Mercurial > repos > galaxyp > psm_to_sam
changeset 4:81b183d8cbc2 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
| author | galaxyp |
|---|---|
| date | Thu, 28 Jan 2016 18:45:02 -0500 |
| parents | ce09f1a1bbad |
| children | 7d02e2e2c8fa |
| files | test-data/Ellis_033_2700_261_07-unrefined-subset.idpDB.gz test-data/dbo_z_20101126_JK_Res_Sens_Set2_H1819_A_07-subset.idpDB.gz test-data/passedPSM.tab tool-data/.RData tool-data/.Rhistory tool-data/exon_anno.RData tool-data/header_refseq_hg19.txt tool-data/ids.RData tool-data/procodingseq.RData tool-data/proseq.RData tool-data/test.fasta_rpkm.fasta tool-data/txdb.sqlite tool_data_table_conf.xml.sample |
| diffstat | 13 files changed, 7 insertions(+), 675 deletions(-) [+] |
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--- a/test-data/passedPSM.tab Thu Jan 28 18:40:54 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,38 +0,0 @@ -spectrum spectrumNativeID start_scan end_scan precursor_neutral_mass assumed_charge index retention_time_sec hit_rank peptide peptide_prev_aa peptide_next_aa protein num_tot_proteins calc_neutral_pep_mass massdiff num_tol_term num_missed_cleavages num_matched_ions tot_num_ions mvh mzFidelity xcorr modification NTT -00463_H12_P003361_B00L_A00_R1.9484.9484.2 controllerType=0 controllerNumber=1 scan=9484 9484 9484 1945.011203902178 2 1604 5941.1121 1 VNPTVFFDIAVDGEPLGR M V ENST00000415933.1|ENSG00000196262.9|OTTHUMG00000023687.5|OTTHUMT00000341788.1|PPIA-007|PPIA|120 4 1944.9945272767 -0.016676625478 2 0 21 31 46.204418394943 81.978491255568 4.2761193008959291 NA 1 -00463_H12_P003361_B00L_A00_R1.9501.9501.2 controllerType=0 controllerNumber=1 scan=9501 9501 9501 1945.01913847249 2 1614 5951.950699999979 1 VNPTVFFDIAVDGEPLGR M V ENST00000415933.1|ENSG00000196262.9|OTTHUMG00000023687.5|OTTHUMT00000341788.1|PPIA-007|PPIA|120 4 1944.9945272767 -0.02461119579 2 0 26 31 60.506052773687 104.253972125002 5.3345391753673557 NA 1 -00463_H12_P003361_B00L_A00_R1.9526.9526.2 controllerType=0 controllerNumber=1 scan=9526 9526 9526 1945.016452925616 2 1631 5963.759599999979 1 VNPTVFFDIAVDGEPLGR M V ENST00000415933.1|ENSG00000196262.9|OTTHUMG00000023687.5|OTTHUMT00000341788.1|PPIA-007|PPIA|120 4 1944.9945272767 -0.021925648916 2 0 22 31 52.51658671853 86.186927014543 5.0573944690853354 NA 1 -00463_H12_P003361_B00L_A00_R1.9551.9551.2 controllerType=0 controllerNumber=1 scan=9551 9551 9551 1945.01572050374 2 1650 5974.70770000002 1 VNPTVFFDIAVDGEPLGR M V ENST00000415933.1|ENSG00000196262.9|OTTHUMG00000023687.5|OTTHUMT00000341788.1|PPIA-007|PPIA|120 4 1944.9945272767 -0.02119322704 2 0 25 31 57.801667421952 104.376405284597 5.0885360433134252 NA 1 -00463_H12_P003361_B00L_A00_R1.5321.5321.2 controllerType=0 controllerNumber=1 scan=5321 5321 5321 1246.617038863116 2 444 3135.20290000002 1 KITIADCGQLE K - ENST00000355968.6|ENSG00000196262.9|OTTHUMG00000023687.5|OTTHUMT00000341783.2|PPIA-002|PPIA|105 3 1246.6227377481 0.005698884984 2 1 12 19 26.789701275346 44.086444435179 2.5089015573740006 7;160.0306484778 2 -00463_H12_P003361_B00L_A00_R1.5335.5335.2 controllerType=0 controllerNumber=1 scan=5335 5335 5335 1246.62265409749 2 446 3145.3746 1 KITIADCGQLE K - ENST00000355968.6|ENSG00000196262.9|OTTHUMG00000023687.5|OTTHUMT00000341783.2|PPIA-002|PPIA|105 3 1246.6227377481 8.36506098949e-05 2 1 12 19 22.053623255921 42.660663132368 2.6259103034973146 7;160.0306484778 2 -00463_H12_P003361_B00L_A00_R1.5355.5355.2 controllerType=0 controllerNumber=1 scan=5355 5355 5355 1246.61923612874 2 452 3156.474 1 KITIADCGQLE K - ENST00000355968.6|ENSG00000196262.9|OTTHUMG00000023687.5|OTTHUMT00000341783.2|PPIA-002|PPIA|105 3 1246.6227377481 0.00350161936 2 1 16 19 34.764799517588 65.279222439398 3.3673483355291189 7;160.0306484778 2 -00463_H12_P003361_B00L_A00_R1.5376.5376.2 controllerType=0 controllerNumber=1 scan=5376 5376 5376 1246.620334761552 2 458 3166.7412 1 KITIADCGQLE K - ENST00000355968.6|ENSG00000196262.9|OTTHUMG00000023687.5|OTTHUMT00000341783.2|PPIA-002|PPIA|105 3 1246.6227377481 0.002402986548 2 1 12 19 27.430886582989 47.577287392774 2.5777545196354388 7;160.0306484778 2 -00463_H12_P003361_B00L_A00_R1.5749.5749.2 controllerType=0 controllerNumber=1 scan=5749 5749 5749 1336.61008293189 2 524 3385.38760000002 1 YALYDATYETK R E ENST00000298159.6|ENSG00000165410.10|OTTHUMG00000029536.7|OTTHUMT00000276638.1|CFL2-001|CFL2|166 12 1336.6186979513 0.00861501941 2 0 14 19 25.105650388807 55.928640379435 2.1785177153468132 NA 2 -00463_H12_P003361_B00L_A00_R1.5754.5754.2 controllerType=0 controllerNumber=1 scan=5754 5754 5754 1336.62167753499 2 525 3389.22919999998 1 YALYDATYETK R E ENST00000298159.6|ENSG00000165410.10|OTTHUMG00000029536.7|OTTHUMT00000276638.1|CFL2-001|CFL2|166 12 1336.6186979513 -0.00297958369 2 0 13 19 24.129759484342 49.379626376266 2.2121857662796973 NA 2 -00463_H12_P003361_B00L_A00_R1.5774.5774.2 controllerType=0 controllerNumber=1 scan=5774 5774 5774 1336.621311324052 2 527 3401.74570000002 1 YALYDATYETK R E ENST00000298159.6|ENSG00000165410.10|OTTHUMG00000029536.7|OTTHUMT00000276638.1|CFL2-001|CFL2|166 12 1336.6186979513 -0.002613372752 2 0 12 19 24.388296643559 44.683514877427 1.7531160330057145 NA 2 -00463_H12_P003361_B00L_A00_R1.7218.7218.2 controllerType=0 controllerNumber=1 scan=7218 7218 7218 1339.777197189702 2 824 4312.7532 1 LGGSAVISLEGKPL K - ENST00000308162.5|ENSG00000172757.8|OTTHUMG00000166602.3|-|CFL1-201|CFL1|166 7 1339.7711162684 -0.006080921302 2 0 16 25 22.681295676754 54.618435522774 2.5399510658740998 NA 2 -00463_H12_P003361_B00L_A00_R1.7221.7221.2 controllerType=0 controllerNumber=1 scan=7221 7221 7221 1339.772800581866 2 825 4314.25129999998 1 LGGSAVISLEGKPL K - ENST00000308162.5|ENSG00000172757.8|OTTHUMG00000166602.3|-|CFL1-201|CFL1|166 7 1339.7711162684 -0.001684313466 2 0 16 25 26.909329916142 50.650277740631 1.9263482891201973 NA 2 -00463_H12_P003361_B00L_A00_R1.7240.7240.2 controllerType=0 controllerNumber=1 scan=7240 7240 7240 1339.778659956866 2 831 4325.60770000002 1 LGGSAVISLEGKPL K - ENST00000308162.5|ENSG00000172757.8|OTTHUMG00000166602.3|-|CFL1-201|CFL1|166 7 1339.7711162684 -0.007543688466 2 0 16 25 36.67045971257 58.855828722104 3.2758580466851592 NA 2 -00463_H12_P003361_B00L_A00_R1.7263.7263.2 controllerType=0 controllerNumber=1 scan=7263 7263 7263 1339.77890409749 2 844 4337.22760000002 1 LGGSAVISLEGKPL K - ENST00000308162.5|ENSG00000172757.8|OTTHUMG00000166602.3|-|CFL1-201|CFL1|166 7 1339.7711162684 -0.00778782909 2 0 20 25 48.296221687223 83.778882039436 4.2370695855587721 NA 2 -00463_H12_P003361_B00L_A00_R1.7286.7286.2 controllerType=0 controllerNumber=1 scan=7286 7286 7286 1339.779148238116 2 857 4347.600899999999 1 LGGSAVISLEGKPL K - ENST00000308162.5|ENSG00000172757.8|OTTHUMG00000166602.3|-|CFL1-201|CFL1|166 7 1339.7711162684 -0.008031969716 2 0 19 25 50.929079797825 74.060801211975 3.5908124986244365 NA 2 -00463_H12_P003361_B00L_A00_R1.7307.7307.2 controllerType=0 controllerNumber=1 scan=7307 7307 7307 1339.781101363116 2 867 4358.570400000001 1 LGGSAVISLEGKPL K - ENST00000308162.5|ENSG00000172757.8|OTTHUMG00000166602.3|-|CFL1-201|CFL1|166 7 1339.7711162684 -0.009985094716 2 0 18 25 30.672214386423 65.432231931785 3.2431760800898073 NA 2 -00463_H12_P003361_B00L_A00_R1.7350.7350.2 controllerType=0 controllerNumber=1 scan=7350 7350 7350 1830.925144331866 2 885 4380.76420000002 1 SIYGEKFEDENFILK K H ENST00000415933.1|ENSG00000196262.9|OTTHUMG00000023687.5|OTTHUMT00000341788.1|PPIA-007|PPIA|120 2 1830.9039809349 -0.021163396966 2 1 12 26 22.49087533635 35.874605053812 2.716855755531788 NA 2 -00463_H12_P003361_B00L_A00_R1.7441.7441.2 