment HCC827ER_EGFR_TAP_2_run1\tUnique Experiment HCC827ER_EGFR_TAP_2_run2\tUnique Experiment HCC827ER_ERBB3_TAP_1_run1\tUnique Experiment HCC827ER_ERBB3_TAP_1_run2\tUnique Experiment HCC827ER_ERBB3_TAP_2_run1\tUnique Experiment HCC827ER_ERBB3_TAP_2_run2\tUnique Experiment HCC827ER_GRB2_TAP_1_run1\tUnique Experiment HCC827ER_GRB2_TAP_1_run2\tUnique Experiment HCC827ER_GRB2_TAP_2_run1\tUnique Experiment HCC827ER_P85B_TAP_1_run1\tUnique Experiment HCC827ER_P85B_TAP_1_run2\tUnique Experiment HCC827ER_P85B_TAP_2_run1\tUnique Experiment HCC827ER_P85B_TAP_2_run2\tIntensity\tIntensity HCC827_EGFR_TAP_1_run1\tIntensity HCC827_EGFR_TAP_1_run2\tIntensity HCC827_EGFR_TAP_2_run1\tIntensity HCC827_EGFR_TAP_2_run2\tIntensity HCC827_ERBB3_TAP_1_run1\tIntensity HCC827_ERBB3_TAP_1_run2\tIntensity HCC827_ERBB3_TAP_2_run1\tIntensity HCC827_ERBB3_TAP_2_run2\tIntensity HCC827_GFP_TAP_1_run1\tIntensity HCC827_GFP_TAP_1_run2\tIntensity HCC827_GFP_TAP_2_run1\tIntensity HCC827_GFP_TAP_2_run2\tIntensity HCC827_GRB2_TAP_1_run1\tIntensity HCC827_GRB2_TAP_1_run2\tIntensity HCC827_GRB2_TAP_2_run1\tIntensity HCC827_GRB2_TAP_2_run2\tIntensity HCC827_P85B_TAP_1_run1\tIntensity HCC827_P85B_TAP_1_run2\tIntensity HCC827_P85B_TAP_2_run1\tIntensity HCC827_P85B_TAP_2_run2\tIntensity HCC827ER_EGFR_TAP_1_run1\tIntensity HCC827ER_EGFR_TAP_1_run2\tIntensity HCC827ER_EGFR_TAP_2_run1\tIntens'..b'1\t1\t1\t1\t1\t\t\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t\t\t\t\t1\t1\t\t\t\t\t\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t\t\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t\t\t\t\t1\t1\t\t\t\t\t\t1\t1\t10260000\t1589800\t1622600\t1264600\t1329700\t279900\t269770\t383040\t345530\t62537\t51054\t0\t0\t250630\t273730\t418810\t414290\t95230\t119930\t151530\t114550\t379040\t363840\t0\t0\t0\t0\t173500\t135360\t0\t0\t0\t0\t0\t80725\t89890\t\t\r\n+567\t125\t574\t6329;6330;6331;6332;6333;6334;6335\t3301\t3301\t\tYLTVATVFR\t1\t1\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t1\t0\t0\t2\t0\t1\t2\t0\t9\t0\t1068.5968\tQ13509\tQ13509\tTUBB3;TUBB4\tTubulin beta-3 chain;Tubulin beta-4 chain;Tubulin beta-III\tno\tno\t2\t0.022807\t90.657\t1\t0\t7\tNaN\tNaN\t\t1\t1\t1\t1\t\t\t\t\t\t\t\t\t\t\t1\t1\t\t\t\t\t1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t777910\t223360\t170920\t135270\t140570\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t42694\t38423\t0\t0\t0\t0\t26674\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t\t\r\n+568\t38\t575\t6336;6337;6338;6339;6340;6341;6342;6343;6344;6345;6346;6347;6348;6349;6350;6351;6352;6353;6354;6355;6356;6357;6358;6359\t3302;3303;3304;3305;3306;3307;3308;3309;3310;3311;3312;3313;3314;3315;3316;3317;3318;3319;3320;3321;3322;3323;3324;3325\t3302\t\tYLVIQGDER\t0\t1\t0\t1\t0\t1\t1\t1\t0\t1\t1\t0\t0\t0\t0\t0\t0\t0\t1\t1\t0\t9\t0\t1091.5611\tP00533\tP00533\tEGFR;ERBB1\tEpidermal growth factor receptor;Proto-oncogene c-ErbB-1;Receptor tyrosine-protein kinase erbB-1\tyes\tyes\t2\t2.0138E-05\t141.48\t1\t0\t24\t1\t0\t24\t1\t1\t2\t1\t1\t\t1\t1\t\t\t\t\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t\t\t\t1\t1\t1\t1\t\t\t\t\t1\t1\t2\t1\t1\t\t1\t1\t\t\t\t\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t\t\t\t1\t1\t1\t1\t\t\t\t\t32392000\t5018100\t5695200\t4607600\t4571800\t30063\t0\t36962\t50585\t0\t0\t0\t0\t818280\t821420\t1090600\t1127900\t56584\t52371\t118980\t70117\t2184800\t1768600\t1774200\t1787900\t0\t0\t0\t0\t241390\t232830\t235430\t0\t0\t0\t0\t\t\r\n+569\t107\t576\t6360;6361;6362;6363;6364;6365\t3326\t3326\t\tYLYTLVITDKEK\t0\t0\t0\t1\t0\t0\t1\t0\t0\t1\t2\t2\t0\t0\t0\t0\t2\t0\t2\t1\t0\t12\t1\t1484.8126\tP63173\tP63173\tRPL38\t60S