| Next changeset 1:ff55700f9d9c (2016-03-15) |
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toolshed_version/GNU Free Documentation License.txt toolshed_version/SAINTexpress_v3.6.1__2015-05-03.zip toolshed_version/saint_wrapper.py toolshed_version/saint_wrapper.xml toolshed_version/test_files/EGFR_MQ_bait_ERvWT.txt toolshed_version/test_files/EGFR_MQ_inter.txt toolshed_version/test_files/EGFR_MQ_prey.txt |
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| diff -r 000000000000 -r 11fe2e7c8fe3 toolshed_version/GNU Free Documentation License.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolshed_version/GNU Free Documentation License.txt Tue Mar 15 16:06:51 2016 -0400 |
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| b'@@ -0,0 +1,451 @@\n+\r\n+ GNU Free Documentation License\r\n+ Version 1.3, 3 November 2008\r\n+\r\n+\r\n+ Copyright (C) 2000, 2001, 2002, 2007, 2008 Free Software Foundation, Inc.\r\n+ <http://fsf.org/>\r\n+ Everyone is permitted to copy and distribute verbatim copies\r\n+ of this license document, but changing it is not allowed.\r\n+\r\n+0. PREAMBLE\r\n+\r\n+The purpose of this License is to make a manual, textbook, or other\r\n+functional and useful document "free" in the sense of freedom: to\r\n+assure everyone the effective freedom to copy and redistribute it,\r\n+with or without modifying it, either commercially or noncommercially.\r\n+Secondarily, this License preserves for the author and publisher a way\r\n+to get credit for their work, while not being considered responsible\r\n+for modifications made by others.\r\n+\r\n+This License is a kind of "copyleft", which means that derivative\r\n+works of the document must themselves be free in the same sense. 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| diff -r 000000000000 -r 11fe2e7c8fe3 toolshed_version/SAINTexpress_v3.6.1__2015-05-03.zip |
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| Binary file toolshed_version/SAINTexpress_v3.6.1__2015-05-03.zip has changed |
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| diff -r 000000000000 -r 11fe2e7c8fe3 toolshed_version/saint_wrapper.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolshed_version/saint_wrapper.py Tue Mar 15 16:06:51 2016 -0400 |
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| @@ -0,0 +1,107 @@ +####################################################################################### +# Python-code: Dotplot Runner +# Author: Adam L Borne +# Contributers: Paul A Stewart, Brent Kuenzi +####################################################################################### +# This runs SAINTexpress found at http://saint-apms.sourceforge.net/Main.html in +# galaxy. +####################################################################################### +# Copyright (C) Adam Borne. +# Permission is granted to copy, distribute and/or modify this document +# under the terms of the GNU Free Documentation License, Version 1.3 +# or any later version published by the Free Software Foundation; +# with no Invariant Sections, no Front-Cover Texts, and no Back-Cover Texts. +# A copy of the license is included in the section entitled "GNU +# Free Documentation License". +####################################################################################### +## REQUIRED INPUT ## + +# 1) list_file: SaintExpress output file. +# 2) FDR1: Primary false discovery rate. (default = 0.01) +# 3) FDR2: Secondary false