controllerType=0 controllerNumber=1 scan=7441 7441 7441 1378.767429488116 2 915 4444.20640000002 1 VSFELFADKVPK R T ENST00000451562.1|ENSG00000196262.9|OTTHUMG00000023687.5|OTTHUMT00000341787.1|PPIA-006|PPIA|121 1 1378.7496525448 -0.017776943316 2 1 16 21 21.321034087967 57.231366553646 2.6742705414295198 NA 2 -00463_H12_P003361_B00L_A00_R1.7457.7457.2 controllerType=0 controllerNumber=1 scan=7457 7457 7457 1378.765598433428 2 922 4454.574499999981 1 VSFELFADKVPK R T ENST00000451562.1|ENSG00000196262.9|OTTHUMG00000023687.5|OTTHUMT00000341787.1|PPIA-006|PPIA|121 1 1378.7496525448 -0.015945888628 2 1 13 21 25.258094726623 42.632914152441 2.9917362130850553 NA 2 -00463_H12_P003361_B00L_A00_R1.7898.7898.2 controllerType=0 controllerNumber=1 scan=7898 7898 7898 1877.938938277178 2 1069 4740.2052 1 LQSSDGEIFEVDVEIAK K Q ENST00000328392.6|ENSG00000113558.14|OTTHUMG00000129117.4|OTTHUMT00000381585.1|SKP1-008|SKP1|158 11 1877.925838589 -0.013099688178 2 0 15 29 30.982918349008 45.100000325963 2.5511644269704821 NA 2 -00463_H12_P003361_B00L_A00_R1.7915.7915.2 controllerType=0 controllerNumber=1 scan=7915 7915 7915 1877.944797652178 2 1075 4750.93900000002 1 LQSSDGEIFEVDVEIAK K Q ENST00000328392.6|ENSG00000113558.14|OTTHUMG00000129117.4|OTTHUMT00000381585.1|SKP1-008|SKP1|158 11 1877.925838589 -0.018959063178 2 0 20 29 42.823475332379 68.583054386532 3.9013459840655327 NA 2 -00463_H12_P003361_B00L_A00_R1.7933.7933.2 controllerType=0 controllerNumber=1 scan=7933 7933 7933 1877.945163863116 2 1079 4762.56970000002 1 LQSSDGEIFEVDVEIAK K Q ENST00000328392.6|ENSG00000113558.14|OTTHUMG00000129117.4|OTTHUMT00000381585.1|SKP1-008|SKP1|158 11 1877.925838589 -0.019325274116 2 0 19 29 33.995138549471 64.962929439795 3.6298434626102449 NA 2 -00463_H12_P003361_B00L_A00_R1.7952.7952.2 controllerType=0 controllerNumber=1 scan=7952 7952 7952 1387.76279081624 2 1086 4775.11819999998 1 ASGQAFELILSPR R S ENST00000357865.2|ENSG00000117632.16|OTTHUMG00000007389.2|OTTHUMT00000019357.1|STMN1-003|STMN1|149 6 1387.7459641504 -0.01682666584 2 0 10 22 23.465486209266 34.687015321513 2.3075107035519555 NA 2 -00463_H12_P003361_B00L_A00_R1.7957.7957.2 controllerType=0 controllerNumber=1 scan=7957 7957 7957 1387.751074142828 2 1089 4777.3443 1 ASGQAFELILSPR R S ENST00000357865.2|ENSG00000117632.16|OTTHUMG00000007389.2|OTTHUMT00000019357.1|STMN1-003|STMN1|149 6 1387.7459641504 -0.005109992428 2 0 14 22 29.433875299502 49.269857725193 2.6334667768120767 NA 2 -00463_H12_P003361_B00L_A00_R1.7966.7966.2 controllerType=0 controllerNumber=1 scan=7966 7966 7966 1877.942724533452 2 1092 4782.29890000002 1 LQSSDGEIFEVDVEIAK K Q ENST00000328392.6|ENSG00000113558.14|OTTHUMG00000129117.4|OTTHUMT00000381585.1|SKP1-008|SKP1|158 11 1877.925838589 -0.016885944452 2 0 13 29 22.326192518883 35.623838450184 2.4770750341773033 NA 2 -00463_H12_P003361_B00L_A00_R1.7972.7972.2 controllerType=0 controllerNumber=1 scan=7972 7972 7972 1387.757175581866 2 1093 4786.41259999998 1 ASGQAFELILSPR R S ENST00000357865.2|ENSG00000117632.16|OTTHUMG00000007389.2|OTTHUMT00000019357.1|STMN1-003|STMN1|149 6 1387.7459641504 -0.011211431466 2 0 14 22 35.87498786185 46.219644010662 2.9282210849818773 NA 2 -00463_H12_P003361_B00L_A00_R1.7988.7988.2 controllerType=0 controllerNumber=1 scan=7988 7988 7988 1387.759983199052 2 1100 4796.7516 1 ASGQAFELILSPR R S ENST00000357865.2|ENSG00000117632.16|OTTHUMG00000007389.2|OTTHUMT00000019357.1|STMN1-003|STMN1|149 6 1387.7459641504 -0.014019048652 2 0 15 22 26.459097532541 56.783446281888 3.0687246401488779 NA 2 -00463_H12_P003361_B00L_A00_R1.8003.8003.2 controllerType=0 controllerNumber=1 scan=8003 8003 8003 1387.760105269366 2 1104 4807.34830000002 1 ASGQAFELILSPR R S ENST00000357865.2|ENSG00000117632.16|OTTHUMG00000007389.2|OTTHUMT00000019357.1|STMN1-003|STMN1|149 6 1387.7459641504 -0.014141118966 2 0 15 22 32.648477269597 60.489969121946 3.0482543933033943 NA 2 -00463_H12_P003361_B00L_A00_R1.8021.8021.2 controllerType=0 controllerNumber=1 scan=8021 8021 8021 1387.76474394124 2 1110 4818.8241 1 ASGQAFELILSPR R S ENST00000357865.2|ENSG00000117632.16|OTTHUMG00000007389.2|OTTHUMT00000019357.1|STMN1-003|STMN1|149 6 1387.7459641504 -0.01877979084 2 0 13 22 24.948802158747 45.99273175144 2.5623559864997865 NA 2 -00463_H12_P003361_B00L_A00_R1.8575.8575.2 controllerType=0 controllerNumber=1 scan=8575 8575 8575 2349.046362228766 2 1287 5218.83700000002 1 NAFACFDEEATGTIQEDYLR R E ENST00000217652.3|ENSG00000101608.8|OTTHUMG00000131509.5|OTTHUMT00000254364.2|MYL12A-001|MYL12A|171 9 2349.0219408701 -0.024421358666 2 0 13 29 26.277655446584 36.709062494236 3.4111691149663521 5;160.0306484778 2 -00463_H12_P003361_B00L_A00_R1.8581.8581.2 controllerType=0 controllerNumber=1 scan=8581 8581 8581 2349.04501737874 2 1288 5222.74060000002 1 NAFACFDEEATGTIQEDYLR R E ENST00000217652.3|ENSG00000101608.8|OTTHUMG00000131509.5|OTTHUMT00000254364.2|MYL12A-001|MYL12A|171 9 2349.0219408701 -0.02307650864 2 0 23 29 50.024579363667 92.315246147479 4.5286496783290753 5;160.0306484778 2 -00463_H12_P003361_B00L_A00_R1.8605.8605.2 controllerType=0 controllerNumber=1 scan=8605 8605 8605 2349.050144331866 2 1301 5233.99309999998 1 NAFACFDEEATGTIQEDYLR R E ENST00000217652.3|ENSG00000101608.8|OTTHUMG00000131509.5|OTTHUMT00000254364.2|MYL12A-001|MYL12A|171 9 2349.0219408701 -0.028203461766 2 0 22 29 52.634472048776 91.483429905977 4.1929949165213589 5;160.0306484778 2 -00463_H12_P003361_B00L_A00_R1.8620.8620.2 controllerType=0 controllerNumber=1 scan=8620 8620 8620 2349.040502853766 2 1310 5241.32689999998 1 NAFACFDEEATGTIQEDYLR R E ENST00000217652.3|ENSG00000101608.8|OTTHUMG00000131509.5|OTTHUMT00000254364.2|MYL12A-001|MYL12A|171 9 2349.0219408701 -0.018561983666 2 0 19 29 31.861371342706 64.997046778589 3.8285629652359816 5;160.0306484778 2 -00463_H12_P003361_B00L_A00_R1.8630.8630.2 controllerType=0 controllerNumber=1 scan=8630 8630 8630 2349.062351363116 2 1317 5245.7199 1 NAFACFDEEATGTIQEDYLR R E ENST00000217652.3|ENSG00000101608.8|OTTHUMG00000131509.5|OTTHUMT00000254364.2|MYL12A-001|MYL12A|171 9 2349.0219408701 -0.040410493016 2 0 18 29 36.68891757627 64.187787867916 4.0132409641103282 5;160.0306484778 2 -00463_H12_P003361_B00L_A00_R1.8637.8637.2 controllerType=0 controllerNumber=1 scan=8637 8637 8637 2349.044409103766 2 1320 5251.05079999998 1 NAFACFDEEATGTIQEDYLR R E ENST00000217652.3|ENSG00000101608.8|OTTHUMG00000131509.5|OTTHUMT00000254364.2|MYL12A-001|MYL12A|171 9 2349.0219408701 -0.022468233666 2 0 19 29 37.546297128072 64.706228542971 3.3201605243652543 5;160.0306484778 2 -00463_H12_P003361_B00L_A00_R1.8644.8644.2 controllerType=0 controllerNumber=1 scan=8644 8644 8644 2349.05600786004 2 1322 5255.85700000002 1 NAFACFDEEATGTIQEDYLR R E ENST00000217652.3|ENSG00000101608.8|OTTHUMG00000131509.5|OTTHUMT00000254364.2|MYL12A-001|MYL12A|171 9 2349.0219408701 -0.034066989941 2 0 16 29 33.932138985108 49.510819522371 3.4363613879741899 5;160.0306484778 2
