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--- finding_genes_of_interest_with_panther_hmms [2026/01/23 15:37] – [Add HMM profile coverage information] 172.20.120.170
+++ finding_genes_of_interest_with_panther_hmms [2026/03/16 14:41] (current) – [Mitochondrial import] 172.20.54.200
@@ Line 144: / Line 144: @@
 </code>
-This yields a file that looks like this
+This yields a file that looks like this (if you did hmmscan)
 <code>
@@ Line 314: / Line 314: @@
 <code>
+function body {
+    IFS= read -r header
+    printf '%s\n' "$header"
+    "$@"
+}
 cat ergo_vs_panther17.filt.ext.domtblout \
     | body rg -f <(cut -f 6 families_of_interest.ATP.upd.list) \
@@ Line 433: / Line 439: @@
 <code>
+IRON_SULFUR_CLUSTER_ASSEMBLY  FeS  Acp1                         PTHR20863.mag.mod    ACYL CARRIER PROTEIN                                            PTHR20863.orig.30.pir
+IRON_SULFUR_CLUSTER_ASSEMBLY  FeS  Acp1                         PTHR20863.SF28.mod   ACYL CARRIER PROTEIN, MITOCHONDRIAL                             PTHR20863.SF28.pir
 IRON_SULFUR_CLUSTER_ASSEMBLY  FeS  Frataxin/FXN                 PTHR16821.mag.mod    FRATAXIN                                                        PTHR16821.orig.30.pir
 IRON_SULFUR_CLUSTER_ASSEMBLY  FeS  Frataxin/FXN                 PTHR16821.SF2.mod    FRATAXIN,_MITOCHONDRIAL                                         PTHR16821.SF2.pir
@@ Line 638: / Line 646: @@
 <code>
-PROTEIN_IMPORT_AND_FOLDING  IMPORT  Tom40                          PTHR10802.mag.mod    MITOCHONDRIAL_IMPORT_RECEPTOR_SUBUNIT_TOM40                               PTHR10802.orig.30.pir
+TRANSLOCASE_OF_THE_OUTER_MEMBRANE  TOM  Tom40                          PTHR10802.mag.mod    MITOCHONDRIAL_IMPORT_RECEPTOR_SUBUNIT_TOM40                               PTHR10802.orig.30.pir
-PROTEIN_IMPORT_AND_FOLDING  IMPORT  Tom40                          PTHR10802.SF2.mod    MITOCHONDRIAL_IMPORT_RECEPTOR_SUBUNIT_TOM40_HOMOLOG_1-RELATED             PTHR10802.SF2.pir
+TRANSLOCASE_OF_THE_OUTER_MEMBRANE  TOM  Tom40                          PTHR10802.SF2.mod    MITOCHONDRIAL_IMPORT_RECEPTOR_SUBUNIT_TOM40_HOMOLOG_1-RELATED             PTHR10802.SF2.pir
-PROTEIN_IMPORT_AND_FOLDING  IMPORT  Sam50                          PTHR12815.SF18.mod   SORTING_AND_ASSEMBLY_MACHINERY_COMPONENT_50_HOMOLOG                       PTHR12815.SF18.pir
+SORTING_AND_ASSEMBLY_MACHINERY     SAM  Sam50                          PTHR12815.SF18.mod   SORTING_AND_ASSEMBLY_MACHINERY_COMPONENT_50_HOMOLOG                       PTHR12815.SF18.pir
-PROTEIN_IMPORT_AND_FOLDING  IMPORT  Sam50                          PTHR12815.mag.mod    SORTING_AND_ASSEMBLY_MACHINERY_SAMM50_PROTEIN_FAMILY_MEMBER               PTHR12815.orig.30.pir
+SORTING_AND_ASSEMBLY_MACHINERY     SAM  Sam50                          PTHR12815.mag.mod    SORTING_AND_ASSEMBLY_MACHINERY_SAMM50_PROTEIN_FAMILY_MEMBER               PTHR12815.orig.30.pir
-PROTEIN_IMPORT_AND_FOLDING  IMPORT  Mia40                          PTHR21622.SF0.mod    AU015836_PROTEIN-RELATED                                                  PTHR21622.SF0.pir