discovery rate. (default = 0.025) +# 4) spec_max: Maximum spectral count. (default = 50) +####################################################################################### + + +import os +import sys + + +inter_file = sys.argv[1] +prey_file = sys.argv[2] +bait_file = sys.argv[3] +num_of_rep = sys.argv[4] +vc_bool = sys.argv[5] +vc_num = sys.argv[6] +go_bool = sys.argv[7] +go_file = sys.argv[8] +output_file = sys.argv[9] +ins_path = sys.argv[10] + + +def first_run_check(): + dirs_list = [] + for (dirpath, dirnames, filename) in os.walk(str(ins_path)): + dirs_list.extend(dirnames) + break + if r"SAINTexpress_v3.6.1__2015-05-03" in dirs_list: + pass + else: + cmd = r"unzip " + str(ins_path) + "/SAINTexpress_v3.6.1__2015-05-03.zip -d " + str(ins_path) + os.system(cmd) + os.chdir(str(ins_path) + "/SAINTexpress_v3.6.1__2015-05-03") + cmd1 = r"make -j" + os.system(cmd1) + + +def default_run(inter_file1, prey_file1, bait_file1, output_file1, num_of_rep1): + # Default is no virtual controls through purification and set replicates number. + cmd = (str(ins_path) + r"/SAINTexpress_v3.6.1__2015-05-03/bin/SAINTexpress-spc " + r"-R" + + str(num_of_rep1) + " " + str(inter_file1) + " " + str(prey_file1) + + " " + str(bait_file1)) + os.system(cmd) + open('list.txt') + os.rename('list.txt', str(output_file1)) + + +def with_L(inter_file1, prey_file1, bait_file1, output_file1, vc_num1, num_of_rep1): + # L is the flag for Virtual Controls through Purification. + cmd = (str(ins_path) + r"/SAINTexpress_v3.6.1__2015-05-03/bin/SAINTexpress-spc "+ r"-R" + + str(num_of_rep1) + " " + r"-L" + str(vc_num1) + " " + str(inter_file1) + " " + + str(prey_file1) + " " + str(bait_file1)) + os.system(cmd) + open('list.txt') + os.rename('list.txt', str(output_file1)) + + +def external_data_no_L(inter_file1, prey_file1, bait_file1, output_file1, go_file1, num_of_rep1): + # Uses external data in the GO file format and no Virtual Controls. + cmd = (str(ins_path) + r"/SAINTexpress_v3.6.1__2015-05-03/bin/SAINTexpress-spc "+ r"-R" + + str(num_of_rep1) + " " + str(inter_file1) + " " + str(prey_file1) + " " + + str(bait_file1) + " " + str(go_file1)) + os.system(cmd) + open('list.txt') + os.rename('list.txt', str(output_file1)) + + +def external_data_with_L(inter_file1, prey_file1, bait_file1, output_file1, go_file1, num_of_rep1, vc_num1): + # Uses external data in the GO file format and Virtual Controls. + cmd = (str(ins_path) + r"/SAINTexpress_v3.6.1__2015-05-03/bin/SAINTexpress-spc "+ r"-R" + + str(num_of_rep1) + " " + r"-L" + str(vc_num1) + " " + str(inter_file1) + " " + + str(prey_file1) + " " + str(bait_file1) + " " + str(go_file1)) + os.system(cmd) + open('list.txt') + os.rename('list.txt', str(output_file1)) + + +first_run_check() +if vc_bool == "true": + if go_bool == "false": + with_L(inter_file, prey_file, bait_file, output_file, vc_num, num_of_rep) + elif go_bool == "true": + external_data_with_L(inter_file, prey_file, bait_file, output_file, go_file, num_of_rep, vc_num) +elif vc_bool == "false": + if go_bool == "false": + default_run(inter_file, prey_file, bait_file, output_file, num_of_rep) + elif go_bool == "true": + external_data_no_L(inter_file, prey_file, bait_file, output_file, go_file, num_of_rep) |
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| diff -r 000000000000 -r 11fe2e7c8fe3 toolshed_version/saint_wrapper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolshed_version/saint_wrapper.xml Tue Mar 15 16:06:51 2016 -0400 |
