.. _dms_editsites: ========================================== ``dms_editsites`` ========================================== .. contents:: Overview ------------- ``dms_editsites`` is a program included with the `dms_tools`_ package. It is designed for renumbering sites, or removing data for specific ones. See `Examples`_ for illustrations of how you might do this. After you install `dms_tools`_, this program will be available to run at the command line. Command-line usage --------------------- .. argparse:: :module: parsearguments :func: EditSitesParser :prog: dms_editsites infile Typically, this file might be a :ref:`preferences_file`, a :ref:`diffpreferences_file`, or a :ref:`dms_counts`. Examples ----------- Renumbering sites ~~~~~~~~~~~~~~~~~~~~~~~ If we have the ``preferences.txt`` file with these contents:: # POSITION WT SITE_ENTROPY PI_A PI_C PI_D PI_E PI_F PI_G PI_H PI_I PI_K PI_L PI_M PI_N PI_P PI_Q PI_R PI_S PI_T PI_V PI_W PI_Y PI_* PI_A_95 PI_C_95 PI_D_95 PI_E_95 PI_F_95 PI_G_95 PI_H_95 PI_I_95 PI_K_95 PI_L_95 PI_M_95 PI_N_95 PI_P_95 PI_Q_95 PI_R_95 PI_S_95 PI_T_95 PI_V_95 PI_W_95 PI_Y_95 PI_*_95 2 K 3.7887 0.00871112 0.0566807 0.00209889 0.0126265 0.123541 0.0419474 0.012759 0.198294 0.0609558 0.0861918 0.0132844 0.0314975 0.0410346 0.0578467 0.0166405 0.0588795 0.0873109 0.0655377 0.00906756 0.0098667 0.0052279 0.00377015,0.0161776 0.0368293,0.0866459 5.25935e-05,0.00750028 0.00147735,0.0305943 0.0838463,0.17365 0.0290031,0.0584818 0.00555741,0.0238828 0.156947,0.244985 0.0549586,0.0681017 0.0664255,0.113842 0.000847956,0.041653 0.0221782,0.0430464 0.0290997,0.0551884 0.0355218,0.091347 0.00758911,0.0250887 0.0443249,0.0761826 0.0677839,0.113325 0.0425034,0.0981422 0.000771089,0.0277961 0.00358541,0.0201952 0.000127331,0.0154344 3 A 2.83514 0.0437537 0.0334546 0.0309614 0.00177409 0.0895918 0.00481327 0.00159833 0.0194826 0.00612203 0.45822 0.00724804 0.0214667 0.00343922 0.0070182 0.00247844 0.019586 0.0234391 0.166837 0.0286347 0.0188882 0.0111935 0.0382826,0.0494847 0.0159482,0.061066 0.0146872,0.054093 3.31649e-05,0.00560408 0.0547333,0.132015 9.98457e-05,0.0141004 4.33912e-05,0.0056256 0.00931897,0.0363372 0.000604372,0.0187545 0.385594,0.531808 0.000164964,0.0337412 0.00394407,0.0612625 0.000229564,0.00835275 0.000259382,0.0237583 0.000710602,0.00561234 0.00861317,0.0325203 0.00902808,0.0448718 0.123725,0.227516 0.00809207,0.0680912 0.00888236,0.0354431 0.00412041,0.0228625 4 K 3.90821 0.0442179 0.0282262 0.00917627 0.0381669 0.00258029 0.00505373 0.117934 0.0259991 0.0512432 0.0905123 0.0170454 0.0126292 0.0614701 0.0848777 0.141501 0.0361854 0.0180969 0.0514335 0.104027 0.0562738 0.0033496 0.0281289,0.0676053 0.0130852,0.0517097 0.00165841,0.0237626 0.00962184,0.0932152 6.39066e-05,0.00890049 0.00132784,0.0114412 0.0783091,0.176141 0.0131793,0.0426951 0.0448744,0.0578793 0.0643019,0.115842 0.00299087,0.0466871 0.00124322,0.0341616 0.0425182,0.0870665 0.0530961,0.124081 0.103449,0.195545 0.0238936,0.0533164 0.009447,0.0303053 0.0345412,0.071387 0.0575267,0.175514 0.0281562,0.0992686 0.000150733,0.00985258 and the ``renumbering_scheme.txt`` file with these contents:: #ORIGINAL_SITE NEW_SITE 2 1 3 2 4 2A then the command:: dms_editsites preferences.txt renumbered_preferences.txt renumber renumbering_scheme.txt creates