Mercurial > repos > eschen42 > mqppep_preproc
changeset 13:28a126da9b28 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
| author | eschen42 |
|---|---|
| date | Tue, 22 Mar 2022 20:47:10 +0000 |
| parents | ae1044bcf13d |
| children | 0380cd493a33 |
| files | macros.xml mqppep_preproc.xml test-data/test_input_for_preproc.tabular test-data/test_kinase_substrate.tabular test-data/test_networkin.tabular test-data/test_regulatory_sites.tabular test-data/test_swissprot.fasta workflow/ppenrich_suite_wf.ga |
| diffstat | 8 files changed, 791 insertions(+), 34 deletions(-) [+] |
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--- a/macros.xml Tue Mar 15 18:17:19 2022 +0000 +++ b/macros.xml Tue Mar 22 20:47:10 2022 +0000 @@ -1,5 +1,5 @@ <macros> - <token name="@TOOL_VERSION@">0.1.3</token> + <token name="@TOOL_VERSION@">0.1.4</token> <token name="@VERSION_SUFFIX@">0</token> <xml name="requirements"> <requirements>
--- a/mqppep_preproc.xml Tue Mar 15 18:17:19 2022 +0000 +++ b/mqppep_preproc.xml Tue Mar 22 20:47:10 2022 +0000 @@ -12,10 +12,10 @@ ) && ( \$CONDA_PREFIX/bin/Rscript '$__tool_directory__/MaxQuantProcessingScript.R' -i '$phosphoSites' - #if $pst_not_py: + #if $pst_py_selector == "y" + --enriched Y + #else --enriched ST - #else - --enriched Y #end if --phosphoCol '$phosphocol_script' --startCol '$startcol_script' @@ -41,10 +41,10 @@ -m '$p_sty_motifs' -p '$psp_kinase_substrate' -r '$psp_regulatory_sites' - #if $pst_not_py: + #if $pst_py_selector == "y" + -P y + #else -P sty - #else - -P y #end if -F $merge_function -o '$mapped_phophopeptides' @@ -101,32 +101,13 @@ <param name="intervalCol" type="integer" value="1" min="1" label="Interval between the intensity column of samples" help="[intervalCol] E.g., 1 if subsequent column is next sample; 2 if next sample is two columns away, etc."/> - <!-- pst_not_py is true when chosing pS/pT, false when choosing pY --> - <param name="pst_not_py" type="boolean" - checked="true" - label="Phospho enrichment pS/pT (rather than pY)" - help="True when samples were enriched for pS and pT; false when enriched for pY" + <param name="pst_py_selector" type="select" + label="Phosphopeptide enrichment type" + help="[enrichment] Were samples enriched for pS and pT, or were they enriched for pY instead?" > + <option value="st" selected="true">pST</option> + <option value="y">pY</option> </param> - <!-- - <conditional name="py_pst"> - <param name="pst_not_py" type="select" - label="Phospho enrichment type" - help="[enriched] Were samples enriched for pS and pT, or were they enriched for pY?" - > - <option value="st" selected="true">pST</option> - <option value="y">pY</option> - </param> - <when value="st"> - <param name="enriched" type="text" value="ST" /> - <param name="phospho_type" type="text" value="sty" /> - </when> - <when value="y"> - <param name="enriched" type="text" value="Y" /> - <param name="phospho_type" type="text" value="y" /> - </when> - </conditional> - --> <param name="collapseFunc" type="select" label="Intensity merge function" help="[collapseFunc] When