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| @@ -0,0 +1,65 @@ +<tool id="saint_wrapper" name="SAINTexpress"> + <description></description> + <command interpreter="python">saint_wrapper.py $inter_input $prey_input $bait_input $rep_num $vc_bool $vc_num $go_bool $go_file $SAINT_output \$INSTALL_RUN_PATH/</command> + <requirements> + <requirement type="set_environment">INSTALL_RUN_PATH</requirement> + </requirements> + <inputs> + <param format="txt" name="inter_input" type="data" label="Interactions File"/> + <param format="txt" name="prey_input" type="data" label="Prey File"/> + <param format="txt" name="bait_input" type="data" label="Bait File"/> + <param name="rep_num" type="integer" value="100" label="Number of Replicates" help="the number of replicates (with largest spectral counts or intensities) to be used for probability calculation in each bait. This option is useful when some baits have more replicates than others." /> + <param type="boolean" name="vc_bool" checked="false" label="Using Virtual Control Purifications by Compression"/> + <param name="vc_num" type="integer" value="1" label="Number of Virtual Controls" /> + <param type="boolean" name="go_bool" checked="false" label="Incorporate External Data Sources" /> + <param format="txt" name="go_file" type="data" optional="true" label="External Data File" help="SAINT can be run with the known interaction data in hand and it will incorporate the number of observed interactions into the statistics to boost identification probability."/> + </inputs> + <outputs> + <data format="txt" name="SAINT_output" /> + </outputs> + <stdio> + <regex match="Error|error" + source="stdout" + level="fatal" + description="Unknown error"/> + <regex match="Error|error" + source="stderr" + level="fatal" + description="Unknown error"/> + <regex match="Error: bad bait" + source="stdout" + level="fatal" + description="Error: bad bait"/> + </stdio> + + <tests> + <test> + <param name="input" value="fa_gc_content_input.fa"/> + <output name="out_file1" file="fa_gc_content_output.txt"/> + </test> + </tests> + <help> +**Running SAINT Express** + +INPUTS: + +Interactions File: Should contain four columns: IP name, bait name, prey name, and spectral counts or intensity values, depending on the mode of quantitation. + +Prey File: Should contain three columns: prey (protein) name, prey protein length, and prey gene name. + +Bait File: Should have three columns: IP name, bait name, and the indicator for test and negative control purifications. + +Number of Replicates: Sets the number of replicates (with largest spectral counts or intensities) to be used for probability calculation in each bait. This option is useful when some baits have more replicates than others. + +Using Virtual Control Purification by Compression: Sets the number of virtual control purifications by compression. For instance, if the user wishes to take 4 largest spectral counts for controls, set Number of Vitual Controls to 4 and this variable to yes. + +Incorporate External Data Sources: To incorporate external data sources for computing the topology-aware probability score (TopoAvgP), the user must also provide the interaction database file that contains two columns: interaction identifier column and interaction/grouping information column. The first column is just for formality and thus can be filled in with anything (no white space) and it will not be utilized in the scoring. The second column must be formatted as a string of prey identifiers (consistent with the first column of the prey file) separated by a white space. + +------ + +**Please cite** + + * Choi, H., Larsen, B., Lin., Z.-Y., Breitkreutz, A., Mellacheruvu, D., Fermin, D., Qin, Z.S., Tyers, M., Gingras, A.-C. and Nesvizhskii, A.I. (2011) SAINT: probabilistic scoring of affinity purification - mass spectrometry data. Nature Methods, 8:70-3. + + </help> +</tool> |