ribosomal protein L38\tyes\tyes\t3\t0.0613\t73.499\t1\t0\t6\t1\t0\t6\t1\t1\t1\t1\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t1\t1\t1\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\t\t\t\t\t\t\t390990\t115330\t86638\t69980\t39359\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t37910\t0\t0\t0\t0\t0\t0\t41774\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t\t\r\n+570\t122\t577\t6366;6367\t3327\t3327\t\tYNKPLPPTPDLPQPHLPPISAPGSSR\t1\t1\t1\t1\t0\t1\t0\t1\t1\t1\t3\t1\t0\t0\t9\t3\t1\t0\t1\t0\t0\t26\t1\t2775.4708\tQ12774\tQ12774\tARHGEF5;TIM\tGuanine nucleotide regulatory protein TIM;Oncogene TIM;p60 TIM;Rho guanine nucleotide exchange factor 5;Transforming immortalized mammary oncogene\tyes\tyes\t3\t0.028867\t67.864\t1\t0\t2\t1\t0\t2\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t489100\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t258500\t230600\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t\t\r\n+571\t26\t578\t6368;6369;6370;6371;6372\t3328;3329\t3329\t\tYQQDQIVKEDSVEAVGAQLK\t2\t0\t0\t2\t0\t4\t2\t1\t0\t1\t1\t2\t0\t0\t0\t1\t0\t0\t1\t3\t0\t20\t1\t2247.1383\tO00459\tO00459\tPIK3R2\tPhosphatidylinositol 3-kinase 85 kDa regulatory subunit beta;Phosphatidylinositol 3-kinase regulatory subunit beta\tyes\tyes\t3\t3.3406E-07\t133.66\t1\t0\t5\t1\t0\t5\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t1\t1\t1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t1\t1\t1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t724070\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t104200\t141790\t233370\t207900\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t36823\t\t\r\n+572\t38\t579\t6373;6374;6375;6376;6377;6378;6379;6380;6381;6382;6383;6384;6385;6386;6387\t3330;3331;3332;3333;3334;3335;3336;3337;3338;3339;3340;3341;3342\t3330\t\tYSFGATCVK\t1\t0\t0\t0\t1\t0\t0\t1\t0\t0\t0\t1\t0\t1\t0\t1\t1\t0\t1\t1\t0\t9\t0\t1031.4746\tP00533\tP00533\tEGFR;ERBB1\tEpidermal growth factor receptor;Proto-oncogene c-ErbB-1;Receptor tyrosine-protein kinase erbB-1\tyes\tyes\t2\t2.1213E-05\t141.2\t1\t0\t15\t1\t0\t15\t1\t1\t1\t1\t\t\t\t\t\t\t\t\t1\t1\t1\t1\t\t\t\t\t1\t1\t1\t1\t\t\t\t\t1\t1\t1\t\t\t\t\t1\t1\t1\t1\t\t\t\t\t\t\t\t\t1\t1\t1\t1\t\t\t\t\t1\t1\t1\t1\t\t\t\t\t1\t1\t1\t\t\t\t\t6491300\t1250600\t1204500\t889280\t992760\t0\t0\t0\t0\t0\t0\t0\t0\t171370\t192640\t209850\t227230\t0\t0\t0\t0\t326160\t312160\t258120\t275490\t0\t0\t0\t0\t51485\t61876\t67776\t0\t0\t0\t0\t\t\r\n+573\t65\t580\t6388;6389;6390;6391;6392;6393\t3343;3344\t3344\t\tYVNILPYDHSR\t0\t1\t1\t1\t0\t0\t0\t0\t1\t1\t1\t0\t0\t0\t1\t1\t0\t0\t2\t1\t0\t11\t0\t1375.6884\tP18433\tP18433\tPTPA;PTPRA;PTPRL2\tReceptor-type tyrosine-protein phosphatase alpha\tyes\tyes\t3\t0.013779\t90.629\t1\t0\t6\t1\t0\t6\t\t\t\t\t\t\t\t\t\t\t\t\t1\t1\t1\t1\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t1\t1\t1\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t1\t\t\t\t\t384240\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t50857\t50062\t102220\t78680\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t51008\t0\t51412\t0\t0\t0\t0\t\t\r\n' |
| b |