a peptide is multiply phosphorylated, how should intensities be merged? [default: sum]" @@ -187,7 +168,7 @@ <param name="p_sty_motifs" ftype="tabular" value="pSTY_motifs.tabular" /> <param name="psp_kinase_substrate" ftype="tabular" value="test_kinase_substrate.tabular" /> <param name="psp_regulatory_sites" ftype="tabular" value="test_regulatory_sites.tabular" /> - <param name="pst_not_py" value="true"/> + <param name="pst_py_selector" value="st"/> <param name="merge_function" value="sum"/> <param name="phosphoCol" value="^Number of Phospho [(][STY][STY]*[)]$"/> @@ -246,10 +227,57 @@ </assert_contents> </output> </test> + <test> + <param name="phosphoSites" ftype="tabular" value="test_input_for_preproc.tabular" /> + <param name="protein_fasta" ftype="fasta" value="test_swissprot.fasta" /> + <param name="networkin" ftype="tabular" value="test_networkin.tabular" /> + <param name="p_sty_motifs" ftype="tabular" value="pSTY_motifs.tabular" /> + <param name="psp_kinase_substrate" ftype="tabular" value="test_kinase_substrate.tabular" /> + <param name="psp_regulatory_sites" ftype="tabular" value="test_regulatory_sites.tabular" /> + <param name="pst_py_selector" value="y"/> + <param name="merge_function" value="sum"/> + + <param name="phosphoCol" value="^Number of Phospho [(][STY][STY]*[)]$"/> + <param name="startCol" value="^Intensity[^_]"/> + <param name="intervalCol" value="1"/> + <param name="collapseFunc" value="sum"/> + <param name="localProbCutoff" value="0.75"/> + <param name="species" value="human"/> + + <output name="phosphoPepIntensities"> + <assert_contents> + <has_text text="Phosphopeptide" /> + <has_text text="pTYVDPFTpYEDPNQAVR" /> + </assert_contents> + </output> + + <output name="preproc_tab"> + <assert_contents> + <has_text text="pTYVDPFTpYEDPNQAVR" /> + <has_text text="EEKHLNQGVRpTYVDPFTYEDP" /> + <has_text text="GVRTYVDPFTpYEDPNQAVREF" /> + <has_text text="HLNQGVRtYVDPFTY" /> + <has_text text="TYVDPFTyEDPNQAV" /> + <has_text text="EPHA4" /> + <has_text text="pT595, pY602" /> + <has_text text="pT544, pY551" /> + <has_text text="P54764;" /> + <has_text text="P54764-2" /> + </assert_contents> + </output> + + <output name="melted_phophopeptide_map"> + <assert_contents> + <has_text text="Casein Kinase II substrate motif (HPRD)" /> + <has_text text="EPHA4_PhosphoSite" /> + <has_text text="EphA4_NetworKIN" /> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[ ========================================================= -Phopsphoproteomic Enrichment Pipeline Preprocessing Steps +Phopsphoproteomic Enrichment Pipeline Preprocessing Steps ========================================================= **Overview** @@ -326,7 +354,7 @@ ``Arthur C. Eschenlauer`` (`ORCiD 0000-0002-2882-0508 <https://orcid.org/0000-0002-2882-0508>`_) adapted the script to run in Galaxy. - + ============================================================= Phopsphoproteomic Enrichment Pipeline Upstream Kinase Mapping =============================================================