+MITOCHONDRIAL_IMPORT_AND_ASSEMBLY  MIA  Mia40                          PTHR21622.SF0.mod    AU015836_PROTEIN-RELATED                                                  PTHR21622.SF0.pir
-PROTEIN_IMPORT_AND_FOLDING  IMPORT  Mia40                          PTHR21622.mag.mod    COILED-COIL-HELIX-COILED-COIL-HELIX_DOMAIN_CONTAINING_4                   PTHR21622.orig.30.pir
+MITOCHONDRIAL_IMPORT_AND_ASSEMBLY  MIA  Mia40                          PTHR21622.mag.mod    COILED-COIL-HELIX-COILED-COIL-HELIX_DOMAIN_CONTAINING_4                   PTHR21622.orig.30.pir
-PROTEIN_IMPORT_AND_FOLDING  IMPORT  Tim8/Tim13                     PTHR19338.mag.mod    TRANSLOCASE_OF_INNER_MITOCHONDRIAL_MEMBRANE_13_HOMOLOG                    PTHR19338.orig.30.pir
+TRANSLOCASE_OF_THE_INNER_MEMBRANE  TIM  Tim8/Tim13                     PTHR19338.mag.mod    TRANSLOCASE_OF_INNER_MITOCHONDRIAL_MEMBRANE_13_HOMOLOG                    PTHR19338.orig.30.pir
-PROTEIN_IMPORT_AND_FOLDING  IMPORT  Tim8/Tim13                     PTHR19338.SF1.mod    MITOCHONDRIAL_IMPORT_INNER_MEMBRANE_TRANSLOCASE_SUBUNIT_TIM8_A-B-RELATED  PTHR19338.SF1.pir
+TRANSLOCASE_OF_THE_INNER_MEMBRANE  TIM  Tim8/Tim13                     PTHR19338.SF1.mod    MITOCHONDRIAL_IMPORT_INNER_MEMBRANE_TRANSLOCASE_SUBUNIT_TIM8_A-B-RELATED  PTHR19338.SF1.pir
-PROTEIN_IMPORT_AND_FOLDING  IMPORT  Tim8/Tim13                     PTHR19338.SF4.mod    MITOCHONDRIAL_IMPORT_INNER_MEMBRANE_TRANSLOCASE_SUBUNIT                   PTHR19338.SF4.pir
+TRANSLOCASE_OF_THE_INNER_MEMBRANE  TIM  Tim8/Tim13                     PTHR19338.SF4.mod    MITOCHONDRIAL_IMPORT_INNER_MEMBRANE_TRANSLOCASE_SUBUNIT                   PTHR19338.SF4.pir
-PROTEIN_IMPORT_AND_FOLDING  IMPORT  Tim9                           PTHR13172.SF5.mod    MITOCHONDRIAL_IMPORT_INNER_MEMBRANE_TRANSLOCASE_SUBUNIT_TIM9              PTHR13172.SF5.pir
+TRANSLOCASE_OF_THE_INNER_MEMBRANE  TIM  Tim9                           PTHR13172.SF5.mod    MITOCHONDRIAL_IMPORT_INNER_MEMBRANE_TRANSLOCASE_SUBUNIT_TIM9              PTHR13172.SF5.pir
-PROTEIN_IMPORT_AND_FOLDING  IMPORT  Tim9                           PTHR13172.mag.mod    MITOCHONDRIAL_IMPORT_INNER_MEMBRANE_TRANSLOCASE_SUBUNIT_TIM9B             PTHR13172.orig.30.pir
+TRANSLOCASE_OF_THE_INNER_MEMBRANE  TIM  Tim9                           PTHR13172.mag.mod    MITOCHONDRIAL_IMPORT_INNER_MEMBRANE_TRANSLOCASE_SUBUNIT_TIM9B             PTHR13172.orig.30.pir
-PROTEIN_IMPORT_AND_FOLDING  IMPORT  Tim10                          PTHR11038.mag.mod    MITOCHONDRIAL_IMPORT_INNER_MEMBRANE_TRANSLOCASE_SUBUNIT_TIM10             PTHR11038.orig.30.pir
+TRANSLOCASE_OF_THE_INNER_MEMBRANE  TIM  Tim10                          PTHR11038.mag.mod    MITOCHONDRIAL_IMPORT_INNER_MEMBRANE_TRANSLOCASE_SUBUNIT_TIM10             PTHR11038.orig.30.pir
-PROTEIN_IMPORT_AND_FOLDING  IMPORT  Tim10                          PTHR11038.SF16.mod   MITOCHONDRIAL_IMPORT_INNER_MEMBRANE_TRANSLOCASE_SUBUNIT_TIM10             PTHR11038.SF16.pir
+TRANSLOCASE_OF_THE_INNER_MEMBRANE  TIM  Tim10                          PTHR11038.SF16.mod   MITOCHONDRIAL_IMPORT_INNER_MEMBRANE_TRANSLOCASE_SUBUNIT_TIM10             PTHR11038.SF16.pir