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| diff -r 000000000000 -r 11fe2e7c8fe3 toolshed_version/test_files/EGFR_MQ_bait_ERvWT.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolshed_version/test_files/EGFR_MQ_bait_ERvWT.txt Tue Mar 15 16:06:51 2016 -0400 |
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| @@ -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 |
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| diff -r 000000000000 -r 11fe2e7c8fe3 toolshed_version/test_files/EGFR_MQ_inter.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolshed_version/test_files/EGFR_MQ_inter.txt Tue Mar 15 16:06:51 2016 -0400 |
| b |
| b'@@ -0,0 +1,10290 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|
| b |
| diff -r 000000000000 -r 11fe2e7c8fe3 toolshed_version/test_files/EGFR_MQ_prey.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolshed_version/test_files/EGFR_MQ_prey.txt Tue Mar 15 16:06:51 2016 -0400 |
| b |
| @@ -0,0 +1,294 @@ +Q8WVM8 642 SCFD1 +Q13049 653 TRIM32 +P35232 272 PHB +O00459 728 PIK3R2 +P09382 135 LGALS1 +P07900 732 HSP90AA1 +Q14568 343 HSP90AA2P +P08238 724 HSP90AB1 +Q58FF8 381 HSP90AB2P +P04259 564 KRT6B +P02538 564 KRT6A +P48668 564 KRT6C +P04264 644 KRT1 +Q96P48 1450 ARAP1 +Q12774 1597 ARHGEF5 +P18433 802 PTPRA +Q07021 282 C1QBP +P42338 1070 PIK3CB +Q96NH3 1257 TBC1D32 +P33992 734 MCM5 +P11021 654 HSPA5 +P13645 584 KRT10 +O95831 613 AIFM1 +O00567 594 NOP56 +P57088 247 TMEM33 +O95782 977 AP2A1 +O94973 939 AP2A2 +O15482 410 TEX28 +P05109 93 S100A8 +O60716 968 CTNND1 +P07437 444 TUBB +P42704 1394 LRPPRC +P38646 679 HSPA9 +P35908 639 KRT2 +Q01546 638 KRT76 +P19013 534 KRT4 +P11142 646 HSPA8 +P54652 639 HSPA2 +Q8TEM1 1887 NUP210 +P62993 217 GRB2 +P00533 1210 EGFR +Q15751 4861 HERC1 +P68363 451 TUBA1B +Q71U36 451 TUBA1A +Q13748 450 TUBA3C +Q6PEY2 450 TUBA3E +Q9NY65 449 TUBA8 +P68366 448 TUBA4A +A5A3E0 1075 POTEF +P0CG38 1075 POTEI +Q6S8J3 1075 POTEE +P68032 377 ACTC1 +P68133 377 ACTA1 +P60709 375 ACTB +P63261 375 ACTG1 +Q9BYX7 375 POTEKP +P62736 377 ACTA2 +P63267 376 ACTG2 +Q9BQE3 449 TUBA1C +Q99615 494 DNAJC7 +P82930 218 MRPS34 +P35568 1242 IRS1 +Q8WX94 980 NLRP7 +P31948 543 STIP1 +Q7Z3Y7 464 KRT28 +Q7Z3Y8 459 KRT27 +Q7Z3Z0 450 KRT25 +P02533 472 KRT14 +P0DMV8 641 HSPA1A +P0DMV9 641 HSPA1B +O00329 1044 PIK3CD +P12236 298 SLC25A6 +P05141 298 SLC25A5 +P42336 1068 PIK3CA +Q8WUY1 208 THEM6 +Q6IE37 1185 OVOS1 +Q9UBL6 633 CPNE7 +Q9HCH3 593 CPNE5 +Q86YQ8 564 CPNE8 +O95741 557 CPNE6 +Q96A23 557 CPNE4 +Q8IYJ1 553 CPNE9 +Q96FN4 548 CPNE2 +O75131 537 CPNE3 +P49411 452 TUFM +P08581 1390 MET +P43246 934 MSH2 +Q8NEG7 585 DENND6B +P62258 255 YWHAE +P31947 248 SFN +P61981 247 YWHAG +Q04917 246 YWHAH +P63104 245 YWHAZ +P27348 245 YWHAQ +Q92552 414 MRPS27 +Q14451 532 GRB7 +Q02978 314 SLC25A11 +Q0VFZ6 552 CCDC173 +Q07889 1333 SOS1 +Q07890 1332 SOS2 +P22681 906 CBL +Q05639 463 EEF1A2 +P68104 462 EEF1A1 +Q5VTE0 462 EEF1A1P5 +P52735 878 VAV2 +Q4G1C9 344 GLIPR1L2 +P21860 1342 ERBB3 +Q8NFI3 743 ENGASE +Q14571 2701 ITPR2 +P42224 750 STAT1 +Q75V66 913 ANO5 +P0CG48 685 UBC +P0CG47 229 UBB +P62979 156 RPS27A +P62987 128 UBA52 +P29353 583 SHC1 +Q7Z794 578 KRT77 +Q86Y46 540 KRT73 +P12035 628 KRT3 +Q9NSB2 600 KRT84 +Q7RTS7 529 KRT74 +Q3SY84 523 KRT71 +Q14CN4 511 KRT72 +O95678 551 KRT75 +Q5XKE5 535 KRT79 +P05787 483 KRT8 +P13647 590 KRT5 +P08729 469 KRT7 +Q06124 597 PTPN11 +P17066 643 HSPA6 +P48741 367 HSPA7 +P53680 142 AP2S1 +P69905 142 HBA1 +P40763 770 STAT3 +A6NK06 481 IRG1 +Q86WR7 435 PROSER2 +P02768 609 ALB +P78527 4128 PRKDC +P35527 623 KRT9 +P04626 1255 ERBB2 +O00264 195 PGRMC1 +P12235 298 SLC25A4 +P43304 727 GPD2 +Q8NDL9 886 AGBL5 +P68371 445 TUBB4B +Q13885 445 TUBB2A +Q9BVA1 445 TUBB2B +Q13509 450 TUBB3 +Q06830 199 PRDX1 +Q13162 271 PRDX4 +P46109 303 CRKL +P07355 339 ANXA2 +A6NMY6 339 ANXA2P2 +Q9GZT3 109 SLIRP +P62249 146 RPS16 +P14678 240 SNRPB +Q8TD57 4116 DNAH3 +Q58FF7 597 HSP90AB3P +Q9Y2R5 130 MRPS17 +Q58FG0 334 HSP90AA5P +P98077 582 SHC2 +Q99611 448 SEPHS2 +P11802 303 CDK4 +P08779 473 KRT16 +Q9NS86 450 LANCL2 +P61978 463 HNRNPK +Q15366 365 PCBP2 +Q13191 982 CBLB +Q4G0P3 5121 HYDIN +Q6P1M0 643 SLC27A4 +P51648 485 ALDH3A2 +P13646 458 KRT13 +Q8IXB1 793 DNAJC10 +P04350 444 TUBB4A +P62269 152 RPS18 +P62829 140 RPL23 +P10809 573 HSPD1 +Q14116 193 IL18 +Q5T9A4 648 ATAD3B +Q9NVI7 634 ATAD3A +Q5T2N8 411 ATAD3C +P08727 400 KRT19 +P05783 430 KRT18 +P0CG39 1038 POTEJ +O43196 834 MSH5 +P63173 70 RPL38 +Q6URK8 271 TEPP +Q99456 494 KRT12 +P19012 456 KRT15 +Q04695 432 KRT17 +A6NNZ2 444 NA +Q3ZCM7 444 TUBB8 +Q9H4B7 451 TUBB1 +Q9NP72 206 RAB18 +Q86SQ7 713 SDCCAG8 +Q2M243 656 CCDC27 +Q96K76 1375 USP47 +Q15165 354 PON2 +Q9BYK8 2649 HELZ2 +Q16543 378 CDC37 +Q8WXH0 6885 SYNE2 +Q9UJM3 462 ERRFI1 +O00461 696 GOLIM4 +Q05655 676 PRKCD +A1L190 88 SYCE3 +P16144 1822 ITGB4 +O95816 211 BAG2 +Q99623 299 PHB2 +Q5JWF2 1037 GNAS +P63092 394 GNAS +P38405 381 GNAL +P04899 355 GNAI2 +A8MTJ3 354 GNAT3 +P08754 354 GNAI3 +P09471 354 GNAO1 +P19087 354 GNAT2 +P63096 354 GNAI1 +P11488 350 GNAT1 +Q92569 461 PIK3R3 +Q8NF37 534 LPCAT1 +Q6Y7W6 1299 GIGYF2 +P49757 651 NUMB +Q9Y6R0 609 NUMBL +P37235 193 HPCAL1 +P61601 193 NCALD +P84074 193 HPCA +Q53GA4 152 PHLDA2 +Q63ZY3 851 KANK2 +Q6PIJ6 1188 FBXO38 +Q15257 358 PPP2R4 +Q96BR5 231 COA7 +P14923 745 JUP +P35222 781 CTNNB1 +Q8IV45 518 UNC5CL +Q86VU5 262 COMTD1 +Q9C0F3 470 ZNF436 +Q69YG0 159 TMEM42 +O94808 682 GFPT2 +Q03989 594 ARID5A +P30825 629 SLC7A1 +Q9NU02 776 ANKEF1 +Q9UBF8 816 PI4KB +Q9BWG4 385 SSBP4 +Q9Y6F6 885 MRVI1 +Q96JB1 4490 DNAH8 +P06702 114 S100A9 +Q99575 1024 POP1 +Q9H069 523 LRRC48 +P60953 191 CDC42 +Q03001 7570 DST +Q9UPN3 7388 MACF1 +Q5VZP5 1158 DUSP27 +A6NCF5 533 KLHL33 +A6NMZ7 2263 COL6A6 +P35498 2009 SCN1A +Q9BWN1 585 PRR14 +Q8IWK6 1321 ADGRA3 +P27986 724 PIK3R1 +Q6NUN0 579 ACSM5 +P68871 147 HBB +Q8WV24 401 PHLDA1 +Q9HCY8 104 S100A14 +Q6PKX4 331 DOK6 +O15440 1437 ABCC5 +O75592 4640 MYCBP2 +P61626 148 LYZ +P11274 1271 BCR +Q12979 859 ABR +Q8IW35 865 CEP97 +Q5D862 2391 FLG2 +P49368 545 CCT3 +Q53GQ0 312 HSD17B12 +P25705 553 ATP5A1 +Q15084 440 PDIA6 +E9PKD4 350 NPIPA5 +Q13946 482 PDE7A +P25205 808 MCM3 +Q9Y4H2 1338 IRS2 +P62266 143 RPS23 +Q6ZU80 1094 CEP128 +Q92859 1461 NEO1 +P62805 103 HIST1H4A +P13639 858 EEF2 +Q58FF6 505 HSP90AB4P +Q8WXI4 607 ACOT11 +P35030 304 PRSS3 +Q15303 1308 ERBB4 +Q8NF91 8797 SYNE1 +Q3BBV2 869 NBPF8 +Q86T75 865 NBPF11 +Q7Z3Y9 468 KRT26 +P02042 147 HBD +Q9H0C2 315 SLC25A31 +P15924 2871 DSP |