--- a/tool-data/.Rhistory Thu Jan 28 18:40:54 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,512 +0,0 @@ -} -channel = sub("\\S+?\\.(iTRAQ\\.\\d+)", "\\1", mergedSampleName, perl=T) -return(paste0(sample, "-", channel)) -} -coreSampleNames = list() -for(i in seq(2, length(multiplexData), 4)) -{ -firstGroupNum = 0.75 * i -print(getMultiplexSampleName(sampleNames[i-1], 1, coreSampleNames)) -sampleNames[i-1] = sub("(\\S+?)_(\\S+?)_(\\S+?)(\\.iTRAQ.\\d+)", "\\1\\4", sampleNames[i-1], perl=T) -sampleNames[i] = sub("(\\S+?)_(\\S+?)_(\\S+?)(\\.iTRAQ.\\d+)", "\\2\\4", sampleNames[i], perl=T) -sampleNames[i+1] = sub("(\\S+?)_(\\S+?)_(\\S+?)(\\.iTRAQ.\\d+)", "\\3\\4", sampleNames[i+1], perl=T) -print(sampleNames[i-1]) -print(sampleNames[i]) -print(sampleNames[i+1]) -#ratios[,firstGroupNum] = ZeroSafeDivide(multiplexData[,i], multiplexData[,i+3]) -#ratios[,firstGroupNum+1] = ZeroSafeDivide(multiplexData[,i+1], multiplexData[,i+3]) -#ratios[,firstGroupNum+2] = ZeroSafeDivide(multiplexData[,i+2], multiplexData[,i+3]) -} -getMultiplexSampleName = function(mergedSampleName, tokenIndex, coreSampleNames) -{ -sample = sub("(\\S+?)_(\\S+?)_(\\S+?)\\.iTRAQ\\.\\d+", paste0("\\", tokenIndex), mergedSampleName, perl=T) -if(is.null(coreSampleNames[[sample]])) -{ -coreSampleNames[[sample]] = 1 -} -else -{ -sample = paste0(sample, incrementChar("A", coreSampleNames[[sample]])) -coreSampleNames[[sample]] = coreSampleNames[[sample]] + 1 -} -channel = sub("\\S+?\\.(iTRAQ\\.\\d+)", "\\1", mergedSampleName, perl=T) -coreSampleNames <<- coreSampleNames -return(paste0(sample, "-", channel)) -} -coreSampleNames = list() -for(i in seq(2, length(multiplexData), 4)) -{ -firstGroupNum = 0.75 * i -print(getMultiplexSampleName(sampleNames[i-1], 1, coreSampleNames)) -sampleNames[i-1] = sub("(\\S+?)_(\\S+?)_(\\S+?)(\\.iTRAQ.\\d+)", "\\1\\4", sampleNames[i-1], perl=T) -sampleNames[i] = sub("(\\S+?)_(\\S+?)_(\\S+?)(\\.iTRAQ.\\d+)", "\\2\\4", sampleNames[i], perl=T) -sampleNames[i+1] = sub("(\\S+?)_(\\S+?)_(\\S+?)(\\.iTRAQ.\\d+)", "\\3\\4", sampleNames[i+1], perl=T) -#print(sampleNames[i-1]) -#print(sampleNames[i]) -#print(sampleNames[i+1]) -#ratios[,firstGroupNum] = ZeroSafeDivide(multiplexData[,i], multiplexData[,i+3]) -#ratios[,firstGroupNum+1] = ZeroSafeDivide(multiplexData[,i+1], multiplexData[,i+3]) -#ratios[,firstGroupNum+2] = ZeroSafeDivide(multiplexData[,i+2], multiplexData[,i+3]) -} -sampleNames = colnames(multiplexData)[-1]#[c(F, rep(c(T,T,T,F), numSamples/3))] -incrementChar = function(c, step=1) { return(rawToChar(as.raw(as.integer(charToRaw(c))+step))); } -getMultiplexSampleName = function(mergedSampleName, tokenIndex, coreSampleNames) -{ -sample = sub("(\\S+?)_(\\S+?)_(\\S+?)\\.iTRAQ\\.\\d+", paste0("\\", tokenIndex), mergedSampleName, perl=T) -if(is.null(coreSampleNames[[sample]])) -{ -coreSampleNames[[sample]] = 1 -} -else -{ -sample = paste0(sample, incrementChar("A", coreSampleNames[[sample]])) -coreSampleNames[[sample]] = coreSampleNames[[sample]] + 1 -} -channel = sub("\\S+?\\.(iTRAQ\\.\\d+)", "\\1", mergedSampleName, perl=T) -coreSampleNames <<- coreSampleNames -return(paste0(sample, "-", channel)) -} -coreSampleNames = list() -for(i in seq(2, length(multiplexData), 4)) -{ -firstGroupNum = 0.75 * i -sampleNames[i-1] = getMultiplexSampleName(sampleNames[i-1], 1, coreSampleNames) -sampleNames[i] = getMultiplexSampleName(sampleNames[i], 2, coreSampleNames) -sampleNames[i+1] = getMultiplexSampleName(sampleNames[i+1], 3, coreSampleNames) -print(sampleNames[i-1]) -print(sampleNames[i]) -print(sampleNames[i+1]) -#ratios[,firstGroupNum] = ZeroSafeDivide(multiplexData[,i], multiplexData[,i+3]) -#ratios[,firstGroupNum+1] = ZeroSafeDivide(multiplexData[,i+1], multiplexData[,i+3]) -#ratios[,firstGroupNum+2] = ZeroSafeDivide(multiplexData[,i+2], multiplexData[,i+3]) -} -sampleNames = colnames(multiplexData)[-1]#[c(F, rep(c(T,T,T,F), numSamples/3))] -incrementChar = function(c, step=1) { return(rawToChar(as.raw(as.integer(charToRaw(c))+step))); } -getMultiplexSampleName = function(mergedSampleName, tokenIndex, coreSampleNames) -{ -sample = sub("(\\S+?)_(\\S+?)_(\\S+?)\\.iTRAQ\\.\\d+", paste0("\\", tokenIndex), mergedSampleName, perl=T) -if(is.null(coreSampleNames[[sample]])) -{ -coreSampleNames[[sample]] = 1 -} -else -{ -sample = paste0(sample, "-", incrementChar("A", coreSampleNames[[sample]])) -coreSampleNames[[sample]] = coreSampleNames[[sample]] + 1 -} -channel = sub("\\S+?\\.(iTRAQ\\.\\d+)", "\\1", mergedSampleName, perl=T) -coreSampleNames <<- coreSampleNames -return(paste0(sample, "-", channel)) -} -coreSampleNames = list() -for(i in seq(2, length(multiplexData), 4)) -{ -firstGroupNum = 0.75 * i -sampleNames[i-1] = getMultiplexSampleName(sampleNames[i-1], 1, coreSampleNames) -sampleNames[i] = getMultiplexSampleName(sampleNames[i], 2, coreSampleNames) -sampleNames[i+1] = getMultiplexSampleName(sampleNames[i+1], 3, coreSampleNames) -print(sampleNames[i-1]) -print(sampleNames[i]) -print(sampleNames[i+1]) -#ratios[,firstGroupNum] = ZeroSafeDivide(multiplexData[,i], multiplexData[,i+3]) -#ratios[,firstGroupNum+1] = ZeroSafeDivide(multiplexData[,i+1], multiplexData[,i+3]) -#ratios[,firstGroupNum+2] = ZeroSafeDivide(multiplexData[,i+2], multiplexData[,i+3]) -} -sampleNames = colnames(multiplexData)[-1]#[c(F, rep(c(T,T,T,F), numSamples/3))] -incrementChar = function(c, step=1) { return(rawToChar(as.raw(as.integer(charToRaw(c))+step))); } -getMultiplexSampleName = function(mergedSampleName, tokenIndex, coreSampleNames) -{ -sample = sub("(\\S+?)_(\\S+?)_(\\S+?)\\.iTRAQ\\.\\d+", paste0("\\", tokenIndex), mergedSampleName, perl=T) -if(is.null(coreSampleNames[[sample]])) -{ -coreSampleNames[[sample]] = 1 -} -else -{ -oldCount = coreSampleNames[[sample]] -sample = paste0(sample, "-", incrementChar("A", oldCount)) -coreSampleNames[[sample]] = oldCount + 1 -} -channel = sub("\\S+?\\.(iTRAQ\\.\\d+)", "\\1", mergedSampleName, perl=T) -coreSampleNames <<- coreSampleNames -return(paste0(sample, "-", channel)) -} -coreSampleNames = list() -for(i in seq(2, length(multiplexData), 4)) -{ -firstGroupNum = 0.75 * i -sampleNames[i-1] = getMultiplexSampleName(sampleNames[i-1], 1, coreSampleNames) -sampleNames[i] = getMultiplexSampleName(sampleNames[i], 2, coreSampleNames) -sampleNames[i+1] = getMultiplexSampleName(sampleNames[i+1], 3, coreSampleNames) -print(sampleNames[i-1]) -print(sampleNames[i]) -print(sampleNames[i+1]) -#ratios[,firstGroupNum] = ZeroSafeDivide(multiplexData[,i], multiplexData[,i+3]) -#ratios[,firstGroupNum+1] = ZeroSafeDivide(multiplexData[,i+1], multiplexData[,i+3]) -#ratios[,firstGroupNum+2] = ZeroSafeDivide(multiplexData[,i+2], multiplexData[,i+3]) -} -sort(coreSampleNames) -sort(coreSampleNames[1]) -coreSampleNames[1] -coreSampleNames[2] -coreSampleNames[1,] -coreSampleNames[,1] -simplify2array(coreSampleNames) -order(coreSampleNames) -order(coreSampleNames[1]) -sort(simplify2array(coreSampleNames)) -order(coreSampleNames) -as.matrix(cores) -as.matrix(coreSampleNames) -order(as.matrix(coreSampleNames)) -names(as.matrix(coreSampleNames)) -names(coreSampleNames) -sort(names(coreSampleNames)) -sort(sampleNames) -sampleNames = sampleNames[c(rep(c(T,T,T,F), numSamples/3))] -sort(sampleNames) -ratios = matrix(nrow=dim(multiplexData)[1], ncol=numSamples, dimnames=list(multiplexData[,1], sampleNames)) -View(ratios) -for(i in seq(2, length(multiplexData), 4)) -{ -firstGroupNum = 0.75 * i -ratios[,firstGroupNum] = ZeroSafeDivide(multiplexData[,i], multiplexData[,i+3]) -ratios[,firstGroupNum+1] = ZeroSafeDivide(multiplexData[,i+1], multiplexData[,i+3]) -ratios[,firstGroupNum+2] = ZeroSafeDivide(multiplexData[,i+2], multiplexData[,i+3]) -} -View(ratios) -filepath = "H:/data/CPTAC/TCGA-Broad-Breast/global-Broad.cct" -outputFilepath = sub(".cct", "-demultiplexed-ratios.cct", filepath, fixed=T) -source('~/.active-rstudio-document') -write.csv(format(ratios, digits=4), file=outputFilepath, quote=F) -demultiplexNetGestaltITRAQ_CCT = function(filepath) -{ -outputFilepath = sub(".cct", "-demultiplexed-ratios.cct", filepath, fixed=T) -multiplexData = read.table(filepath, sep="\t", header=T) -numSamples = 0.75*(dim(multiplexData)[2]-1) -sampleNames = colnames(multiplexData)[-1]#[c(F, rep(c(T,T,T,F), numSamples/3))] -coreSampleNames = list() -for(i in seq(2, length(multiplexData), 4)) -{ -firstGroupNum = 0.75 * i -sampleNames[i-1] = getMultiplexSampleName(sampleNames[i-1], 1, coreSampleNames) -sampleNames[i] = getMultiplexSampleName(sampleNames[i], 2, coreSampleNames) -sampleNames[i+1] = getMultiplexSampleName(sampleNames[i+1], 3, coreSampleNames) -} -sampleNames = sampleNames[c(rep(c(T,T,T,F), numSamples/3))] -ratios = matrix(nrow=dim(multiplexData)[1], ncol=numSamples, dimnames=list(multiplexData[,1], sampleNames)) -for(i in seq(2, length(multiplexData), 4)) -{ -firstGroupNum = 0.75 * i -ratios[,firstGroupNum] = ZeroSafeDivide(multiplexData[,i], multiplexData[,i+3]) -ratios[,firstGroupNum+1] = ZeroSafeDivide(multiplexData[,i+1], multiplexData[,i+3]) -ratios[,firstGroupNum+2] = ZeroSafeDivide(multiplexData[,i+2], multiplexData[,i+3]) -} -write.csv(format(ratios, digits=4), file=outputFilepath, quote=F) -} -source('~/.active-rstudio-document') -source('~/.active-rstudio-document') -write.table(format(ratios, digits=4), file=outputFilepath, quote=F, row.names=T, sep="\t") -write.table(format(ratios, digits=4), file=outputFilepath, quote=F, row.names=T, col.names=T, sep="\t") -write.table(format(cbind(rownames(ratios), ratios), digits=4), file=outputFilepath, quote=F, row.names=F, sep="\t") -write.table(format(cbind(c("GeneSymbol", rownames(ratios)), ratios), digits=4), file=outputFilepath, quote=F, row.names=F, sep="\t") -c("GeneSymbol", rownames(ratios)) -head(c("GeneSymbol", rownames(ratios))) -cbind(c("GeneSymbol", rownames(ratios)), ratios), digits=4) -cbind(c("GeneSymbol", rownames(ratios)) -) -cbind(c("GeneSymbol", rownames(ratios)), ratios) -write.table(format(cbind(c(GeneSymbol=rownames(ratios)), ratios), digits=4), file=outputFilepath, quote=F, row.names=F, sep="\t") -write.table(format(cbind(c(GeneSymbol=rownames(ratios)), ratios), digits=4), file=outputFilepath, quote=F, row.names=F, sep="\t") -write.table(format(cbind(GeneSymbol=rownames(ratios), ratios), digits=4), file=outputFilepath, quote=F, row.names=F, sep="\t") -source('~/.active-rstudio-document') -write.table(format(cbind(GeneSymbol=rownames(ratios), ratios), digits=4), file=outputFilepath, quote=F, row.names=F, sep="\t", options(digits=2)) -write.table(cbind(GeneSymbol=rownames(ratios), ratios), file=outputFilepath, quote=F, row.names=F, sep="\t", options(digits=4)) -options(digits=4) -write.table(cbind(GeneSymbol=rownames(ratios), ratios), file=outputFilepath, quote=F, row.names=F, sep="\t") -source('~/.active-rstudio-document') -demultiplexNetGestaltITRAQ_CCT("H:/data/CPTAC/TCGA-Broad-Breast/phospho-Broad.cct") -demultiplexNetGestaltITRAQ_CCT("H:/data/CPTAC/TCGA-Broad-Breast/phospho-Broad.cct") -rm("*") -rm("") -rm -rm() -?rm -getMultiplexSampleName = function(mergedSampleName, tokenIndex, coreSampleNames) -{ -innerSampleNames = coreSampleNames -sample = sub("(\\S+?)_(\\S+?)_(\\S+?)\\.iTRAQ\\.\\d+", paste0("\\", tokenIndex), mergedSampleName, perl=T) -if(is.null(innerSampleNames[[sample]])) -{ -innerSampleNames[[sample]] = 1 -} -else -{ -oldCount = innerSampleNames[[sample]] -sample = paste0(sample, "-", incrementChar("A", oldCount)) -innerSampleNames[[sample]] = oldCount + 1 -} -channel = sub("\\S+?\\.(iTRAQ\\.\\d+)", "\\1", mergedSampleName, perl=T) -eval.parent(substitute(coreSampleNames = innerSampleNames)) -return(paste0(sample, "-", channel)) -} -demultiplexNetGestaltITRAQ_CCT = function(filepath) -{ -outputFilepath = sub(".cct", "-demultiplexed-ratios.cct", filepath, fixed=T) -multiplexData = read.table(filepath, sep="\t", header=T) -numSamples = 0.75*(dim(multiplexData)[2]-1) -sampleNames = colnames(multiplexData)[-1]#[c(F, rep(c(T,T,T,F), numSamples/3))] -coreSampleNames = list() -for(i in seq(2, length(multiplexData), 4)) -{ -firstGroupNum = 0.75 * i -sampleNames[i-1] = getMultiplexSampleName(sampleNames[i-1], 1, coreSampleNames) -sampleNames[i] = getMultiplexSampleName(sampleNames[i], 2, coreSampleNames) -sampleNames[i+1] = getMultiplexSampleName(sampleNames[i+1], 3, coreSampleNames) -} -sampleNames = sampleNames[c(rep(c(T,T,T,F), numSamples/3))] -ratios = matrix(nrow=dim(multiplexData)[1], ncol=numSamples, dimnames=list(multiplexData[,1], sampleNames)) -for(i in seq(2, length(multiplexData), 4)) -{ -firstGroupNum = 0.75 * i -ratios[,firstGroupNum] = ZeroSafeDivide(multiplexData[,i], multiplexData[,i+3]) -ratios[,firstGroupNum+1] = ZeroSafeDivide(multiplexData[,i+1], multiplexData[,i+3]) -ratios[,firstGroupNum+2] = ZeroSafeDivide(multiplexData[,i+2], multiplexData[,i+3]) -} -options(digits=4) -write.table(cbind(GeneSymbol=rownames(ratios), ratios), file=outputFilepath, quote=F, row.names=F, sep="\t") -} -demultiplexNetGestaltITRAQ_CCT("H:/data/CPTAC/TCGA-Broad-Breast/phospho-Broad.cct") -?substittue -?substitute -getMultiplexSampleName = function(mergedSampleName, tokenIndex, coreSampleNames) -{ -innerSampleNames = coreSampleNames -sample = sub("(\\S+?)_(\\S+?)_(\\S+?)\\.iTRAQ\\.\\d+", paste0("\\", tokenIndex), mergedSampleName, perl=T) -if(is.null(innerSampleNames[[sample]])) -{ -innerSampleNames[[sample]] = 1 -} -else -{ -oldCount = innerSampleNames[[sample]] -sample = paste0(sample, "-", incrementChar("A", oldCount)) -innerSampleNames[[sample]] = oldCount + 1 -} -channel = sub("\\S+?\\.(iTRAQ\\.\\d+)", "\\1", mergedSampleName, perl=T) -eval.parent(substitute(coreSampleNames<-innerSampleNames)) -return(paste0(sample, "-", channel)) -} -demultiplexNetGestaltITRAQ_CCT = function(filepath) -{ -outputFilepath = sub(".cct", "-demultiplexed-ratios.cct", filepath, fixed=T) -multiplexData = read.table(filepath, sep="\t", header=T) -numSamples = 0.75*(dim(multiplexData)[2]-1) -sampleNames = colnames(multiplexData)[-1]#[c(F, rep(c(T,T,T,F), numSamples/3))] -coreSampleNames = list() -for(i in seq(2, length(multiplexData), 4)) -{ -firstGroupNum = 0.75 * i -sampleNames[i-1] = getMultiplexSampleName(sampleNames[i-1], 1, coreSampleNames) -sampleNames[i] = getMultiplexSampleName(sampleNames[i], 2, coreSampleNames) -sampleNames[i+1] = getMultiplexSampleName(sampleNames[i+1], 3, coreSampleNames) -} -sampleNames = sampleNames[c(rep(c(T,T,T,F), numSamples/3))] -ratios = matrix(nrow=dim(multiplexData)[1], ncol=numSamples, dimnames=list(multiplexData[,1], sampleNames)) -for(i in seq(2, length(multiplexData), 4)) -{ -firstGroupNum = 0.75 * i -ratios[,firstGroupNum] = ZeroSafeDivide(multiplexData[,i], multiplexData[,i+3]) -ratios[,firstGroupNum+1] = ZeroSafeDivide(multiplexData[,i+1], multiplexData[,i+3]) -ratios[,firstGroupNum+2] = ZeroSafeDivide(multiplexData[,i+2], multiplexData[,i+3]) -} -options(digits=4) -write.table(cbind(GeneSymbol=rownames(ratios), ratios), file=outputFilepath, quote=F, row.names=F, sep="\t") -} -demultiplexNetGestaltITRAQ_CCT("H:/data/CPTAC/TCGA-Broad-Breast/phospho-Broad.cct") -demultiplexNetGestaltITRAQ_CCT("H:/data/CPTAC/TCGA-Broad-Breast/global-Broad.cct") -demultiplexNetGestaltITRAQ_CCT("H:/data/CPTAC/TCGA-PNNL-Ovarian/phospho-PNNL.cct") -demultiplexNetGestaltITRAQ_CCT("H:/data/CPTAC/TCGA-PNNL-Ovarian/global-PNNL.cct") -demultiplexNetGestaltITRAQ_CCT("H:/data/CPTAC/TCGA-PNNL-Ovarian/phospho-PNNL.cct") -demultiplexNetGestaltITRAQ_CCT("H:/data/CPTAC/TCGA-PNNL-Ovarian/global-PNNL.cct") -ratios_ordered = ratios[,order(names(ratios))] -ratios_ordered = ratios[order(names(ratios)),] -names(ratios) -colnames(ratios) -ratios_ordered = ratios[order(colnames(ratios)),] -ratios_ordered = ratios[,order(colnames(ratios))] -View(ratios_ordered) -source('~/.active-rstudio-document') -source('~/.active-rstudio-document') -source('~/.active-rstudio-document') -source('~/.active-rstudio-document') -biocLite("RGalaxy") -source("https://bioconductor.org/biocLite.R") -biocLite("RGalaxy") -source('~/.active-rstudio-document') -source('~/.active-rstudio-document') -source('~/.active-rstudio-document') -galaxyHome="/galaxy-central" -galaxy("addTwoNumbers", -galaxyConfig= -GalaxyConfig(galaxyHome, "mytool", "Test Section", -"testSectionId") -) -galaxyHome="C:\\Users\\chambem2\\.vagrant\\precise64\\bingomics-galaxy\\vagrant\\export\\src\\galaxy" -galaxy("addTwoNumbers", -galaxyConfig= -GalaxyConfig(galaxyHome, "mytool", "Test Section", -"testSectionId") -) -galaxyHome="C:\\Users\\chambem2\\.vagrant\\precise64\\bingomics-galaxy\\vagrant\\export\\src\\galaxy" -galaxy("addTwoNumbers", -galaxyConfig= -GalaxyConfig(galaxyHome, "mytool", "Test Section", -"testSectionId") -) -?GalaxyConfig -galaxyHome="C:\\Users\\chambem2\\.vagrant\\precise64\\bingomics-galaxy\\vagrant\\export\\src\\galaxy" -galaxy("addTwoNumbers", -galaxyConfig= -GalaxyConfig(galaxyHome, "mytool", "Test Section", -"testSectionId") -) -galaxyHome="C:\\Users\\chambem2\\.vagrant\\precise64\\bingomics-galaxy\\vagrant\\export\\src\\galaxy" -galaxy("addTwoNumbers", -galaxyConfig= -GalaxyConfig(galaxyHome, "mytool", "Test Section", -"testSectionId") -) -source('~/.active-rstudio-document') -galaxyHome="C:\\Users\\chambem2\\.vagrant\\precise64\\bingomics-galaxy\\vagrant\\export\\src\\galaxy" -galaxy("addTwoNumbers", -galaxyConfig= -GalaxyConfig(galaxyHome, "mytool", "Test Section", -"testSectionId") -) -galaxyHome="C:\\Users\\chambem2\\.vagrant\\precise64\\bingomics-galaxy\\vagrant\\export\\src\\galaxy" -galaxy("addTwoNumbers", -galaxyConfig= -GalaxyConfig(galaxyHome, "mytool", "Test Section", -"testSectionId") -) -galaxyHome="C:\\Users\\chambem2\\.vagrant\\precise64\\bingomics-galaxy\\vagrant\\export\\src\\galaxy" -galaxy("PrepareAnnotationGENCODE_g", -galaxyConfig= -GalaxyConfig(galaxyHome, "mytool", "Test Section", -"testSectionId") -) -PrepareAnnotationGENCODE_g <- function() {} -galaxyHome="C:\\Users\\chambem2\\.vagrant\\precise64\\bingomics-galaxy\\vagrant\\export\\src\\galaxy" -galaxy("PrepareAnnotationGENCODE_g", -galaxyConfig= -GalaxyConfig(galaxyHome, "mytool", "Test Section", -"testSectionId") -) -PrepareAnnotationGENCODE_g <- function(gtfFile = GalaxyInputFile(required = TRUE), -CDSfasta = GalaxyInputFile(required = TRUE), -pepfasta = GalaxyInputFile(required = TRUE), -annotation_path = GalaxyCharacterParam(required = TRUE), -dbsnp = GalaxySelectParam(c(`First Choice` = "NULL", `Second Choice` = -"snp135")), splice_matrix = GalaxyLogicalParam(checked = TRUE), -COSMIC = GalaxyLogicalParam(checked = TRUE), ...) -{ -} -PrepareAnnotationGENCODE_g <- function(gtfFile = GalaxyInputFile(required = TRUE), -CDSfasta = GalaxyInputFile(required = TRUE), -pepfasta = GalaxyInputFile(required = TRUE), -annotation_path = GalaxyCharacterParam(required = TRUE), -dbsnp = GalaxySelectParam(c(`First Choice` = "NULL", `Second Choice` = -"snp135")), splice_matrix = GalaxyLogicalParam(checked = TRUE), -COSMIC = GalaxyLogicalParam(checked = TRUE), ...) -{ -} -galaxyHome="C:\\Users\\chambem2\\.vagrant\\precise64\\bingomics-galaxy\\vagrant\\export\\src\\galaxy" -galaxy("PrepareAnnotationGENCODE_g", -galaxyConfig= -GalaxyConfig(galaxyHome, "mytool", "Test Section", -"testSectionId") -) -source('~/.active-rstudio-document') -PrepareAnnotationGENCODE_g <- function(gtfFile = GalaxyInputFile(required = TRUE), -CDSfasta = GalaxyInputFile(required = TRUE), -pepfasta = GalaxyInputFile(required = TRUE), -annotation_path = GalaxyCharacterParam(required = TRUE), -dbsnp = GalaxySelectParam(c(`First Choice` = "NULL", `Second Choice` = -"snp135")), splice_matrix = GalaxyLogicalParam(checked = TRUE), -COSMIC = GalaxyLogicalParam(checked = TRUE), ...) -{ -} -galaxyHome="C:\\Users\\chambem2\\.vagrant\\precise64\\bingomics-galaxy\\vagrant\\export\\src\\galaxy" -galaxy("PrepareAnnotationGENCODE_g", -galaxyConfig= -GalaxyConfig(galaxyHome, "mytool", "Test Section", -"testSectionId") -) -source('~/.active-rstudio-document') -source('~/.active-rstudio-document') -source('~/.active-rstudio-document') -source('~/.active-rstudio-document') -source('~/.active-rstudio-document') -source('~/.active-rstudio-document') -source('~/.active-rstudio-document') -source('~/.active-rstudio-document') -?wtf -print "why doesn't this work" -print( )"why doesn't this work") -print("why doesn't this work") -source('~/.active-rstudio-document') -galaxyHome="C:\\Users\\chambem2\\.vagrant\\precise64\\bingomics-galaxy\\vagrant\\export\\src\\galaxy" -galaxy("addTwoNumbers", -galaxyConfig= -GalaxyConfig(galaxyHome, "mytool", "Test Section", -"testSectionId") -) -source('~/.active-rstudio-document') -source('~/.active-rstudio-document') -PrepareAnnotationGENCODE <- function(gtfFile = GalaxyInputFile(required = TRUE), -CDSfasta = GalaxyInputFile(required = TRUE), -pepfasta = GalaxyInputFile(required = TRUE), -annotation_path = GalaxyCharacterParam(required = TRUE), -COSMIC = GalaxyLogicalParam(checked = TRUE), -output = GalaxyOutput("sum", "txt")) -{ -print("why doesn't this work") -} -source('~/.active-rstudio-document') -source('~/.active-rstudio-document') -source('~/.active-rstudio-document') -library(RGalaxy) -source('~/.active-rstudio-document') -galaxyHome="C:\\Users\\chambem2\\.vagrant\\precise64\\bingomics-galaxy\\vagrant\\export\\src\\galaxy" -galaxy("PrepareAnnotationGENCODE", -galaxyConfig= -GalaxyConfig(galaxyHome, "mytool", "Test Section", -"testSectionId") -) -source('~/.active-rstudio-document') -str(addTwoNumbers) -addTwoNumbers -packageName() -packageName(addTwoNumbers) -packageName("addTwoNumbers") -source('~/.active-rstudio-document') -source('~/.active-rstudio-document', echo=TRUE) -source('~/.active-rstudio-document', echo=TRUE) -str(addTwoNumbers) -str(addTwoNumbers2) -env(addTwoNumbers) -environmentName -environmentName() -env.profile() -namespace:base -library(namespace) -source('~/.active-rstudio-document', echo=TRUE) -source("https://bioconductor.org/biocLite.R") -biocLite("customProDB") -library("customProDB", lib.loc="C:/Users/chambem2/Google Drive/Marvin Documents/R/win-library/3.1") -setwd("C:/Users/chambem2/.vagrant/precise64/bingomics-galaxy/vagrant/export/src/tools-galaxyp-chambm/tools/bumbershoot/psm_to_sam/tool-data") -bamFile <- system.file("extdata/bams", "test1_sort.bam", package="customProDB") -easyRun(bamFile=bamFile, annotation_path=".") -easyRun(bamFile=bamFile, annotation_path=".") -easyRun(bamFile=bamFile, annotation_path=".", outfile_path=".", outfile_name="test.fasta")