-PROTEIN_IMPORT_AND_FOLDING  IMPORT  Tim22                          PTHR14110.mag.mod    MITOCHONDRIAL_IMPORT_INNER_MEMBRANE_TRANSLOCASE_SUBUNIT_TIM22             PTHR14110.orig.30.pir
+TRANSLOCASE_OF_THE_INNER_MEMBRANE  TIM  Tim22                          PTHR14110.mag.mod    MITOCHONDRIAL_IMPORT_INNER_MEMBRANE_TRANSLOCASE_SUBUNIT_TIM22             PTHR14110.orig.30.pir
-PROTEIN_IMPORT_AND_FOLDING  IMPORT  Tim22                          PTHR14110.SF0.mod    MITOCHONDRIAL_IMPORT_INNER_MEMBRANE_TRANSLOCASE_SUBUNIT_TIM22             PTHR14110.SF0.pir
+TRANSLOCASE_OF_THE_INNER_MEMBRANE  TIM  Tim22                          PTHR14110.SF0.mod    MITOCHONDRIAL_IMPORT_INNER_MEMBRANE_TRANSLOCASE_SUBUNIT_TIM22             PTHR14110.SF0.pir
-PROTEIN_IMPORT_AND_FOLDING  IMPORT  Tim23                          PTHR15371.SF0.mod    MITOCHONDRIAL_IMPORT_INNER_MEMBRANE_TRANSLOCASE_SUBUNIT_TIM23             PTHR15371.SF0.pir
+TRANSLOCASE_OF_THE_INNER_MEMBRANE  TIM  Tim23                          PTHR15371.SF0.mod    MITOCHONDRIAL_IMPORT_INNER_MEMBRANE_TRANSLOCASE_SUBUNIT_TIM23             PTHR15371.SF0.pir
-PROTEIN_IMPORT_AND_FOLDING  IMPORT  Tim23                          PTHR15371.mag.mod    TIM23                                                                     PTHR15371.orig.30.pir
+TRANSLOCASE_OF_THE_INNER_MEMBRANE  TIM  Tim23                          PTHR15371.mag.mod    TIM23                                                                     PTHR15371.orig.30.pir
 PROTEIN_IMPORT_AND_FOLDING  IMPORT  Pam18/Tim14                    PTHR12763.mag.mod    UNCHARACTERIZED                                                           PTHR12763.orig.30.pir
 PROTEIN_IMPORT_AND_FOLDING  IMPORT  Pam18/Tim14                    PTHR12763.SF28.mod   GEO10507P1-RELATED                                                        PTHR12763.SF28.pir
@@ Line 703: / Line 711: @@
 PROTEIN_IMPORT_AND_FOLDING  IMPORT  Atp23                          PTHR21711.mag.mod    MITOCHONDRIAL_INNER_MEMBRANE_PROTEASE                                     PTHR21711.orig.30.pir
 PROTEIN_IMPORT_AND_FOLDING  IMPORT  Atp23                          PTHR21711.SF0.mod    MITOCHONDRIAL_INNER_MEMBRANE_PROTEASE_ATP23_HOMOLOG                       PTHR21711.SF0.pir
+PROTEIN_IMPORT_AND_FOLDING  IMPORT  Imp1                           PTHR12383.mag.mod    PROTEASE FAMILY S26 MITOCHONDRIAL INNER MEMBRANE PROTEASE-RELATED         PTHR12383.orig.30.pir
+PROTEIN_IMPORT_AND_FOLDING  IMPORT  Imp1                           PTHR12383.SF16.mod   MITOCHONDRIAL INNER MEMBRANE PROTEASE SUBUNIT 1                           PTHR12383.SF16.pir
+PROTEIN_IMPORT_AND_FOLDING  IMPORT  Imp1                           PTHR12383.SF32.mod   MITOCHONDRIAL INNER MEMBRANE PROTEASE SUBUNIT                             PTHR12383.SF32.pir
+PROTEIN_IMPORT_AND_FOLDING  IMPORT  Imp1                           PTHR12383.SF33.mod   MITOCHONDRIAL INNER MEMBRANE PROTEASE SUBUNIT 1                           PTHR12383.SF33.pir
+PROTEIN_IMPORT_AND_FOLDING  IMPORT  Imp2                           PTHR46041.mag.mod    MITOCHONDRIAL INNER MEMBRANE PROTEASE SUBUNIT 2                           PTHR46041.orig.30.pir