| diff -r 6a6c1b3b186c -r 843ee18d6065 test_files/scaffold_EGFR.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test_files/scaffold_EGFR.txt Tue Mar 15 15:58:57 2016 -0400 |
| [ |
| b'@@ -0,0 +1,137 @@\n+EGFR_TAP, Samples report created on 12/08/2015\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+Experiment: EGFR_TAP\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\tPeak List Generator: unknown\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\tVersion: unknown\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\tCharge States Calculated: unknown\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\tDeisotoped: unknown\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\tTextual Annotation: unknown\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\tDatabase Set: 1 Database\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\tDatabase Name: the SwissProt_2015_09 database\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\tVersion: unknown\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\tTaxonomy: Homo sapiens\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\tNumber of Proteins: 20205\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\tDoes database contain common contaminants?: unknown\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\tSearch Engine Set: 1 Search Engine\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\tSearch Engine: Mascot\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\tVersion: 2.4.1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\tSamples: All Samples\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\tFragment Tolerance: 0.80 Da (Monoisotopic)\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\tParent Tolerance: 1.2 Da (Monoisotopic)\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\tFixed Modifications: \t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\tVariable Modifications: +16 on M (Oxidation), +57 on C (Carbamidomethyl)\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\tDatabase: the SwissProt_2015_09 database (selected for Homo sapiens, unknown version, 20205 entries)\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\tDigestion Enzyme: Trypsin\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\tMax Missed Cleavages: 2\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\tProbability Model: \t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t04112012_JL_HCC827_EGFR_TAP_1_run1.RAW (F001988): Peptide Prophet with Delta Mass Correction (No decoys found) [all charge states]\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t04112012_JL_HCC827_EGFR_TAP_1_run2.RAW (F001989): Peptide Prophet with Delta Mass Correction (No decoys found) [all charge states]\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t04112012_JL_HCC827_EGFR_TAP_2_run1.RAW (F001990): Peptide Prophet with Delta Mass Correction (No decoys found) [all charge states]\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t04112012_JL_HCC827_EGFR_TAP_2_run2.RAW (F001991): Peptide Prophet with Delta Mass Correction (No decoys found) [all charge states]\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t04112012_JL_HCC827_ERBB3_TAP_1_run1.RAW (F001992): Peptide Prophet with Delta Mass Correction (No decoys found) [all charge states]\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t04112012_JL_HCC827_ERBB3_TAP_1_run2.RAW (F001993): Peptide