--- a/tool-data/header_refseq_hg19.txt Thu Jan 28 18:40:54 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,95 +0,0 @@ -@HD VN:1.0 SO:coordinate -@SQ SN:chr1 LN:249250621 -@SQ SN:chr10 LN:135534747 -@SQ SN:chr11 LN:135006516 -@SQ SN:chr11_gl000202_random LN:40103 -@SQ SN:chr12 LN:133851895 -@SQ SN:chr13 LN:115169878 -@SQ SN:chr14 LN:107349540 -@SQ SN:chr15 LN:102531392 -@SQ SN:chr16 LN:90354753 -@SQ SN:chr17 LN:81195210 -@SQ SN:chr17_ctg5_hap1 LN:1680828 -@SQ SN:chr17_gl000203_random LN:37498 -@SQ SN:chr17_gl000204_random LN:81310 -@SQ SN:chr17_gl000205_random LN:174588 -@SQ SN:chr17_gl000206_random LN:41001 -@SQ SN:chr18 LN:78077248 -@SQ SN:chr18_gl000207_random LN:4262 -@SQ SN:chr19 LN:59128983 -@SQ SN:chr19_gl000208_random LN:92689 -@SQ SN:chr19_gl000209_random LN:159169 -@SQ SN:chr1_gl000191_random LN:106433 -@SQ SN:chr1_gl000192_random LN:547496 -@SQ SN:chr2 LN:243199373 -@SQ SN:chr20 LN:63025520 -@SQ SN:chr21 LN:48129895 -@SQ SN:chr21_gl000210_random LN:27682 -@SQ SN:chr22 LN:51304566 -@SQ SN:chr3 LN:198022430 -@SQ SN:chr4 LN:191154276 -@SQ SN:chr4_ctg9_hap1 LN:590426 -@SQ SN:chr4_gl000193_random LN:189789 -@SQ SN:chr4_gl000194_random LN:191469 -@SQ SN:chr5 LN:180915260 -@SQ SN:chr6 LN:171115067 -@SQ SN:chr6_apd_hap1 LN:4622290 -@SQ SN:chr6_cox_hap2 LN:4795371 -@SQ SN:chr6_dbb_hap3 LN:4610396 -@SQ SN:chr6_mann_hap4 LN:4683263 -@SQ SN:chr6_mcf_hap5 LN:4833398 -@SQ SN:chr6_qbl_hap6 LN:4611984 -@SQ SN:chr6_ssto_hap7 LN:4928567 -@SQ SN:chr7 LN:159138663 -@SQ SN:chr7_gl000195_random LN:182896 -@SQ SN:chr8 LN:146364022 -@SQ SN:chr8_gl000196_random LN:38914 -@SQ SN:chr8_gl000197_random LN:37175 -@SQ SN:chr9 LN:141213431 -@SQ SN:chr9_gl000198_random LN:90085 -@SQ SN:chr9_gl000199_random LN:169874 -@SQ SN:chr9_gl000200_random LN:187035 -@SQ SN:chr9_gl000201_random LN:36148 -@SQ SN:chrM LN:16571 -@SQ SN:chrUn_gl000211 LN:166566 -@SQ SN:chrUn_gl000212 LN:186858 -@SQ SN:chrUn_gl000213 LN:164239 -@SQ SN:chrUn_gl000214 LN:137718 -@SQ SN:chrUn_gl000215 LN:172545 -@SQ SN:chrUn_gl000216 LN:172294 -@SQ SN:chrUn_gl000217 LN:172149 -@SQ SN:chrUn_gl000218 LN:161147 -@SQ SN:chrUn_gl000219 LN:179198 -@SQ SN:chrUn_gl000220 LN:161802 -@SQ SN:chrUn_gl000221 LN:155397 -@SQ SN:chrUn_gl000222 LN:186861 -@SQ SN:chrUn_gl000223 LN:180455 -@SQ SN:chrUn_gl000224 LN:179693 -@SQ SN:chrUn_gl000225 LN:211173 -@SQ SN:chrUn_gl000226 LN:15008 -@SQ SN:chrUn_gl000227 LN:128374 -@SQ SN:chrUn_gl000228 LN:129120 -@SQ SN:chrUn_gl000229 LN:19913 -@SQ SN:chrUn_gl000230 LN:43691 -@SQ SN:chrUn_gl000231 LN:27386 -@SQ SN:chrUn_gl000232 LN:40652 -@SQ SN:chrUn_gl000233 LN:45941 -@SQ SN:chrUn_gl000234 LN:40531 -@SQ SN:chrUn_gl000235 LN:34474 -@SQ SN:chrUn_gl000236 LN:41934 -@SQ SN:chrUn_gl000237 LN:45867 -@SQ SN:chrUn_gl000238 LN:39939 -@SQ SN:chrUn_gl000239 LN:33824 -@SQ SN:chrUn_gl000240 LN:41933 -@SQ SN:chrUn_gl000241 LN:42152 -@SQ SN:chrUn_gl000242 LN:43523 -@SQ SN:chrUn_gl000243 LN:43341 -@SQ SN:chrUn_gl000244 LN:39929 -@SQ SN:chrUn_gl000245 LN:36651 -@SQ SN:chrUn_gl000246 LN:38154 -@SQ SN:chrUn_gl000247 LN:36422 -@SQ SN:chrUn_gl000248 LN:39786 -@SQ SN:chrUn_gl000249 LN:38502 -@SQ SN:chrX LN:155270560 -@SQ SN:chrY LN:59373566 -@PG ID:proBAM
--- a/tool-data/test.fasta_rpkm.fasta Thu Jan 28 18:40:54 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,30 +0,0 @@ ->NP_001258807 |46361.0485|NM_001271878|KHDRBS1|KH domain-containing, RNA-binding, signal transduction-associated protein 1 isoform 2 -MQRRDDPAARMSRSSGRSGSMDPSGAHPSVRQTPSRQPPLPHRSRGGGGGSRGGARASPATQPPPLLPPSATGPDATVGGPAPTPLLPPSATASVKMEPENKYLPELMAEKDSLDPSFTHAMQLLTAEIEKIQKGDSKKDDEENYLDLFSHKNMKLKERVLIPVKQYPKEEELRKGGDPKYAHLNMDLHVFIEVFGPPCEAYALMAHAMEEVKKFLVPDMMDDICQEQFLELSYLNGVPEPSRGRGVPVRGRGAAPPPPPVPRGRGVGPPRGALVRGTPVRGAITRGATVTRGVPPPPTVRGAPAPRARTAGIQRIPLPPPPAPETYEEYGYDDTYAEQSYEGYEGYYSQSQGDSEYYDYGHGEVQDSYEAYGQDDWNGTRPSLKAPPARPVKGAYREHPYGRY ->NP_006550 |45056.7445|NM_006559|KHDRBS1|KH domain-containing, RNA-binding, signal transduction-associated protein 1 isoform 1 -MQRRDDPAARMSRSSGRSGSMDPSGAHPSVRQTPSRQPPLPHRSRGGGGGSRGGARASPATQPPPLLPPSATGPDATVGGPAPTPLLPPSATASVKMEPENKYLPELMAEKDSLDPSFTHAMQLLTAEIEKIQKGDSKKDDEENYLDLFSHKNMKLKERVLIPVKQYPKFNFVGKILGPQGNTIKRLQEETGAKISVLGKGSMRDKAKEEELRKGGDPKYAHLNMDLHVFIEVFGPPCEAYALMAHAMEEVKKFLVPDMMDDICQEQFLELSYLNGVPEPSRGRGVPVRGRGAAPPPPPVPRGRGVGPPRGALVRGTPVRGAITRGATVTRGVPPPPTVRGAPAPRARTAGIQRIPLPPPPAPETYEEYGYDDTYAEQSYEGYEGYYSQSQGDSEYYDYGHGEVQDSYEAYGQDDWNGTRPSLKAPPARPVKGAYREHPYGRY ->NP_004439 |40248.8323|NM_004448|ERBB2|receptor tyrosine-protein kinase erbB-2 isoform a precursor -MELAALCRWGLLLALLPPGAASTQVCTGTDMKLRLPASPETHLDMLRHLYQGCQVVQGNLELTYLPTNASLSFLQDIQEVQGYVLIAHNQVRQVPLQRLRIVRGTQLFEDNYALAVLDNGDPLNNTTPVTGASPGGLRELQLRSLTEILKGGVLIQRNPQLCYQDTILWKDIFHKNNQLALTLIDTNRSRACHPCSPMCKGSRCWGESSEDCQSLTRTVCAGGCARCKGPLPTDCCHEQCAAGCTGPKHSDCLACLHFNHSGICELHCPALVTYNTDTFESMPNPEGRYTFGASCVTACPYNYLSTDVGSCTLVCPLHNQEVTAEDGTQRCEKCSKPCARVCYGLGMEHLREVRAVTSANIQEFAGCKKIFGSLAFLPESFDGDPASNTAPLQPEQLQVFETLEEITGYLYISAWPDSLPDLSVFQNLQVIRGRILHNGAYSLTLQGLGISWLGLRSLRELGSGLALIHHNTHLCFVHTVPWDQLFRNPHQALLHTANRPEDECVGEGLACHQLCARGHCWGPGPTQCVNCSQFLRGQECVEECRVLQGLPREYVNARHCLPCHPECQPQNGSVTCFGPEADQCVACAHYKDPPFCVARCPSGVKPDLSYMPIWKFPDEEGACQPCPINCTHSCVDLDDKGCPAEQRASPLTSIISAVVGILLVVVLGVVFGILIKRRQQKIRKYTMRRLLQETELVEPLTPSGAMPNQAQMRILKETELRKVKVLGSGAFGTVYKGIWIPDGENVKIPVAIKVLRENTSPKANKEILDEAYVMAGVGSPYVSRLLGICLTSTVQLVTQLMPYGCLLDHVRENRGRLGSQDLLNWCMQIAKGMSYLEDVRLVHRDLAARNVLVKSPNHVKITDFGLARLLDIDETEYHADGGKVPIKWMALESILRRRFTHQSDVWSYGVTVWELMTFGAKPYDGIPAREIPDLLEKGERLPQPPICTIDVYMIMVKCWMIDSECRPRFRELVSEFSRMARDPQRFVVIQNEDLGPASPLDSTFYRSLLEDDDMGDLVDAEEYLVPQQGFFCPDPAPGAGGMVHHRHRSSSTRSGGGDLTLGLEPSEEEAPRSPLAPSEGAGSDVFDGDLGMGAAKGLQSLPTHDPSPLQRYSEDPTVPLPSETDGYVAPLTCSPQPEYVNQPDVRPQPPSPREGPLPAARPAGATLERPKTLSPGKNGVVKDVFAFGGAVENPEYLTPQGGAAPQPHPPPAFSPAFDNLYYWDQDPPERGAPPSTFKGTPTAENPEYLGLDVPV ->NP_001005862 |38529.7828|NM_001005862|ERBB2|receptor tyrosine-protein kinase erbB-2 isoform b -MKLRLPASPETHLDMLRHLYQGCQVVQGNLELTYLPTNASLSFLQDIQEVQGYVLIAHNQVRQVPLQRLRIVRGTQLFEDNYALAVLDNGDPLNNTTPVTGASPGGLRELQLRSLTEILKGGVLIQRNPQLCYQDTILWKDIFHKNNQLALTLIDTNRSRACHPCSPMCKGSRCWGESSEDCQSLTRTVCAGGCARCKGPLPTDCCHEQCAAGCTGPKHSDCLACLHFNHSGICELHCPALVTYNTDTFESMPNPEGRYTFGASCVTACPYNYLSTDVGSCTLVCPLHNQEVTAEDGTQRCEKCSKPCARVCYGLGMEHLREVRAVTSANIQEFAGCKKIFGSLAFLPESFDGDPASNTAPLQPEQLQVFETLEEITGYLYISAWPDSLPDLSVFQNLQVIRGRILHNGAYSLTLQGLGISWLGLRSLRELGSGLALIHHNTHLCFVHTVPWDQLFRNPHQALLHTANRPEDECVGEGLACHQLCARGHCWGPGPTQCVNCSQFLRGQECVEECRVLQGLPREYVNARHCLPCHPECQPQNGSVTCFGPEADQCVACAHYKDPPFCVARCPSGVKPDLSYMPIWKFPDEEGACQPCPINCTHSCVDLDDKGCPAEQRASPLTSIISAVVGILLVVVLGVVFGILIKRRQQKIRKYTMRRLLQETELVEPLTPSGAMPNQAQMRILKETELRKVKVLGSGAFGTVYKGIWIPDGENVKIPVAIKVLRENTSPKANKEILDEAYVMAGVGSPYVSRLLGICLTSTVQLVTQLMPYGCLLDHVRENRGRLGSQDLLNWCMQIAKGMSYLEDVRLVHRDLAARNVLVKSPNHVKITDFGLARLLDIDETEYHADGGKVPIKWMALESILRRRFTHQSDVWSYGVTVWELMTFGAKPYDGIPAREIPDLLEKGERLPQPPICTIDVYMIMVKCWMIDSECRPRFRELVSEFSRMARDPQRFVVIQNEDLGPASPLDSTFYRSLLEDDDMGDLVDAEEYLVPQQGFFCPDPAPGAGGMVHHRHRSSSTRSGGGDLTLGLEPSEEEAPRSPLAPSEGAGSDVFDGDLGMGAAKGLQSLPTHDPSPLQRYSEDPTVPLPSETDGYVAPLTCSPQPEYVNQPDVRPQPPSPREGPLPAARPAGATLERPKTLSPGKNGVVKDVFAFGGAVENPEYLTPQGGAAPQPHPPPAFSPAFDNLYYWDQDPPERGAPPSTFKGTPTAENPEYLGLDVPV ->NP_001268421 |6531.5159|NM_001281492|MSH6|DNA mismatch repair protein Msh6 isoform 2 -MSRQSTLYSFFPKSPALSDANKASARASREGGRAAAAPGASPSPGGDAAWSEAGPGPRPLARSASPPKAKNLNGGLRRSVGTTYVTDKSEEDNEIESEEEVQPKTQGSRRSSRQIKKRRVISDSESDIGGSDVEFKPDTKEEGSSDEISSGVGDSESEGLNSPVKVARKRKRMVTGNGSLKRKSSRKETPSATKQATSISSETKNTLRAFSAPQNSESQAHVSGGGDDSSRPTVWYHETLEWLKEEKRRDEHRRRPDHPDFDASTLYVPEDFLNSCTPGMRKWWQIKSQNFDLVICYKVGKFYELYHMDALIGVSELGLVFMKGNWAHSGFPEIAFGRYSDSLVQKGYKVARVEQTETPEMMEARCRKMAHISKYDRVVRREICRIITKGTQTYSVLEGDPSENYSKYLLSLKEKEEDSSGHTRAYGVCFVDTSLGKFFIGQFSDDRHCSRFRTLVAHYPPVQVLFEKGNLSKETKTILKSSLSCSLQEGLIPGSQFWDASKTLRTLLEEEYFREKLSDGIGVMLPQVLKGMTSESDSIGLTPGEKSELALSALGGCVFYLKKCLIDQELLSMANFEEYIPLDSDTVSTTRSGAIFTKAYQRMVLDAVTLNNLEIFLNGTNGSTEGTLLERVDTCHTPFGKRLLKQWLCAPLCNHYAINDRLDAIEDLMVVPDKISEVVELLKKLPDLERLLSKIHNVGSPLKSQNHPDSRAIMYEETTYSKKKIIDFLSALEGFKVMCKIIGIMEEVADGFKSKILKQVISLQTKNPEGRFPDLTVELNRWDTAFDHEKARKTGLITPKAGFDSDYDQALADIRENEQSLLEYLEKQRNRIGCRTIVYWGIGRNRYQLEIPENFTTRNLPEEYELKSTKKGCKRYWTKTIEKKLANLINAEERRDVSLKDCMRRLFYNFDKNYKDWQSAVECIAVLDVLLCLANYSRGGDGPMCRPVILLPEDTPPFLELKGSRHPCITKTFFGDDFIPNDILIGCEEEEQENGKAYCVLVTGPNMGGKSTLMRQAGLLAVMAQMGCYVPAEVCRLTPIDRVFTRLGASDRIMSGESTFFVELSETASILMHATAHSLVLVDELGRGTATFDGTAIANAVVKELAETIKCRTLFSTHYHSLVEDYSQNVAVRLGHMACMVENECEDPSQETITFLYKFIKGACPKSYGFNAARLANLPEEVIQKGHRKAREFEKMNQSLRLFREVCLASERSTVDAEAVHKLLTLIKEL ->NP_001268422 |6318.4888|NM_001281493|MSH6|DNA mismatch repair protein Msh6 isoform 3 -MVTGNGSLKRKSSRKETPSATKQATSISSETKNTLRAFSAPQNSESQAHVSGGGDDSSRPTVWYHETLEWLKEEKRRDEHRRRPDHPDFDASTLYVPEDFLNSCTPGMRKWWQIKSQNFDLVICYKVGKFYELYHMDALIGVSELGLVFMKGNWAHSGFPEIAFGRYSDSLVQKGYKVARVEQTETPEMMEARCRKMAHISKYDRVVRREICRIITKGTQTYSVLEGDPSENYSKYLLSLKEKEEDSSGHTRAYGVCFVDTSLGKFFIGQFSDDRHCSRFRTLVAHYPPVQVLFEKGNLSKETKTILKSSLSCSLQEGLIPGSQFWDASKTLRTLLEEEYFREKLSDGIGVMLPQVLKGMTSESDSIGLTPGEKSELALSALGGCVFYLKKCLIDQELLSMANFEEYIPLDSDTVSTTRSGAIFTKAYQRMVLDAVTLNNLEIFLNGTNGSTEGTLLERVDTCHTPFGKRLLKQWLCAPLCNHYAINDRLDAIEDLMVVPDKISEVVELLKKLPDLERLLSKIHNVGSPLKSQNHPDSRAIMYEETTYSKKKIIDFLSALEGFKVMCKIIGIMEEVADGFKSKILKQVISLQTKNPEGRFPDLTVELNRWDTAFDHEKARKTGLITPKAGFDSDYDQALADIRENEQSLLEYLEKQRNRIGCRTIVYWGIGRNRYQLEIPENFTTRNLPEEYELKSTKKGCKRYWTKTIEKKLANLINAEERRDVSLKDCMRRLFYNFDKNYKDWQSAVECIAVLDVLLCLANYSRGGDGPMCRPVILLPEDTPPFLELKGSRHPCITKTFFGDDFIPNDILIGCEEEEQENGKAYCVLVTGPNMGGKSTLMRQAGLLAVMAQMGCYVPAEVCRLTPIDRVFTRLGASDRIMSGESTFFVELSETASILMHATAHSLVLVDELGRGTATFDGTAIANAVVKELAETIKCRTLFSTHYHSLVEDYSQNVAVRLGHMACMVENECEDPSQETITFLYKFIKGACPKSYGFNAARLANLPEEVIQKGHRKAREFEKMNQSLRLFREVCLASERSTVDAEAVHKLLTLIKEL ->NP_001268423 |6240.1342|NM_001281494|MSH6|DNA mismatch repair protein Msh6 isoform 3 -MVTGNGSLKRKSSRKETPSATKQATSISSETKNTLRAFSAPQNSESQAHVSGGGDDSSRPTVWYHETLEWLKEEKRRDEHRRRPDHPDFDASTLYVPEDFLNSCTPGMRKWWQIKSQNFDLVICYKVGKFYELYHMDALIGVSELGLVFMKGNWAHSGFPEIAFGRYSDSLVQKGYKVARVEQTETPEMMEARCRKMAHISKYDRVVRREICRIITKGTQTYSVLEGDPSENYSKYLLSLKEKEEDSSGHTRAYGVCFVDTSLGKFFIGQFSDDRHCSRFRTLVAHYPPVQVLFEKGNLSKETKTILKSSLSCSLQEGLIPGSQFWDASKTLRTLLEEEYFREKLSDGIGVMLPQVLKGMTSESDSIGLTPGEKSELALSALGGCVFYLKKCLIDQELLSMANFEEYIPLDSDTVSTTRSGAIFTKAYQRMVLDAVTLNNLEIFLNGTNGSTEGTLLERVDTCHTPFGKRLLKQWLCAPLCNHYAINDRLDAIEDLMVVPDKISEVVELLKKLPDLERLLSKIHNVGSPLKSQNHPDSRAIMYEETTYSKKKIIDFLSALEGFKVMCKIIGIMEEVADGFKSKILKQVISLQTKNPEGRFPDLTVELNRWDTAFDHEKARKTGLITPKAGFDSDYDQALADIRENEQSLLEYLEKQRNRIGCRTIVYWGIGRNRYQLEIPENFTTRNLPEEYELKSTKKGCKRYWTKTIEKKLANLINAEERRDVSLKDCMRRLFYNFDKNYKDWQSAVECIAVLDVLLCLANYSRGGDGPMCRPVILLPEDTPPFLELKGSRHPCITKTFFGDDFIPNDILIGCEEEEQENGKAYCVLVTGPNMGGKSTLMRQAGLLAVMAQMGCYVPAEVCRLTPIDRVFTRLGASDRIMSGESTFFVELSETASILMHATAHSLVLVDELGRGTATFDGTAIANAVVKELAETIKCRTLFSTHYHSLVEDYSQNVAVRLGHMACMVENECEDPSQETITFLYKFIKGACPKSYGFNAARLANLPEEVIQKGHRKAREFEKMNQSLRLFREVCLASERSTVDAEAVHKLLTLIKEL ->NP_000170 |6197.6532|NM_000179|MSH6|DNA mismatch repair protein Msh6 isoform 1 -MSRQSTLYSFFPKSPALSDANKASARASREGGRAAAAPGASPSPGGDAAWSEAGPGPRPLARSASPPKAKNLNGGLRRSVAPAAPTSCDFSPGDLVWAKMEGYPWWPCLVYNHPFDGTFIREKGKSVRVHVQFFDDSPTRGWVSKRLLKPYTGSKSKEAQKGGHFYSAKPEILRAMQRADEALNKDKIKRLELAVCDEPSEPEEEEEMEVGTTYVTDKSEEDNEIESEEEVQPKTQGSRRSSRQIKKRRVISDSESDIGGSDVEFKPDTKEEGSSDEISSGVGDSESEGLNSPVKVARKRKRMVTGNGSLKRKSSRKETPSATKQATSISSETKNTLRAFSAPQNSESQAHVSGGGDDSSRPTVWYHETLEWLKEEKRRDEHRRRPDHPDFDASTLYVPEDFLNSCTPGMRKWWQIKSQNFDLVICYKVGKFYELYHMDALIGVSELGLVFMKGNWAHSGFPEIAFGRYSDSLVQKGYKVARVEQTETPEMMEARCRKMAHISKYDRVVRREICRIITKGTQTYSVLEGDPSENYSKYLLSLKEKEEDSSGHTRAYGVCFVDTSLGKFFIGQFSDDRHCSRFRTLVAHYPPVQVLFEKGNLSKETKTILKSSLSCSLQEGLIPGSQFWDASKTLRTLLEEEYFREKLSDGIGVMLPQVLKGMTSESDSIGLTPGEKSELALSALGGCVFYLKKCLIDQELLSMANFEEYIPLDSDTVSTTRSGAIFTKAYQRMVLDAVTLNNLEIFLNGTNGSTEGTLLERVDTCHTPFGKRLLKQWLCAPLCNHYAINDRLDAIEDLMVVPDKISEVVELLKKLPDLERLLSKIHNVGSPLKSQNHPDSRAIMYEETTYSKKKIIDFLSALEGFKVMCKIIGIMEEVADGFKSKILKQVISLQTKNPEGRFPDLTVELNRWDTAFDHEKARKTGLITPKAGFDSDYDQALADIRENEQSLLEYLEKQRNRIGCRTIVYWGIGRNRYQLEIPENFTTRNLPEEYELKSTKKGCKRYWTKTIEKKLANLINAEERRDVSLKDCMRRLFYNFDKNYKDWQSAVECIAVLDVLLCLANYSRGGDGPMCRPVILLPEDTPPFLELKGSRHPCITKTFFGDDFIPNDILIGCEEEEQENGKAYCVLVTGPNMGGKSTLMRQAGLLAVMAQMGCYVPAEVCRLTPIDRVFTRLGASDRIMSGESTFFVELSETASILMHATAHSLVLVDELGRGTATFDGTAIANAVVKELAETIKCRTLFSTHYHSLVEDYSQNVAVRLGHMACMVENECEDPSQETITFLYKFIKGACPKSYGFNAARLANLPEEVIQKGHRKAREFEKMNQSLRLFREVCLASERSTVDAEAVHKLLTLIKEL ->NP_001137462 |3840.1782|NM_001143990|WRAP53|telomerase Cajal body protein 1 -MKTLETQPLAPDCCPSDQDPAPAHPSPHASPMNKNADSELMPPPPERGDPPRLSPDPVAGSAVSQELREGDPVSLSTPLETEFGSPSELSPRIEEQELSENTSLPAEEANGSLSEEEANGPELGSGKAMEDTSGEPAAEDEGDTAWNYSFSQLPRFLSGSWSEFSTQPENFLKGCKWAPDGSCILTNSADNILRIYNLPPELYHEGEQVEYAEMVPVLRMVEGDTIYDYCWYSLMSSAQPDTSYVASSSRENPIHIWDAFTGELRASFRAYNHLDELTAAHSLCFSPDGSQLFCGFNRTVRVFSTARPGRDCEVRATFAKKQGQSGIISCIAFSPAQPLYACGSYGRSLGLYAWDDGSPLALLGGHQGGITHLCFHPDGNRFFSGARKDAELLCWDLRQSGYPLWSLGREVTTNQRIYFDLDPTGQFLVSGSTSGAVSVWDTDGPGNDGKPEPVLSFLPQKDCTNGVSLHPSLPLLATASGQRVFPEPTESGDEGEELGLPLLSTRHVHLECRLQLWWCGGAPDSSIPDDHQGEKGQGGTEGGVGELI ->NP_001137463 |1105.5494|NM_001143991|WRAP53|telomerase Cajal body protein 1 -MKTLETQPLAPDCCPSDQDPAPAHPSPHASPMNKNADSELMPPPPERGDPPRLSPDPVAGSAVSQELREGDPVSLSTPLETEFGSPSELSPRIEEQELSENTSLPAEEANGSLSEEEANGPELGSGKAMEDTSGEPAAEDEGDTAWNYSFSQLPRFLSGSWSEFSTQPENFLKGCKWAPDGSCILTNSADNILRIYNLPPELYHEGEQVEYAEMVPVLRMVEGDTIYDYCWYSLMSSAQPDTSYVASSSRENPIHIWDAFTGELRASFRAYNHLDELTAAHSLCFSPDGSQLFCGFNRTVRVFSTARPGRDCEVRATFAKKQGQSGIISCIAFSPAQPLYACGSYGRSLGLYAWDDGSPLALLGGHQGGITHLCFHPDGNRFFSGARKDAELLCWDLRQSGYPLWSLGREVTTNQRIYFDLDPTGQFLVSGSTSGAVSVWDTDGPGNDGKPEPVLSFLPQKDCTNGVSLHPSLPLLATASGQRVFPEPTESGDEGEELGLPLLSTRHVHLECRLQLWWCGGAPDSSIPDDHQGEKGQGGTEGGVGELI ->NP_000029 |239.7121|NM_000038|APC|adenomatous polyposis coli protein isoform b -MAAASYDQLLKQVEALKMENSNLRQELEDNSNHLTKLETEASNMKEVLKQLQGSIEDEAMASSGQIDLLERLKELNLDSSNFPGVKLRSKMSLRSYGSREGSVSSRSGECSPVPMGSFPRRGFVNGSRESTGYLEELEKERSLLLADLDKEEKEKDWYYAQLQNLTKRIDSLPLTENFSLQTDMTRRQLEYEARQIRVAMEEQLGTCQDMEKRAQRRIARIQQIEKDILRIRQLLQSQATEAERSSQNKHETGSHDAERQNEGQGVGEINMATSGNGQGSTTRMDHETASVLSSSSTHSAPRRLTSHLGTKVEMVYSLLSMLGTHDKDDMSRTLLAMSSSQDSCISMRQSGCLPLLIQLLHGNDKDSVLLGNSRGSKEARARASAALHNIIHSQPDDKRGRREIRVLHLLEQIRAYCETCWEWQEAHEPGMDQDKNPMPAPVEHQICPAVCVLMKLSFDEEHRHAMNELGGLQAIAELLQVDCEMYGLTNDHYSITLRRYAGMALTNLTFGDVANKATLCSMKGCMRALVAQLKSESEDLQQVIASVLRNLSWRADVNSKKTLREVGSVKALMECALEVKKESTLKSVLSALWNLSAHCTENKADICAVDGALAFLVGTLTYRSQTNTLAIIESGGGILRNVSSLIATNEDHRQILRENNCLQTLLQHLKSHSLTIVSNACGTLWNLSARNPKDQEALWDMGAVSMLKNLIHSKHKMIAMGSAAALRNLMANRPAKYKDANIMSPGSSLPSLHVRKQKALEAELDAQHLSETFDNIDNLSPKASHRSKQRHKQSLYGDYVFDTNRHDDNRSDNFNTGNMTVLSPYLNTTVLPSSSSSRGSLDSSRSEKDRSLERERGIGLGNYHPATENPGTSSKRGLQISTTAAQIAKVMEEVSAIHTSQEDRSSGSTTELHCVTDERNALRRSSAAHTHSNTYNFTKSENSNRTCSMPYAKLEYKRSSNDSLNSVSSSDGYGKRGQMKPSIESYSEDDESKFCSYGQYPADLAHKIHSANHMDDNDGELDTPINYSLKYSDEQLNSGRQSPSQNERWARPKHIIEDEIKQSEQRQSRNQSTTYPVYTESTDDKHLKFQPHFGQQECVSPYRSRGANGSETNRVGSNHGINQNVSQSLCQEDDYEDDKPTNYSERYSEEEQHEEEERPTNYSIKYNEEKRHVDQPIDYSLKYATDIPSSQKQSFSFSKSSSGQSSKTEHMSSSSENTSTPSSNAKRQNQLHPSSAQSRSGQPQKAATCKVSSINQETIQTYCVEDTPICFSRCSSLSSLSSAEDEIGCNQTTQEADSANTLQIAEIKEKIGTRSAEDPVSEVPAVSQHPRTKSSRLQGSSLSSESARHKAVEFSSGAKSPSKSGAQTPKSPPEHYVQETPLMFSRCTSVSSLDSFESRSIASSVQSEPCSGMVSGIISPSDLPDSPGQTMPPSRSKTPPPPPQTAQTKREVPKNKAPTAEKRESGPKQAAVNAAVQRVQVLPDADTLLHFATESTPDGFSCSSSLSALSLDEPFIQKDVELRIMPPVQENDNGNETESEQPKESNENQEKEAEKTIDSEKDLLDDSDDDDIEILEECIISAMPTKSSRKAKKPAQTASKLPPPVARKPSQLPVYKLLPSQNRLQPQKHVSFTPGDDMPRVYCVEGTPINFSTATSLSDLTIESPPNELAAGEGVRGGAQSGEFEKRDTIPTEGRSTDEAQGGKTSSVTIPELDDNKAEEGDILAECINSAMPKGKSHKPFRVKKIMDQVQQASASSSAPNKNQLDGKKKKPTSPVKPIPQNTEYRTRVRKNADSKNNLNAERVFSDNKDSKKQNLKNNSKVFNDKLPNNEDRVRGSFAFDSPHHYTPIEGTPYCFSRNDSLSSLDFDDDDVDLSREKAELRKAKENKESEAKVTSHTELTSNQQSANKTQAIAKQPINRGQPKPILQKQSTFPQSSKDIPDRGAATDEKLQNFAIENTPVCFSHNSSLSSLSDIDQENNNKENEPIKETEPPDSQGEPSKPQASGYAPKSFHVEDTPVCFSRNSSLSSLSIDSEDDLLQECISSAMPKKKKPSRLKGDNEKHSPRNMGGILGEDLTLDLKDIQRPDSEHGLSPDSENFDWKAIQEGANSIVSSLHQAAAAACLSRQASSDSDSILSLKSGISLGSPFHLTPDQEEKPFTSNKGPRILKPGEKSTLETKKIESESKGIKGGKKVYKSLITGKVRSNSEISGQMKQPLQANMPSISRGRTMIHIPGVRNSSSSTSPVSKKGPPLKTPASKSPSEGQTATTSPRGAKPSVKSELSPVARQTSQIGGSSKAPSRSGSRDSTPSRPAQQPLSRPIQSPGRNSISPGRNGISPPNKLSQLPRTSSPSTASTKSSGSGKMSYTSPGRQMSQQNLTKQTGLSKNASSIPRSESASKGLNQMNNGNGANKKVELSRMSSTKSSGSESDRSERPVLVRQSTFIKEAPSPTLRRKLEESASFESLSPSSRPASPTRSQAQTPVLSPSLPDMSLSTHSSVQAGGWRKLPPNLSPTIEYNDGRPAKRHDIARSHSESPSRLPINRSGTWKREHSKHSSSLPRVSTWRRTGSSSSILSASSESSEKAKSEDEKHVNSISGTKQSKENQVSAKGTWRKIKENEFSPTNSTSQTVSSGATNGAESKTLIYQMAPAVSKTEDVWVRIEDCPINNPRSGRSPTGNTPPVIDSVSEKANPNIKDSKDNQAKQNVGNGSVPMRTVGLENRLNSFIQVDAPDQKGTEIKPGQNNPVPVSETNESSIVERTPFSSSSSSKHSSPSGTVAARVTPFNYNPSPRKSSADSTSARPSQIPTPVNNNTKKRDSKTDSTESSGTQSPKRHSGSYLVTSV ->NP_001120982 |237.3234|NM_001127510|APC|adenomatous polyposis coli protein isoform b -MAAASYDQLLKQVEALKMENSNLRQELEDNSNHLTKLETEASNMKEVLKQLQGSIEDEAMASSGQIDLLERLKELNLDSSNFPGVKLRSKMSLRSYGSREGSVSSRSGECSPVPMGSFPRRGFVNGSRESTGYLEELEKERSLLLADLDKEEKEKDWYYAQLQNLTKRIDSLPLTENFSLQTDMTRRQLEYEARQIRVAMEEQLGTCQDMEKRAQRRIARIQQIEKDILRIRQLLQSQATEAERSSQNKHETGSHDAERQNEGQGVGEINMATSGNGQGSTTRMDHETASVLSSSSTHSAPRRLTSHLGTKVEMVYSLLSMLGTHDKDDMSRTLLAMSSSQDSCISMRQSGCLPLLIQLLHGNDKDSVLLGNSRGSKEARARASAALHNIIHSQPDDKRGRREIRVLHLLEQIRAYCETCWEWQEAHEPGMDQDKNPMPAPVEHQICPAVCVLMKLSFDEEHRHAMNELGGLQAIAELLQVDCEMYGLTNDHYSITLRRYAGMALTNLTFGDVANKATLCSMKGCMRALVAQLKSESEDLQQVIASVLRNLSWRADVNSKKTLREVGSVKALMECALEVKKESTLKSVLSALWNLSAHCTENKADICAVDGALAFLVGTLTYRSQTNTLAIIESGGGILRNVSSLIATNEDHRQILRENNCLQTLLQHLKSHSLTIVSNACGTLWNLSARNPKDQEALWDMGAVSMLKNLIHSKHKMIAMGSAAALRNLMANRPAKYKDANIMSPGSSLPSLHVRKQKALEAELDAQHLSETFDNIDNLSPKASHRSKQRHKQSLYGDYVFDTNRHDDNRSDNFNTGNMTVLSPYLNTTVLPSSSSSRGSLDSSRSEKDRSLERERGIGLGNYHPATENPGTSSKRGLQISTTAAQIAKVMEEVSAIHTSQEDRSSGSTTELHCVTDERNALRRSSAAHTHSNTYNFTKSENSNRTCSMPYAKLEYKRSSNDSLNSVSSSDGYGKRGQMKPSIESYSEDDESKFCSYGQYPADLAHKIHSANHMDDNDGELDTPINYSLKYSDEQLNSGRQSPSQNERWARPKHIIEDEIKQSEQRQSRNQSTTYPVYTESTDDKHLKFQPHFGQQECVSPYRSRGANGSETNRVGSNHGINQNVSQSLCQEDDYEDDKPTNYSERYSEEEQHEEEERPTNYSIKYNEEKRHVDQPIDYSLKYATDIPSSQKQSFSFSKSSSGQSSKTEHMSSSSENTSTPSSNAKRQNQLHPSSAQSRSGQPQKAATCKVSSINQETIQTYCVEDTPICFSRCSSLSSLSSAEDEIGCNQTTQEADSANTLQIAEIKEKIGTRSAEDPVSEVPAVSQHPRTKSSRLQGSSLSSESARHKAVEFSSGAKSPSKSGAQTPKSPPEHYVQETPLMFSRCTSVSSLDSFESRSIASSVQSEPCSGMVSGIISPSDLPDSPGQTMPPSRSKTPPPPPQTAQTKREVPKNKAPTAEKRESGPKQAAVNAAVQRVQVLPDADTLLHFATESTPDGFSCSSSLSALSLDEPFIQKDVELRIMPPVQENDNGNETESEQPKESNENQEKEAEKTIDSEKDLLDDSDDDDIEILEECIISAMPTKSSRKAKKPAQTASKLPPPVARKPSQLPVYKLLPSQNRLQPQKHVSFTPGDDMPRVYCVEGTPINFSTATSLSDLTIESPPNELAAGEGVRGGAQSGEFEKRDTIPTEGRSTDEAQGGKTSSVTIPELDDNKAEEGDILAECINSAMPKGKSHKPFRVKKIMDQVQQASASSSAPNKNQLDGKKKKPTSPVKPIPQNTEYRTRVRKNADSKNNLNAERVFSDNKDSKKQNLKNNSKVFNDKLPNNEDRVRGSFAFDSPHHYTPIEGTPYCFSRNDSLSSLDFDDDDVDLSREKAELRKAKENKESEAKVTSHTELTSNQQSANKTQAIAKQPINRGQPKPILQKQSTFPQSSKDIPDRGAATDEKLQNFAIENTPVCFSHNSSLSSLSDIDQENNNKENEPIKETEPPDSQGEPSKPQASGYAPKSFHVEDTPVCFSRNSSLSSLSIDSEDDLLQECISSAMPKKKKPSRLKGDNEKHSPRNMGGILGEDLTLDLKDIQRPDSEHGLSPDSENFDWKAIQEGANSIVSSLHQAAAAACLSRQASSDSDSILSLKSGISLGSPFHLTPDQEEKPFTSNKGPRILKPGEKSTLETKKIESESKGIKGGKKVYKSLITGKVRSNSEISGQMKQPLQANMPSISRGRTMIHIPGVRNSSSSTSPVSKKGPPLKTPASKSPSEGQTATTSPRGAKPSVKSELSPVARQTSQIGGSSKAPSRSGSRDSTPSRPAQQPLSRPIQSPGRNSISPGRNGISPPNKLSQLPRTSSPSTASTKSSGSGKMSYTSPGRQMSQQNLTKQTGLSKNASSIPRSESASKGLNQMNNGNGANKKVELSRMSSTKSSGSESDRSERPVLVRQSTFIKEAPSPTLRRKLEESASFESLSPSSRPASPTRSQAQTPVLSPSLPDMSLSTHSSVQAGGWRKLPPNLSPTIEYNDGRPAKRHDIARSHSESPSRLPINRSGTWKREHSKHSSSLPRVSTWRRTGSSSSILSASSESSEKAKSEDEKHVNSISGTKQSKENQVSAKGTWRKIKENEFSPTNSTSQTVSSGATNGAESKTLIYQMAPAVSKTEDVWVRIEDCPINNPRSGRSPTGNTPPVIDSVSEKANPNIKDSKDNQAKQNVGNGSVPMRTVGLENRLNSFIQVDAPDQKGTEIKPGQNNPVPVSETNESSIVERTPFSSSSSSKHSSPSGTVAARVTPFNYNPSPRKSSADSTSARPSQIPTPVNNNTKKRDSKTDSTESSGTQSPKRHSGSYLVTSV ->NP_001120983 |221.0652|NM_001127511|APC|adenomatous polyposis coli protein isoform a -MYASLGSGPVAPLPASVPPSVLGSWSTGGSRSCVRQETKSPGGARTSGHWASVWQEVLKQLQGSIEDEAMASSGQIDLLERLKELNLDSSNFPGVKLRSKMSLRSYGSREGSVSSRSGECSPVPMGSFPRRGFVNGSRESTGYLEELEKERSLLLADLDKEEKEKDWYYAQLQNLTKRIDSLPLTENFSLQTDMTRRQLEYEARQIRVAMEEQLGTCQDMEKRAQRSSQNKHETGSHDAERQNEGQGVGEINMATSGNGQGSTTRMDHETASVLSSSSTHSAPRRLTSHLGTKVEMVYSLLSMLGTHDKDDMSRTLLAMSSSQDSCISMRQSGCLPLLIQLLHGNDKDSVLLGNSRGSKEARARASAALHNIIHSQPDDKRGRREIRVLHLLEQIRAYCETCWEWQEAHEPGMDQDKNPMPAPVEHQICPAVCVLMKLSFDEEHRHAMNELGGLQAIAELLQVDCEMYGLTNDHYSITLRRYAGMALTNLTFGDVANKATLCSMKGCMRALVAQLKSESEDLQQVIASVLRNLSWRADVNSKKTLREVGSVKALMECALEVKKESTLKSVLSALWNLSAHCTENKADICAVDGALAFLVGTLTYRSQTNTLAIIESGGGILRNVSSLIATNEDHRQILRENNCLQTLLQHLKSHSLTIVSNACGTLWNLSARNPKDQEALWDMGAVSMLKNLIHSKHKMIAMGSAAALRNLMANRPAKYKDANIMSPGSSLPSLHVRKQKALEAELDAQHLSETFDNIDNLSPKASHRSKQRHKQSLYGDYVFDTNRHDDNRSDNFNTGNMTVLSPYLNTTVLPSSSSSRGSLDSSRSEKDRSLERERGIGLGNYHPATENPGTSSKRGLQISTTAAQIAKVMEEVSAIHTSQEDRSSGSTTELHCVTDERNALRRSSAAHTHSNTYNFTKSENSNRTCSMPYAKLEYKRSSNDSLNSVSSSDGYGKRGQMKPSIESYSEDDESKFCSYGQYPADLAHKIHSANHMDDNDGELDTPINYSLKYSDEQLNSGRQSPSQNERWARPKHIIEDEIKQSEQRQSRNQSTTYPVYTESTDDKHLKFQPHFGQQECVSPYRSRGANGSETNRVGSNHGINQNVSQSLCQEDDYEDDKPTNYSERYSEEEQHEEEERPTNYSIKYNEEKRHVDQPIDYSLKYATDIPSSQKQSFSFSKSSSGQSSKTEHMSSSSENTSTPSSNAKRQNQLHPSSAQSRSGQPQKAATCKVSSINQETIQTYCVEDTPICFSRCSSLSSLSSAEDEIGCNQTTQEADSANTLQIAEIKEKIGTRSAEDPVSEVPAVSQHPRTKSSRLQGSSLSSESARHKAVEFSSGAKSPSKSGAQTPKSPPEHYVQETPLMFSRCTSVSSLDSFESRSIASSVQSEPCSGMVSGIISPSDLPDSPGQTMPPSRSKTPPPPPQTAQTKREVPKNKAPTAEKRESGPKQAAVNAAVQRVQVLPDADTLLHFATESTPDGFSCSSSLSALSLDEPFIQKDVELRIMPPVQENDNGNETESEQPKESNENQEKEAEKTIDSEKDLLDDSDDDDIEILEECIISAMPTKSSRKAKKPAQTASKLPPPVARKPSQLPVYKLLPSQNRLQPQKHVSFTPGDDMPRVYCVEGTPINFSTATSLSDLTIESPPNELAAGEGVRGGAQSGEFEKRDTIPTEGRSTDEAQGGKTSSVTIPELDDNKAEEGDILAECINSAMPKGKSHKPFRVKKIMDQVQQASASSSAPNKNQLDGKKKKPTSPVKPIPQNTEYRTRVRKNADSKNNLNAERVFSDNKDSKKQNLKNNSKVFNDKLPNNEDRVRGSFAFDSPHHYTPIEGTPYCFSRNDSLSSLDFDDDDVDLSREKAELRKAKENKESEAKVTSHTELTSNQQSANKTQAIAKQPINRGQPKPILQKQSTFPQSSKDIPDRGAATDEKLQNFAIENTPVCFSHNSSLSSLSDIDQENNNKENEPIKETEPPDSQGEPSKPQASGYAPKSFHVEDTPVCFSRNSSLSSLSIDSEDDLLQECISSAMPKKKKPSRLKGDNEKHSPRNMGGILGEDLTLDLKDIQRPDSEHGLSPDSENFDWKAIQEGANSIVSSLHQAAAAACLSRQASSDSDSILSLKSGISLGSPFHLTPDQEEKPFTSNKGPRILKPGEKSTLETKKIESESKGIKGGKKVYKSLITGKVRSNSEISGQMKQPLQANMPSISRGRTMIHIPGVRNSSSSTSPVSKKGPPLKTPASKSPSEGQTATTSPRGAKPSVKSELSPVARQTSQIGGSSKAPSRSGSRDSTPSRPAQQPLSRPIQSPGRNSISPGRNGISPPNKLSQLPRTSSPSTASTKSSGSGKMSYTSPGRQMSQQNLTKQTGLSKNASSIPRSESASKGLNQMNNGNGANKKVELSRMSSTKSSGSESDRSERPVLVRQSTFIKEAPSPTLRRKLEESASFESLSPSSRPASPTRSQAQTPVLSPSLPDMSLSTHSSVQAGGWRKLPPNLSPTIEYNDGRPAKRHDIARSHSESPSRLPINRSGTWKREHSKHSSSLPRVSTWRRTGSSSSILSASSESSEKAKSEDEKHVNSISGTKQSKENQVSAKGTWRKIKENEFSPTNSTSQTVSSGATNGAESKTLIYQMAPAVSKTEDVWVRIEDCPINNPRSGRSPTGNTPPVIDSVSEKANPNIKDSKDNQAKQNVGNGSVPMRTVGLENRLNSFIQVDAPDQKGTEIKPGQNNPVPVSETNESSIVERTPFSSSSSSKHSSPSGTVAARVTPFNYNPSPRKSSADSTSARPSQIPTPVNNNTKKRDSKTDSTESSGTQSPKRHSGSYLVTSV ->NP_001137464 |195.7615|NM_001143992|WRAP53|telomerase Cajal body protein 1 -MKTLETQPLAPDCCPSDQDPAPAHPSPHASPMNKNADSELMPPPPERGDPPRLSPDPVAGSAVSQELREGDPVSLSTPLETEFGSPSELSPRIEEQELSENTSLPAEEANGSLSEEEANGPELGSGKAMEDTSGEPAAEDEGDTAWNYSFSQLPRFLSGSWSEFSTQPENFLKGCKWAPDGSCILTNSADNILRIYNLPPELYHEGEQVEYAEMVPVLRMVEGDTIYDYCWYSLMSSAQPDTSYVASSSRENPIHIWDAFTGELRASFRAYNHLDELTAAHSLCFSPDGSQLFCGFNRTVRVFSTARPGRDCEVRATFAKKQGQSGIISCIAFSPAQPLYACGSYGRSLGLYAWDDGSPLALLGGHQGGITHLCFHPDGNRFFSGARKDAELLCWDLRQSGYPLWSLGREVTTNQRIYFDLDPTGQFLVSGSTSGAVSVWDTDGPGNDGKPEPVLSFLPQKDCTNGVSLHPSLPLLATASGQRVFPEPTESGDEGEELGLPLLSTRHVHLECRLQLWWCGGAPDSSIPDDHQGEKGQGGTEGGVGELI ->NP_060551 |93.5926|NM_018081|WRAP53|telomerase Cajal body protein 1 -MKTLETQPLAPDCCPSDQDPAPAHPSPHASPMNKNADSELMPPPPERGDPPRLSPDPVAGSAVSQELREGDPVSLSTPLETEFGSPSELSPRIEEQELSENTSLPAEEANGSLSEEEANGPELGSGKAMEDTSGEPAAEDEGDTAWNYSFSQLPRFLSGSWSEFSTQPENFLKGCKWAPDGSCILTNSADNILRIYNLPPELYHEGEQVEYAEMVPVLRMVEGDTIYDYCWYSLMSSAQPDTSYVASSSRENPIHIWDAFTGELRASFRAYNHLDELTAAHSLCFSPDGSQLFCGFNRTVRVFSTARPGRDCEVRATFAKKQGQSGIISCIAFSPAQPLYACGSYGRSLGLYAWDDGSPLALLGGHQGGITHLCFHPDGNRFFSGARKDAELLCWDLRQSGYPLWSLGREVTTNQRIYFDLDPTGQFLVSGSTSGAVSVWDTDGPGNDGKPEPVLSFLPQKDCTNGVSLHPSLPLLATASGQRVFPEPTESGDEGEELGLPLLSTRHVHLECRLQLWWCGGAPDSSIPDDHQGEKGQGGTEGGVGELI
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Thu Jan 28 18:45:02 2016 -0500 @@ -0,0 +1,7 @@ +<tables> + <!-- Locations of all customProDB annotations under genome directory --> + <table name="customProDB" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/customProDB.loc" /> + </table> +</tables>