the file ``renumbered_preferences.txt`` with these contents:: # POSITION WT SITE_ENTROPY PI_A PI_C PI_D PI_E PI_F PI_G PI_H PI_I PI_K PI_L PI_M PI_N PI_P PI_Q PI_R PI_S PI_T PI_V PI_W PI_Y PI_* PI_A_95 PI_C_95 PI_D_95 PI_E_95 PI_F_95 PI_G_95 PI_H_95 PI_I_95 PI_K_95 PI_L_95 PI_M_95 PI_N_95 PI_P_95 PI_Q_95 PI_R_95 PI_S_95 PI_T_95 PI_V_95 PI_W_95 PI_Y_95 PI_*_95 1 K 3.7887 0.00871112 0.0566807 0.00209889 0.0126265 0.123541 0.0419474 0.012759 0.198294 0.0609558 0.0861918 0.0132844 0.0314975 0.0410346 0.0578467 0.0166405 0.0588795 0.0873109 0.0655377 0.00906756 0.0098667 0.0052279 0.00377015,0.0161776 0.0368293,0.0866459 5.25935e-05,0.00750028 0.00147735,0.0305943 0.0838463,0.17365 0.0290031,0.0584818 0.00555741,0.0238828 0.156947,0.244985 0.0549586,0.0681017 0.0664255,0.113842 0.000847956,0.041653 0.0221782,0.0430464 0.0290997,0.0551884 0.0355218,0.091347 0.00758911,0.0250887 0.0443249,0.0761826 0.0677839,0.113325 0.0425034,0.0981422 0.000771089,0.0277961 0.00358541,0.0201952 0.000127331,0.0154344 2 A 2.83514 0.0437537 0.0334546 0.0309614 0.00177409 0.0895918 0.00481327 0.00159833 0.0194826 0.00612203 0.45822 0.00724804 0.0214667 0.00343922 0.0070182 0.00247844 0.019586 0.0234391 0.166837 0.0286347 0.0188882 0.0111935 0.0382826,0.0494847 0.0159482,0.061066 0.0146872,0.054093 3.31649e-05,0.00560408 0.0547333,0.132015 9.98457e-05,0.0141004 4.33912e-05,0.0056256 0.00931897,0.0363372 0.000604372,0.0187545 0.385594,0.531808 0.000164964,0.0337412 0.00394407,0.0612625 0.000229564,0.00835275 0.000259382,0.0237583 0.000710602,0.00561234 0.00861317,0.0325203 0.00902808,0.0448718 0.123725,0.227516 0.00809207,0.0680912 0.00888236,0.0354431 0.00412041,0.0228625 2A K 3.90821 0.0442179 0.0282262 0.00917627 0.0381669 0.00258029 0.00505373 0.117934 0.0259991 0.0512432 0.0905123 0.0170454 0.0126292 0.0614701 0.0848777 0.141501 0.0361854 0.0180969 0.0514335 0.104027 0.0562738 0.0033496 0.0281289,0.0676053 0.0130852,0.0517097 0.00165841,0.0237626 0.00962184,0.0932152 6.39066e-05,0.00890049 0.00132784,0.0114412 0.0783091,0.176141 0.0131793,0.0426951 0.0448744,0.0578793 0.0643019,0.115842 0.00299087,0.0466871 0.00124322,0.0341616 0.0425182,0.0870665 0.0530961,0.124081 0.103449,0.195545 0.0238936,0.0533164 0.009447,0.0303053 0.0345412,0.071387 0.0575267,0.175514 0.0281562,0.0992686 0.000150733,0.00985258 Removing sites ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ If we have the ``preferences.txt`` file with these contents:: # POSITION WT SITE_ENTROPY PI_A PI_C PI_D PI_E PI_F PI_G PI_H PI_I PI_K PI_L PI_M PI_N PI_P PI_Q PI_R PI_S PI_T PI_V PI_W PI_Y PI_* PI_A_95 PI_C_95 PI_D_95 PI_E_95 PI_F_95 PI_G_95 PI_H_95 PI_I_95 PI_K_95 PI_L_95 PI_M_95 PI_N_95 PI_P_95 PI_Q_95 PI_R_95 PI_S_95 PI_T_95 PI_V_95 PI_W_95 PI_Y_95 PI_*_95 2 K 3.7887 0.00871112 0.0566807 0.00209889 0.0126265 0.123541 0.0419474 0.012759 0.198294 0.0609558 0.0861918 0.0132844 0.0314975 0.0410346 0.0578467 0.0166405 0.0588795 0.0873109 0.0655377 0.00906756 0.0098667 0.0052279 0.00377015,0.0161776 0.0368293,0.0866459 5.25935e-05,0.00750028 0.00147735,0.0305943 0.0838463,0.17365 0.0290031,0.0584818 0.00555741,0.0238828 0.156947,0.244985 0.0549586,0.0681017 0.0664255,0.113842 0.000847956,0.041653 0.0221782,0.0430464 0.0290997,0.0551884 0.0355218,0.091347 0.00758911,0.0250887 0.0443249,0.0761826 