Prophet with Delta Mass Correction (No decoys found) [all charge states]\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t04112012_JL_HCC827_ERBB3_TAP_2_run1.RAW (F001994): Peptide Prophet with Delta Mass Correction (No decoys found) [all charge states]\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t04112012_JL_HCC827_ERBB3_TAP_2_run2.RAW (F001995): Peptide Prophet with Delta Mass Correction (No decoys found) [all charge states]\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t04112012_JL_HCC827_GFP_TAP_1_run1.RAW (F001996): Peptide Prophet with Delta Mass Correction (No decoys found) [all charge states]\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t04112012_JL_HCC827_GFP_TAP_1_run2.RAW (F001997): Peptide Prophet with Delta Mass Correction (No decoys found) [all charge states]\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t04112012_JL_HCC827_GFP_TAP_2_run1.RAW (F001998): Peptide Prophet with Delta Mass Correction (No decoys found) [all charge states]\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t04112012_JL_HCC827_GFP_TAP_2_run2.RAW (F001999): Pe'..b'tor-type tyrosine-protein phosphatase alpha OS=Homo sapiens GN=PTPRA PE=1 SV=2\tPTPRA_HUMAN\t91 kDa\t\t\tunknown\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t3\t3\t3\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t3\t2\t0\t0\t0\t0\t0\t0\r\n+28\tTRUE\tEmpty\tComplement component 1 Q subcomponent-binding protein, mitochondrial OS=Homo sapiens GN=C1QBP PE=1 SV=1\tC1QBP_HUMAN\t31 kDa\t\t\tunknown\t0\t0\t0\t0\t0\t0\t0\t0\t7\t5\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n+29\tTRUE\tEmpty\tSHC-transforming protein 1 OS=Homo sapiens GN=SHC1 PE=1 SV=4\tSHC1_HUMAN\t63 kDa\t\t\tunknown\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t2\t3\t3\t2\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t1\t0\t0\t0\t0\t0\t0\r\n+30\tTRUE\tEmpty\tTyrosine-protein phosphatase non-receptor type 11 OS=Homo sapiens GN=PTPN11 PE=1 SV=2\tPTN11_HUMAN\t68 kDa\t\t\tunknown\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t1\t1\t1\t2\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n+31\tTRUE\tEmpty\tSerum paraoxonase/arylesterase 2 OS=Homo sapiens GN=PON2 PE=1 SV=3\tPON2_HUMAN\t39 kDa\t\t\tunknown\t1\t2\t1\t1\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t2\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n+32\tTRUE\tEmpty\tHepatocyte growth factor receptor OS=Homo sapiens GN=MET PE=1 SV=4\tMET_HUMAN\t156 kDa\t\t\tunknown\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t1\t0\t0\t0\t0\t1\t1\t0\t0\t0\t0\t1\t0\t2\t2\t0\t0\t0\t0\t1\t1\r\n+33\tTRUE\tEmpty\tCrk-like protein OS=Homo sapiens GN=CRKL PE=1 SV=1\tCRKL_HUMAN\t34 kDa\t\t\tunknown\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t2\t1\t1\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n+34\tTRUE\tEmpty\tE3 ubiquitin-protein ligase CBL OS=Homo sapiens GN=CBL PE=1 SV=2\tCBL_HUMAN\t100 kDa\t\t\tunknown\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t2\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n+35\tTRUE\tEmpty\tPleckstrin homology-like domain family A member 2 OS=Homo sapiens GN=PHLDA2 PE=1 SV=2\tPHLA2_HUMAN\t17 kDa\t\t\tunknown\t1\t1\t0\t1\t2\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n+36\tTRUE\tEmpty\t28S ribosomal protein S27, mitochondrial OS=Homo sapiens GN=MRPS27 PE=1 SV=3\tRT27_HUMAN\t48 