--- a/test-data/test_input_for_preproc.tabular Tue Mar 15 18:17:19 2022 +0000 +++ b/test-data/test_input_for_preproc.tabular Tue Mar 22 20:47:10 2022 +0000 @@ -36,3 +36,4 @@ sp|Q15836|VAMP3_HUMAN;sp|P63027|VAMP2_HUMAN;sp|P23763-2|VAMP1_HUMAN;sp|P23763-3|VAMP1_HUMAN;sp|P23763|VAMP1_HUMAN 44;61;63;63;63 sp|Q15836|VAMP3_HUMAN sp|Q15836|VAMP3_HUMAN 1 65.4951 2.36E-06 126.19 98.602 65.495 1 S MRVNVDKVLERDQKLSELDDRADALQAGASQ X;X;X;X;X;X;X;X;X;X;X;X;X;X;X;Phospho (STY);X;X;X;X;X;X;X;X;X;X;X;X;X;X;X XXXXXXXXXXXPPPPPPPPPPXXXXXXXXXX DQKLS(1)ELDDR DQKLS(65.5)ELDDR 5 3 -0.72518 By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS 412950000 412950000 0 0 NaN 75542000 44814000 32924000 35016000 11023000 4669900 NaN NaN NaN NaN NaN NaN 75542000 0 0 44814000 0 0 32924000 0 0 35016000 0 0 11023000 0 0 4669900 0 0 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 4443 2836 44 44 4530 5083 37093;37094;37095;37096;37097;37098;37099;37100;37101;37102;37103;37104 34712;34713;34714;34715;34716;34717;34718;34719 37100 34719 QE05102 18436 37093 34712 QE05097 18245 37093 34712 QE05097 18245 sp|Q15836|VAMP3_HUMAN 11 sp|Q15836|VAMP3_HUMAN sp|Q15836|VAMP3_HUMAN 0.97018 15.1316 0.000117365 79.652 72.041 79.652 1 S _____MSTGPTAATGSNRRLQQTQNQVDEVV X;X;X;X;X;X;X;X;X;X;X;X;X;X;X;Phospho (STY);X;X;X;X;X;X;X;X;X;X;X;X;X;X;X XXXXXXPPPPPPPPPPPPPXXXXXXXXXXXX STGPTAAT(0.03)GS(0.97)NRR S(-66.94)T(-63.48)GPT(-42.47)AAT(-15.13)GS(15.13)NRR 10 2 -0.15791 By matching By matching By MS/MS By matching By matching By MS/MS 34280000 34280000 0 0 NaN 3057100 4718800 12052000 5047700 1070900 8333500 NaN NaN NaN NaN NaN NaN 3057100 0 0 4718800 0 0 12052000 0 0 5047700 0 0 1070900 0 0 8333500 0 0 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 4444 2836 11 11 20280 22978 162490;162491;162492;162493;162494;162495 144222;144223 162490 144222 QE05099 7582 162490 144222 QE05099 7582 162490 144222 QE05099 7582 sp|Q9BV40|VAMP8_HUMAN 55 sp|Q9BV40|VAMP8_HUMAN sp|Q9BV40|VAMP8_HUMAN 0.959784 13.7778 3.78E-05 91.969 27.98 91.969 1 S NLEHLRNKTEDLEATSEHFKTTSQKVARKFW X;X;X;X;X;X;X;X;X;X;X;X;X;X;X;Phospho (STY);X;X;X;X;X;X;X;X;X;X;X;X;X;X;X XXXXXXXXPPPPPPPPPPPPXXXXXXXXXXX TEDLEAT(0.04)S(0.96)EHFK T(-83.18)EDLEAT(-13.78)S(13.78)EHFK 8 2 0.40785 By matching By matching By matching By MS/MS 114520000 114520000 0 0 NaN 20400000 9738500 7862300 0 0 76518000 NaN NaN NaN NaN NaN NaN 20400000 0 0 9738500 0 0 7862300 0 0 0 0 0 0 0 0 76518000 0 0 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 7902 4687 55 55 21013 23827 168874;168875;168876;168877 150433 168874 150433 QE05102 19524 168874 150433 QE05102 19524 168874 150433 QE05102 19524 +sp|P54764-2|EPHA4_HUMAN;sp|P54764|EPHA4_HUMAN 551;602 sp|P54764-2|EPHA4_HUMAN sp|P54764-2|EPHA4_HUMAN 0.871707 6.48916 4.61E-08 65.374 58.758 65.374 + 2 Y KHLNQGVRTYVDPFTYEDPNQAVREFAKEID X;X;X;X;X;X;X;X;Phospho (STY);X;X;X;X;X;X;Phospho (STY);X;X;X;X;X;X;X;X;X;X;X;X;X;X;X XXXXXXXXPPPPPPPPPPPPPPPPXXXXXXX T(0.499)Y(0.501)VDPFT(0.128)Y(0.872)EDPNQAVR T(0.85)Y(-0.85)VDPFT(-6.49)Y(6.49)EDPNQAVR 8 3 0.97415 By matching By MS/MS By matching By matching 3679100 0 3679100 0 NaN 725460 0 1651300 655850 646420 0 NaN NaN NaN NaN NaN NaN 0 725460 0 0 0 0 0 1651300 0 0 655850 0 0 646420 0 0 0 0 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 242 260 551 551 972 999 4968;4969;4970;4971 3421 4968 3421 QE04980 9557 4968 3421 QE04980 9557 4968 3421 QE04980 9557