0.0677839,0.113325 0.0425034,0.0981422 0.000771089,0.0277961 0.00358541,0.0201952 0.000127331,0.0154344 3 A 2.83514 0.0437537 0.0334546 0.0309614 0.00177409 0.0895918 0.00481327 0.00159833 0.0194826 0.00612203 0.45822 0.00724804 0.0214667 0.00343922 0.0070182 0.00247844 0.019586 0.0234391 0.166837 0.0286347 0.0188882 0.0111935 0.0382826,0.0494847 0.0159482,0.061066 0.0146872,0.054093 3.31649e-05,0.00560408 0.0547333,0.132015 9.98457e-05,0.0141004 4.33912e-05,0.0056256 0.00931897,0.0363372 0.000604372,0.0187545 0.385594,0.531808 0.000164964,0.0337412 0.00394407,0.0612625 0.000229564,0.00835275 0.000259382,0.0237583 0.000710602,0.00561234 0.00861317,0.0325203 0.00902808,0.0448718 0.123725,0.227516 0.00809207,0.0680912 0.00888236,0.0354431 0.00412041,0.0228625 4 K 3.90821 0.0442179 0.0282262 0.00917627 0.0381669 0.00258029 0.00505373 0.117934 0.0259991 0.0512432 0.0905123 0.0170454 0.0126292 0.0614701 0.0848777 0.141501 0.0361854 0.0180969 0.0514335 0.104027 0.0562738 0.0033496 0.0281289,0.0676053 0.0130852,0.0517097 0.00165841,0.0237626 0.00962184,0.0932152 6.39066e-05,0.00890049 0.00132784,0.0114412 0.0783091,0.176141 0.0131793,0.0426951 0.0448744,0.0578793 0.0643019,0.115842 0.00299087,0.0466871 0.00124322,0.0341616 0.0425182,0.0870665 0.0530961,0.124081 0.103449,0.195545 0.0238936,0.0533164 0.009447,0.0303053 0.0345412,0.071387 0.0575267,0.175514 0.0281562,0.0992686 0.000150733,0.00985258 and the file ``remove_sites.txt`` with these contents:: #sites to remove 2 then the command:: dms_editsites preferences.txt pruned_preferences.txt remove remove_sites.txt creates the file ``pruned_preferences.txt`` with these contents:: # POSITION WT SITE_ENTROPY PI_A PI_C PI_D PI_E PI_F PI_G PI_H PI_I PI_K PI_L PI_M PI_N PI_P PI_Q PI_R PI_S PI_T PI_V PI_W PI_Y PI_* PI_A_95 PI_C_95 PI_D_95 PI_E_95 PI_F_95 PI_G_95 PI_H_95 PI_I_95 PI_K_95 PI_L_95 PI_M_95 PI_N_95 PI_P_95 PI_Q_95 PI_R_95 PI_S_95 PI_T_95 PI_V_95 PI_W_95 PI_Y_95 PI_*_95 3 A 2.83514 0.0437537 0.0334546 0.0309614 0.00177409 0.0895918 0.00481327 0.00159833 0.0194826 0.00612203 0.45822 0.00724804 0.0214667 0.00343922 0.0070182 0.00247844 0.019586 0.0234391 0.166837 0.0286347 0.0188882 0.0111935 0.0382826,0.0494847 0.0159482,0.061066 0.0146872,0.054093 3.31649e-05,0.00560408 0.0547333,0.132015 9.98457e-05,0.0141004 4.33912e-05,0.0056256 0.00931897,0.0363372 0.000604372,0.0187545 0.385594,0.531808 0.000164964,0.0337412 0.00394407,0.0612625 0.000229564,0.00835275 0.000259382,0.0237583 0.000710602,0.00561234 0.00861317,0.0325203 0.00902808,0.0448718 0.123725,0.227516 0.00809207,0.0680912 0.00888236,0.0354431 0.00412041,0.0228625 4 K 3.90821 0.0442179 0.0282262 0.00917627 0.0381669 0.00258029 0.00505373 0.117934 0.0259991 0.0512432 0.0905123 0.0170454 0.0126292 0.0614701 0.0848777 0.141501 0.0361854 0.0180969 0.0514335 0.104027 0.0562738 0.0033496 0.0281289,0.0676053 0.0130852,0.0517097 0.00165841,0.0237626 0.00962184,0.0932152 6.39066e-05,0.00890049 0.00132784,0.0114412 0.0783091,0.176141 0.0131793,0.0426951 0.0448744,0.0578793 0.0643019,0.115842 0.00299087,0.0466871 0.00124322,0.0341616 0.0425182,0.0870665 0.0530961,0.124081 0.103449,0.195545 0.0238936,0.0533164 0.009447,0.0303053 0.0345412,0.071387 0.0575267,0.175514 0.0281562,0.0992686 0.000150733,0.00985258 .. include:: weblinks.txt