kDa\t\t\tunknown\t0\t0\t0\t0\t1\t2\t1\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t1\t0\t0\t0\t0\t0\t0\t0\t0\r\n+37\tTRUE\tEmpty\tMitochondrial 2-oxoglutarate/malate carrier protein OS=Homo sapiens GN=SLC25A11 PE=1 SV=3\tM2OM_HUMAN\t34 kDa\t\t\tunknown\t1\t0\t1\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n+38\tTRUE\tEmpty\tSignal transducer and activator of transcription 1-alpha/beta OS=Homo sapiens GN=STAT1 PE=1 SV=2\tSTAT1_HUMAN\t87 kDa\t\t\tunknown\t3\t2\t1\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n+39\tTRUE\tEmpty\tSRA stem-loop-interacting RNA-binding protein, mitochondrial OS=Homo sapiens GN=SLIRP PE=1 SV=1\tSLIRP_HUMAN\t12 kDa\t\t\tunknown\t2\t1\t2\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n+40\tTRUE\tEmpty\tPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform OS=Homo sapiens GN=PIK3CD PE=1 SV=2\tPK3CD_HUMAN\t119 kDa\tTRUE\t\tunknown\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t2\t2\t2\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n+41\tTRUE\tEmpty\tStress-70 protein, mitochondrial OS=Homo sapiens GN=HSPA9 PE=1 SV=2\tGRP75_HUMAN\t74 kDa\t\t\tunknown\t1\t2\t1\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n+42\tTRUE\tEmpty\tApoptosis-inducing factor 1, mitochondrial OS=Homo sapiens GN=AIFM1 PE=1 SV=1\tAIFM1_HUMAN\t67 kDa\t\t\tunknown\t0\t0\t0\t0\t1\t1\t1\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n+43\tTRUE\tEmpty\tProhibitin OS=Homo sapiens GN=PHB PE=1 SV=1\tPHB_HUMAN\t30 kDa\t\t\tunknown\t2\t1\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n+44\tTRUE\tEmpty\tHeterogeneous nuclear ribonucleoprotein K OS=Homo sapiens GN=HNRNPK PE=1 SV=1\tHNRPK_HUMAN\t51 kDa\t\t\tunknown\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t1\t2\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n+45\tTRUE\tEmpty\tTransmembrane protein 33 OS=Homo sapiens GN=TMEM33 PE=1 SV=2\tTMM33_HUMAN\t28 kDa\t\t\tunknown\t2\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n+46\tTRUE\tEmpty\t28S ribosomal protein S34, mitochondrial OS=Homo sapiens GN=MRPS34 PE=1 SV=2\tRT34_HUMAN\t26 kDa\t\t\tunknown\t0\t0\t0\t0\t1\t0\t1\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n+\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+END OF FILE\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\n\\ No newline at end of file\n' |
| b |
| diff -r 6a6c1b3b186c -r 843ee18d6065 test_files/scaffold_bait.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test_files/scaffold_bait.txt Tue Mar 15 15:58:57 2016 -0400 |
| b |
| @@ -0,0 +1,36 @@ +WT_EGFR1_1 WT_EGFR T +WT_EGFR1_2 WT_EGFR T +WT_EGFR2_1 WT_EGFR T +WT_EGFR2_2 WT_EGFR T +WT_ERBB31_1 WT_ERBB3 T +WT_ERBB31_2 WT_ERBB3 T +WT_ERBB32_1 WT_ERBB3 T +WT_ERBB32_2 WT_ERBB3 T +WT_GFP1_1 WT_GFP C +WT_GFP1_2 WT_GFP C +WT_GFP2_1 WT_GFP C +WT_GFP2_2 WT_GFP C +WT_GRB21_1 WT_GRB2 T +WT_GRB21_2 WT_GRB2 T +WT_GRB22_1 WT_GRB2 T +WT_GRB22_2 WT_GRB2 T +WT_P85B1_1 WT_P85B T +WT_P85B1_2 WT_P85B T +WT_P85B2_1 WT_P85B T +WT_P85B2_2 WT_P85B T +ER_EGFR1_1 ER_EGFR T +ER_EGFR1_2 ER_EGFR T +ER_EGFR2_1 ER_EGFR T +ER_EGFR2_2 ER_EGFR T +ER_ERBB31_1 ER_ERBB3 T +ER_ERBB31_2 ER_ERBB3 T +ER_ERBB32_1 ER_ERBB3 T +ER_ERBB32_2 ER_ERBB3 T +ER_GRB21_1 ER_GRB2 T +ER_GRB21_2 ER_GRB2 T +ER_GRB22_1 ER_GRB2 T +ER_GRB22_2 ER_GRB2 T +ER_P85B1_1 ER_P85B T +ER_P85B1_2 ER_P85B T +ER_P85B2_1 ER_P85B T +ER_P85B2_2 ER_P85B T \ No newline at end of file |