+PROTEIN_IMPORT_AND_FOLDING  IMPORT  Imp2                           PTHR46041.SF1.mod    MITOCHONDRIAL INNER MEMBRANE PROTEASE SUBUNIT 2                           PTHR46041.SF1.pir
+PROTEIN_IMPORT_AND_FOLDING  IMPORT  Imp2                           PTHR46041.SF2.mod    MITOCHONDRIAL INNER MEMBRANE PROTEASE SUBUNIT 2                           PTHR46041.SF2.pir
+PROTEIN_IMPORT_AND_FOLDING  IMPORT  Imp2                           PTHR46041.SF3.mod    MITOCHONDRIAL INNER MEMBRANE PROTEASE SUBUNIT 2                           PTHR46041.SF3.pir
+PROTEIN_IMPORT_AND_FOLDING  IMPORT  Imp2                           PTHR46041.SF4.mod    MITOCHONDRIAL INNER MEMBRANE PROTEASE SUBUNIT 2                           PTHR46041.SF4.pir
+PROTEIN_IMPORT_AND_FOLDING  IMPORT  Oxa1                           PTHR12428.mag.mod       OXA1                                                                   PTHR12428.orig.30.pir
+PROTEIN_IMPORT_AND_FOLDING  IMPORT  Oxa1                           PTHR12428.SF66.mod      MITOCHONDRIAL INNER MEMBRANE PROTEIN OXA1L                             PTHR12428.SF66.pir
+PROTEIN_IMPORT_AND_FOLDING  IMPORT  Oxa1                           PTHR12428.SF60.mod      MITOCHONDRIAL INNER MEMBRANE PROTEIN OXA1-LIKE                         PTHR12428.SF60.pir
+PROTEIN_IMPORT_AND_FOLDING  IMPORT  Oxa1                           PTHR12428.SF63.mod      MITOCHONDRIAL INNER MEMBRANE PROTEIN OXA1-2                            PTHR12428.SF63.pir
+PROTEIN_IMPORT_AND_FOLDING  IMPORT  Oxa1                           PTHR12428.SF34.mod      MITOCHONDRIAL INNER MEMBRANE PROTEIN OXA1                              PTHR12428.SF34.pir
+PROTEIN_IMPORT_AND_FOLDING  IMPORT  Oxa1                           PTHR12428.SF49.mod      OXAA/YIDC-LIKE MEMBRANE INSERTION PROTEIN                              PTHR12428.SF49.pir
+PROTEIN_IMPORT_AND_FOLDING  IMPORT  Oxa1                           PTHR12428.SF64.mod      MITOCHONDRIAL INNER MEMBRANE PROTEIN OXA1-LIKE                         PTHR12428.SF64.pir
+PROTEIN_IMPORT_AND_FOLDING  IMPORT  Mdm10                          PTHR28035.mag.mod       MITOCHONDRIAL DISTRIBUTION AND MORPHOLOGY PROTEIN 10                   PTHR28035.orig.30.pir
+PROTEIN_IMPORT_AND_FOLDING  IMPORT  Mdm10                          PTHR28035.SF1.mod       MITOCHONDRIAL DISTRIBUTION AND MORPHOLOGY PROTEIN 10                   PTHR28035.SF1.pir
 </code>
@@ Line 1009: / Line 1037: @@
 MEMBRANE_FUSION_BETWEEN_GAMETES  HAP2     hap2       PTHR31764.mag.mod  PROTEIN_HAPLESS_2                                               PTHR31764.orig.30.pir
 MEMBRANE_FUSION_BETWEEN_GAMETES  HAP2     hap2       PTHR31764.SF0.mod  HAP2-GCS1_DOMAIN-CONTAINING_PROTEIN                             PTHR31764.SF0.pir
 </code>
-==== Polyadenylation machinery ====
+==== polyA machinary====
 <code>
-POLYA_MACHINERY CPSF    CPSF1/CPSF160   PTHR10644.mag.mod       DNA REPAIR/RNA PROCESSING CPSF FAMILY
+POLYA_MACHINERY CPSF    CPSF1/CPSF160   PTHR10644.mag.mod       DNA REPAIR/RNA PROCESSING CPSF FAMILY   PTHR10644.orig.30.pir