--- a/test-data/test_kinase_substrate.tabular Tue Mar 15 18:17:19 2022 +0000 +++ b/test-data/test_kinase_substrate.tabular Tue Mar 22 20:47:10 2022 +0000 @@ -1,2 +1,5 @@ GENE KINASE KIN_ACC_ID KIN_ORGANISM SUBSTRATE SUB_GENE_ID SUB_ACC_ID SUB_GENE SUB_ORGANISM SUB_MOD_RSD SITE_GRP_ID SITE_+/-7_AA DOMAIN IN_VIVO_RXN IN_VITRO_RXN CST_CAT# Csnk2a1 CK2A1 Q60737 human VAMP4 53330 O70480 Vamp4 human S30 454285 RNLLEDDsDEEEDFF X +EPHA2 EphA2 P29317 human EphA2 1969 P29317 EPHA2 human Y588 450859 QLkPLktyVDPHtyE EphA2_TM X X 7423; 12677 +EPHA4 EphA4 P54764 human EphA4 2043 P54764 EPHA4 human Y596 450856 LNQGVRtyVDPFtyE EphA2_TM X +EPHA4 EphA4 P54764 human EphA4 2043 P54764 EPHA4 human Y602 450857 tyVDPFtyEDPNQAV EphA2_TM X
--- a/test-data/test_networkin.tabular Tue Mar 15 18:17:19 2022 +0000 +++ b/test-data/test_networkin.tabular Tue Mar 22 20:47:10 2022 +0000 @@ -31,3 +31,71 @@ ERC1 (ENSP00000354158) 191 HIPK2 2.2748 KIN HIPK1_HIPK2_group 0.0463 ENSP00000354158 0.4159 ERC1 IKTFWsPELKK "ENSP00000263551, 0.7696 ENSP00000286332, 0.7192 ENSP00000354158" VAMP3 (ENSP00000054666) 11 PKCzeta 2.0773 KIN PKC_group 0.4633 ENSP00000054666 0.4263 VAMP3 TAATGsNRRLQ "ENSP00000367830, 0.7688 ENSP00000320935, 0.796 ENSP00000054666" SSRP1 (ENSP00000278412) 659 DNAPK 2.0042 KIN DNAPK 0.0584 ENSP00000278412 0.56 SSRP1 RQLSEsFKSKE "ENSP00000313420, 0.448 ENSP00000278412" +EPHA4 (ENSP00000386829) 602 EphA4 35.9325 KIN Eph_group 0.1443 ENSP00000281821 1 EPHA4 VDPFTyEDPNQ 1 KIN +EPHA4 (ENSP00000386829) 596 EphA4 35.921 KIN Eph_group 0.1442 ENSP00000281821 1 EPHA4 QGVRTyVDPFT 1 KIN +EPHA4 (ENSP00000386829) 779 EphA4 17.3679 KIN Eph_group 0.0482 ENSP00000281821 1 EPHA4 DPEAAyTTRGG 1 KIN +EPHA4 (ENSP00000386829) 798 EphA4 17.3679 KIN Eph_group 0.0482 ENSP00000281821 1 EPHA4 PEAIAyRKFTS 1 KIN +EPHA4 (ENSP00000386829) 928 EphA4 17.3679 KIN Eph_group 0.0482 ENSP00000281821 1 EPHA4 IKMDRyKDNFT 1 KIN +EPHA4 (ENSP00000386829) 602 EphA1 5.7706 KIN Eph_group 0.1443 ENSP00000281821 0.907 EPHA4 VDPFTyEDPNQ "ENSP00000275815, 0.7256 ENSP00000281821" +EPHA4 (ENSP00000386829) 596 EphA1 5.7688 KIN Eph_group 0.1442 ENSP00000281821 0.907 EPHA4 QGVRTyVDPFT "ENSP00000275815, 0.7256 ENSP00000281821" +EPHA4 (ENSP00000386829) 602 EphA2 5.7678 KIN Eph_group 0.1443 ENSP00000281821 0.904 EPHA4 VDPFTyEDPNQ "ENSP00000351209, 0.7232 ENSP00000281821" +EPHA4 (ENSP00000386829) 602 EphA3 5.7678 KIN Eph_group 0.1443 ENSP00000281821 0.904 EPHA4 VDPFTyEDPNQ "ENSP00000337451, 0.7232 ENSP00000281821" +EPHA4 (ENSP00000386829) 602 EphA5 5.7678 KIN Eph_group 0.1443 ENSP00000281821 0.904 EPHA4 VDPFTyEDPNQ "ENSP00000273854, 0.7232 ENSP00000281821" +EPHA4 (ENSP00000386829) 602 EphA7 5.7678 KIN Eph_group 0.1443 ENSP00000281821 0.904 EPHA4 VDPFTyEDPNQ "ENSP00000358309, 0.7232 ENSP00000281821" +EPHA4 (ENSP00000386829) 602 EphA6 5.7668 KIN Eph_group 0.1443 ENSP00000281821 0.903 EPHA4 VDPFTyEDPNQ "ENSP00000374323, 0.7224 ENSP00000281821" +EPHA4 (ENSP00000386829) 596 EphA2 5.7659 KIN Eph_group 0.1442 ENSP00000281821 0.904 EPHA4 QGVRTyVDPFT "ENSP00000351209, 0.7232 ENSP00000281821" +EPHA4 (ENSP00000386829) 596 EphA3 5.7659 KIN Eph_group 0.1442 ENSP00000281821 0.904 EPHA4 QGVRTyVDPFT "ENSP00000337451, 0.7232 ENSP00000281821" +EPHA4 (ENSP00000386829) 596 EphA5 5.7659 KIN Eph_group 0.1442 ENSP00000281821 0.904 EPHA4 QGVRTyVDPFT "ENSP00000273854, 0.7232 ENSP00000281821" +EPHA4 (ENSP00000386829) 596 EphA7 5.7659 KIN Eph_group 0.1442 ENSP00000281821 0.904 EPHA4 QGVRTyVDPFT "ENSP00000358309, 0.7232 ENSP00000281821" +EPHA4 (ENSP00000386829) 596 EphA6 5.765 KIN Eph_group 0.1442 ENSP00000281821 0.903 EPHA4 QGVRTyVDPFT "ENSP00000374323, 0.7224 ENSP00000281821" +EPHA4 (ENSP00000386829) 779 Abl 5.6735 KIN Abl_group 0.0573 ENSP00000281821 0.806 EPHA4 DPEAAyTTRGG "ENSP00000361423, 0.6448 ENSP00000281821" +EPHA4 (ENSP00000386829) 602 EphA8 3.8493 KIN Eph_group 0.1443 ENSP00000281821 0.576 EPHA4 VDPFTyEDPNQ "ENSP00000166244, 0.7984 ENSP00000403005, 0.78 ENSP00000281821" +EPHA4 (ENSP00000386829) 596 EphA8 3.8481 KIN Eph_group 0.1442 ENSP00000281821 0.576 EPHA4 QGVRTyVDPFT "ENSP00000166244, 0.7984 ENSP00000403005, 0.78 ENSP00000281821" +EPHA4 (ENSP00000386829) 596 Abl 3.757 KIN Abl_group 0.0432 ENSP00000281821 0.806 EPHA4 QGVRTyVDPFT "ENSP00000361423, 0.6448 ENSP00000281821" +EPHA4 (ENSP00000386829) 602 Fgr 3.5442 KIN Src_group 0.0705 ENSP00000281821 0.902 EPHA4 VDPFTyEDPNQ "ENSP00000363115, 0.7216 ENSP00000281821" +EPHA4 (ENSP00000386829) 602 Yes 3.5442 KIN Src_group 0.0705 ENSP00000281821 0.902 EPHA4 VDPFTyEDPNQ "ENSP00000324740, 0.7216 ENSP00000281821" +EPHA4 (ENSP00000386829) 602 BLK 3.5431 KIN Src_group 0.0705 ENSP00000281821 0.9 EPHA4 VDPFTyEDPNQ "ENSP00000259089, 0.72 ENSP00000281821" +EPHA4 (ENSP00000386829) 779 Fgr 2.8234 KIN Src_group 0.0583 ENSP00000281821 0.902 EPHA4 DPEAAyTTRGG "ENSP00000363115, 0.7216 ENSP00000281821" +EPHA4 (ENSP00000386829) 779 Yes 2.8234 KIN Src_group 0.0583 ENSP00000281821 0.902 EPHA4 DPEAAyTTRGG "ENSP00000324740, 0.7216 ENSP00000281821" +EPHA4 (ENSP00000386829) 779 BLK 2.8225 KIN Src_group 0.0583 ENSP00000281821 0.9 EPHA4 DPEAAyTTRGG "ENSP00000259089, 0.72 ENSP00000281821" +EPHA4 (ENSP00000386829) 779 EphA1 2.7892 KIN Eph_group 0.0482 ENSP00000281821 0.907 EPHA4 DPEAAyTTRGG "ENSP00000275815, 0.7256 ENSP00000281821" +EPHA4 (ENSP00000386829) 798 EphA1 2.7892 KIN Eph_group 0.0482 ENSP00000281821 0.907 EPHA4 PEAIAyRKFTS "ENSP00000275815, 0.7256 ENSP00000281821" +EPHA4 (ENSP00000386829) 928 EphA1 2.7892 KIN Eph_group 0.0482 ENSP00000281821 0.907 EPHA4 IKMDRyKDNFT "ENSP00000275815, 0.7256 ENSP00000281821" +EPHA4 (ENSP00000386829) 779 EphA2 2.7878 KIN Eph_group 0.0482 ENSP00000281821 0.904 EPHA4 DPEAAyTTRGG "ENSP00000351209, 0.7232 ENSP00000281821" +EPHA4 (ENSP00000386829) 779 EphA3 2.7878 KIN Eph_group 0.0482 ENSP00000281821 0.904 EPHA4 DPEAAyTTRGG "ENSP00000337451, 0.7232 ENSP00000281821" +EPHA4 (ENSP00000386829) 779 EphA5 2.7878 KIN Eph_group 0.0482 ENSP00000281821 0.904 EPHA4 DPEAAyTTRGG "ENSP00000273854, 0.7232 ENSP00000281821" +EPHA4 (ENSP00000386829) 779 EphA7 2.7878 KIN Eph_group 0.0482 ENSP00000281821 0.904 EPHA4 DPEAAyTTRGG "ENSP00000358309, 0.7232 ENSP00000281821" +EPHA4 (ENSP00000386829) 798 EphA2 2.7878 KIN Eph_group 0.0482 ENSP00000281821 0.904 EPHA4 PEAIAyRKFTS "ENSP00000351209, 0.7232 ENSP00000281821" +EPHA4 (ENSP00000386829) 798 EphA3 2.7878 KIN Eph_group 0.0482 ENSP00000281821 0.904 EPHA4 PEAIAyRKFTS "ENSP00000337451, 0.7232 ENSP00000281821" +EPHA4 (ENSP00000386829) 798 EphA5 2.7878 KIN Eph_group 0.0482 ENSP00000281821 0.904 EPHA4 PEAIAyRKFTS "ENSP00000273854, 0.7232 ENSP00000281821" +EPHA4 (ENSP00000386829) 798 EphA7 2.7878 KIN Eph_group 0.0482 ENSP00000281821 0.904 EPHA4 PEAIAyRKFTS "ENSP00000358309, 0.7232 ENSP00000281821" +EPHA4 (ENSP00000386829) 928 EphA2 2.7878 KIN Eph_group 0.0482 ENSP00000281821 0.904 EPHA4 IKMDRyKDNFT "ENSP00000351209, 0.7232 ENSP00000281821" +EPHA4 (ENSP00000386829) 928 EphA3 2.7878 KIN Eph_group 0.0482 ENSP00000281821 0.904 EPHA4 IKMDRyKDNFT "ENSP00000337451, 0.7232 ENSP00000281821" +EPHA4 (ENSP00000386829) 928 EphA5 2.7878 KIN Eph_group 0.0482 ENSP00000281821 0.904 EPHA4 IKMDRyKDNFT "ENSP00000273854, 0.7232 ENSP00000281821" +EPHA4 (ENSP00000386829) 928 EphA7 2.7878 KIN Eph_group 0.0482 ENSP00000281821 0.904 EPHA4 IKMDRyKDNFT "ENSP00000358309, 0.7232 ENSP00000281821" +EPHA4 (ENSP00000386829) 779 EphA6 2.7874 KIN Eph_group 0.0482 ENSP00000281821 0.903 EPHA4 DPEAAyTTRGG "ENSP00000374323, 0.7224 ENSP00000281821" +EPHA4 (ENSP00000386829) 798 EphA6 2.7874 KIN Eph_group 0.0482 ENSP00000281821 0.903 EPHA4 PEAIAyRKFTS "ENSP00000374323, 0.7224 ENSP00000281821" +EPHA4 (ENSP00000386829) 928 EphA6 2.7874 KIN Eph_group 0.0482 ENSP00000281821 0.903 EPHA4 IKMDRyKDNFT "ENSP00000374323, 0.7224 ENSP00000281821" +EPHA4 (ENSP00000386829) 596 Fgr 2.7541 KIN Src_group 0.036 ENSP00000281821 0.902 EPHA4 QGVRTyVDPFT "ENSP00000363115, 0.7216 ENSP00000281821" +EPHA4 (ENSP00000386829) 596 Yes 2.7541 KIN Src_group 0.036 ENSP00000281821 0.902 EPHA4 QGVRTyVDPFT "ENSP00000324740, 0.7216 ENSP00000281821" +EPHA4 (ENSP00000386829) 596 BLK 2.7532 KIN Src_group 0.036 ENSP00000281821 0.9 EPHA4 QGVRTyVDPFT "ENSP00000259089, 0.72 ENSP00000281821" +EPHA4 (ENSP00000386829) 798 Fgr 2.7477 KIN Src_group 0.0263 ENSP00000281821 0.902 EPHA4 PEAIAyRKFTS "ENSP00000363115, 0.7216 ENSP00000281821" +EPHA4 (ENSP00000386829) 798 Yes 2.7477 KIN Src_group 0.0263 ENSP00000281821 0.902 EPHA4 PEAIAyRKFTS "ENSP00000324740, 0.7216 ENSP00000281821" +EPHA4 (ENSP00000386829) 928 Fgr 2.7472 KIN Src_group 0.0257 ENSP00000281821 0.902 EPHA4 IKMDRyKDNFT "ENSP00000363115, 0.7216 ENSP00000281821" +EPHA4 (ENSP00000386829) 928 Yes 2.7472 KIN Src_group 0.0257 ENSP00000281821 0.902 EPHA4 IKMDRyKDNFT "ENSP00000324740, 0.7216 ENSP00000281821" +EPHA4 (ENSP00000386829) 798 BLK 2.7468 KIN Src_group 0.0263 ENSP00000281821 0.9 EPHA4 PEAIAyRKFTS "ENSP00000259089, 0.72 ENSP00000281821" +EPHA4 (ENSP00000386829) 928 BLK 2.7463 KIN Src_group 0.0257 ENSP00000281821 0.9 EPHA4 IKMDRyKDNFT "ENSP00000259089, 0.72 ENSP00000281821" +EPHA4 (ENSP00000386829) 596 HCK 2.7098 KIN Src_group 0.036 ENSP00000281821 0.899 EPHA4 QGVRTyVDPFT "ENSP00000365012, 0.7192 ENSP00000281821" +EPHA4 (ENSP00000386829) 602 HCK 2.7098 KIN Src_group 0.0705 ENSP00000281821 0.899 EPHA4 VDPFTyEDPNQ "ENSP00000365012, 0.7192 ENSP00000281821" +EPHA4 (ENSP00000386829) 779 HCK 2.7098 KIN Src_group 0.0583 ENSP00000281821 0.899 EPHA4 DPEAAyTTRGG "ENSP00000365012, 0.7192 ENSP00000281821" +EPHA4 (ENSP00000386829) 798 HCK 2.7098 KIN Src_group 0.0263 ENSP00000281821 0.899 EPHA4 PEAIAyRKFTS "ENSP00000365012, 0.7192 ENSP00000281821" +EPHA4 (ENSP00000386829) 928 HCK 2.7098 KIN Src_group 0.0257 ENSP00000281821 0.899 EPHA4 IKMDRyKDNFT "ENSP00000365012, 0.7192 ENSP00000281821" +EPHA4 (ENSP00000386829) 780 PKCalpha 2.5567 KIN PKC_group 0.3699 ENSP00000281821 0.401 EPHA4 PEAAYtTRGGK "ENSP00000284384, 0.7464 ENSP00000244007, 0.7784 ENSP00000281821" +EPHA4 (ENSP00000386829) 780 PKCbeta 2.4948 KIN PKC_group 0.3699 ENSP00000281821 0.3759 EPHA4 PEAAYtTRGGK "ENSP00000305355, 0.7464 ENSP00000244007, 0.7296 ENSP00000281821" +EPHA4 (ENSP00000386829) 602 Abl 2.1653 KIN Abl_group 0.0221 ENSP00000281821 0.806 EPHA4 VDPFTyEDPNQ "ENSP00000361423, 0.6448 ENSP00000281821" +EPHA4 (ENSP00000386829) 798 Abl 2.1376 KIN Abl_group 0.0221 ENSP00000281821 0.806 EPHA4 PEAIAyRKFTS "ENSP00000361423, 0.6448 ENSP00000281821" +EPHA4 (ENSP00000386829) 928 Abl 2.1099 KIN Abl_group 0.0221 ENSP00000281821 0.806 EPHA4 IKMDRyKDNFT "ENSP00000361423, 0.6448 ENSP00000281821" +EPHA4 (ENSP00000386829) 602 EphB6 2.04 KIN Eph_group 0.1443 ENSP00000281821 0.5258 EPHA4 VDPFTyEDPNQ "ENSP00000376684, 0.7976 ENSP00000226091, 0.7976 ENSP00000281821" +EPHA4 (ENSP00000386829) 596 EphB6 2.0393 KIN Eph_group 0.1442 ENSP00000281821 0.5258 EPHA4 QGVRTyVDPFT "ENSP00000376684, 0.7976 ENSP00000226091, 0.7976 ENSP00000281821" +EPHA4 (ENSP00000386829) 602 EphB3 2.0282 KIN Eph_group 0.1443 ENSP00000281821 0.5231 EPHA4 VDPFTyEDPNQ "ENSP00000332118, 0.7976 ENSP00000226091, 0.7936 ENSP00000281821" +EPHA4 (ENSP00000386829) 596 EphB3 2.0276 KIN Eph_group 0.1442 ENSP00000281821 0.5231 EPHA4 QGVRTyVDPFT "ENSP00000332118, 0.7976 ENSP00000226091, 0.7936 ENSP00000281821"
--- a/test-data/test_regulatory_sites.tabular Tue Mar 15 18:17:19 2022 +0000 +++ b/test-data/test_regulatory_sites.tabular Tue Mar 22 20:47:10 2022 +0000 @@ -6,3 +6,4 @@ VAMP8 VAMP8 "Membrane protein, integral; Vesicle" Q9BV40 8673 2p11.2 human S55-p 12738929 TEDLEATsEHFKTTS Synaptobrevin "activity, inhibited" 27402227 1 8 0 "abolish function in SNARE complex during mast cell secretion, reduces in vitro ensemble vesicle fusion" ENSA ENSA "Inhibitor; Protein phosphatase, regulatory subunit" O43768 2029 1q21.3 human S67-p 455934 KGQKYFDsGDYNMAK Endosulfine "molecular association, regulation" cell cycle regulation PPP2CA(INDUCES) 27889260 3 56 47 Vamp4 VAMP4 "Membrane protein, integral; Vesicle" O70480 53330 1 H2.1|1 70.29 cM mouse S30-p 454285 RNLLEDDsDEEEDFF "molecular association, regulation; intracellular localization" PACS-1(INDUCES) 14608369 1 64 10 +EPHA4 EphA4 "EC 2.7.10.1; KINASE; Kinase, protein; Membrane protein, integral; Protein kinase, TK; Protein kinase, tyrosine (receptor)" P54764 2043 2q36.1 human Y602-p 450857 TYVDPFTyEDPNQAV EphA2_TM "molecular association, regulation" Fyn(INDUCES) 8622893 6 16 155
--- a/test-data/test_swissprot.fasta Tue Mar 15 18:17:19 2022 +0000 +++ b/test-data/test_swissprot.fasta Tue Mar 22 20:47:10 2022 +0000 @@ -66,3 +66,7 @@ MAILFAVVARGTTILAKHAWCGGNFLEDFERSRAFNFLNEIKKRFQTTYGSRAQTALPYAMNSEFSSVLAAQLKHHSENKGLDKVMETQAQVDELKGIMVRNIDLVAQRGERLELLIDKTENLVDSSVTFKTTSRNLARAMCMKNLKLTIIIIIVSIVFIYIIVSPLCGGFTWPSCVKK >sp|Q9BV40|VAMP8_HUMAN_Vesicle-associated membrane protein 8 OS=Homo sapiens OX=9606 GN=VAMP8 PE=1 SV=1 MEEASEGGGNDRVRNLQSEVEGVKNIMTQNVERILARGENLEHLRNKTEDLEATSEHFKTTSQKVARKFWWKNVKMIVLICVIVFIIILFIVLFATGAFS +>sp|P54764|EPHA4_HUMAN Ephrin type-A receptor 4 OS=Homo sapiens OX=9606 GN=EPHA4 PE=1 SV=1 +MAGIFYFALFSCLFGICDAVTGSRVYPANEVTLLDSRSVQGELGWIASPLEGGWEEVSIMDEKNTPIRTYQVCNVMEPSQNNWLRTDWITREGAQRVYIEIKFTLRDCNSLPGVMGTCKETFNLYYYESDNDKERFIRENQFVKIDTIAADESFTQVDIGDRIMKLNTEIRDVGPLSKKGFYLAFQDVGACIALVSVRVFYKKCPLTVRNLAQFPDTITGADTSSLVEVRGSCVNNSEEKDVPKMYCGADGEWLVPIGNCLCNAGHEERSGECQACKIGYYKALSTDATCAKCPPHSYSVWEGATSCTCDRGFFRADNDAASMPCTRPPSAPLNLISNVNETSVNLEWSSPQNTGGRQDISYNVVCKKCGAGDPSKCRPCGSGVHYTPQQNGLKTTKVSITDLLAHTNYTFEIWAVNGVSKYNPNPDQSVSVTVTTNQAAPSSIALVQAKEVTRYSVALAWLEPDRPNGVILEYEVKYYEKDQNERSYRIVRTAARNTDIKGLNPLTSYVFHVRARTAAGYGDFSEPLEVTTNTVPSRIIGDGANSTVLLVSVSGSVVLVVILIAAFVISRRRSKYSKAKQEADEEKHLNQGVRTYVDPFTYEDPNQAVREFAKEIDASCIKIEKVIGVGEFGEVCSGRLKVPGKREICVAIKTLKAGYTDKQRRDFLSEASIMGQFDHPNIIHLEGVVTKCKPVMIITEYMENGSLDAFLRKNDGRFTVIQLVGMLRGIGSGMKYLSDMSYVHRDLAARNILVNSNLVCKVSDFGMSRVLEDDPEAAYTTRGGKIPIRWTAPEAIAYRKFTSASDVWSYGIVMWEVMSYGERPYWDMSNQDVIKAIEEGYRLPPPMDCPIALHQLMLDCWQKERSDRPKFGQIVNMLDKLIRNPNSLKRTGTESSRPNTALLDPSSPEFSAVVSVGDWLQAIKMDRYKDNFTAAGYTTLEAVVHVNQEDLARIGITAITHQNKILSSVQAMRTQMQQMHGRMVPV +>sp|P54764-2|EPHA4_HUMAN Isoform 2 of Ephrin type-A receptor 4 OS=Homo sapiens OX=9606 GN=EPHA4 +MKWEEVSIMDEKNTPIRTYQVCNVMEPSQNNWLRTDWITREGAQRVYIEIKFTLRDCNSLPGVMGTCKETFNLYYYESDNDKERFIRENQFVKIDTIAADESFTQVDIGDRIMKLNTEIRDVGPLSKKGFYLAFQDVGACIALVSVRVFYKKCPLTVRNLAQFPDTITGADTSSLVEVRGSCVNNSEEKDVPKMYCGADGEWLVPIGNCLCNAGHEERSGECQACKIGYYKALSTDATCAKCPPHSYSVWEGATSCTCDRGFFRADNDAASMPCTRPPSAPLNLISNVNETSVNLEWSSPQNTGGRQDISYNVVCKKCGAGDPSKCRPCGSGVHYTPQQNGLKTTKVSITDLLAHTNYTFEIWAVNGVSKYNPNPDQSVSVTVTTNQAAPSSIALVQAKEVTRYSVALAWLEPDRPNGVILEYEVKYYEKDQNERSYRIVRTAARNTDIKGLNPLTSYVFHVRARTAAGYGDFSEPLEVTTNTVPSRIIGDGANSTVLLVSVSGSVVLVVILIAAFVISRRRSKYSKAKQEADEEKHLNQGVRTYVDPFTYEDPNQAVREFAKEIDASCIKIEKVIGVGEFGEVCSGRLKVPGKREICVAIKTLKAGYTDKQRRDFLSEASIMGQFDHPNIIHLEGVVTKCKPVMIITEYMENGSLDAFLRKNDGRFTVIQLVGMLRGIGSGMKYLSDMSYVHRDLAARNILVNSNLVCKVSDFGMSRVLEDDPEAAYTTRGGKIPIRWTAPEAIAYRKFTSASDVWSYGIVMWEVMSYGERPYWDMSNQDVIKAIEEGYRLPPPMDCPIALHQLMLDCWQKERSDRPKFGQIVNMLDKLIRNPNSLKRTGTESSRPNTALLDPSSPEFSAVVSVGDWLQAIKMDRYKDNFTAAGYTTLEAVVHVNQEDLARIGITAITHQNKILSSVQAMRTQMQQMHGRMVPV
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