-POLYA_MACHINERY CPSF    CPSF1/CPSF160   PTHR10644.SF2.mod       CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 1
+POLYA_MACHINERY CPSF    CPSF1/CPSF160   PTHR10644.SF2.mod       CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 1       PTHR10644.SF2.pir
-POLYA_MACHINERY CPSF    CPSF1/CPSF160   PTHR10644.SF6.mod       CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR (CPSF) A SUBUNIT PROTEIN
+POLYA_MACHINERY CPSF    CPSF1/CPSF160   PTHR10644.SF6.mod       CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR (CPSF) A SUBUNIT PROTEIN          PTHR10644.SF6.pir
-POLYA_MACHINERY CPSF    CPSF2/CPSF100   PTHR45922.mag.mod       CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 2
+POLYA_MACHINERY CPSF    CPSF2/CPSF100   PTHR45922.mag.mod       CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 2       PTHR45922.orig.30.pir
-POLYA_MACHINERY CPSF    CPSF2/CPSF100   PTHR45922.SF1.mod       CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 2
+POLYA_MACHINERY CPSF    CPSF2/CPSF100   PTHR45922.SF1.mod       CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 2       PTHR45922.SF1.pir
-POLYA_MACHINERY CPSF    CPSF3/CPSF73    PTHR11203.mag.mod       CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR FAMILY MEMBER
+POLYA_MACHINERY CPSF    CPSF3/CPSF73    PTHR11203.mag.mod       CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR FAMILY MEMBER   PTHR11203.orig.30.pir
-POLYA_MACHINERY CPSF    CPSF3/CPSF73    PTHR11203.SF11.mod      CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 3
+POLYA_MACHINERY CPSF    CPSF3/CPSF73    PTHR11203.SF11.mod      CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 3       PTHR11203.SF11.pir
-POLYA_MACHINERY CPSF    CPSF4/CPSF30    PTHR23102.mag.mod       CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 4-RELATED
+POLYA_MACHINERY CPSF    CPSF4/CPSF30    PTHR23102.mag.mod       CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 4-RELATED       PTHR23102.orig.30.pir
-POLYA_MACHINERY CPSF    CPSF4/CPSF30    PTHR23102.SF18.mod      CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 4
+POLYA_MACHINERY CPSF    CPSF4/CPSF30    PTHR23102.SF18.mod      CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 4       PTHR23102.SF18.pir
-POLYA_MACHINERY CstF    CstF1/CstF50    PTHR44133.mag.mod       CLEAVAGE STIMULATION FACTOR SUBUNIT 1
+POLYA_MACHINERY CPSF    CPSF4/CPSF30    PTHR23102.SF24.mod      CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 4       PTHR23102.SF24.pir
-POLYA_MACHINERY CstF    CstF1/CstF50    PTHR44133.SF2.mod       CLEAVAGE STIMULATION FACTOR SUBUNIT 1
+POLYA_MACHINERY CPSF    CPSF4/CPSF30    PTHR23102.SF19.mod      CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 4-LIKE PROTEIN-RELATED       PTHR23102.SF19.pir
-POLYA_MACHINERY CstF    CstF2/CstF64    PTHR45735.mag.mod       CLEAVAGE STIMULATION FACTOR SUBUNIT 2
+POLYA_MACHINERY CstF    CstF1/CstF50    PTHR44133.mag.mod       CLEAVAGE STIMULATION FACTOR SUBUNIT 1   PTHR44133.orig.30.pir
-POLYA_MACHINERY CstF    CstF2/CstF64    PTHR45735.SF6.mod       CLEAVAGE STIMULATION FACTOR SUBUNIT 2
+POLYA_MACHINERY CstF    CstF1/CstF50    PTHR44133.SF2.mod       CLEAVAGE STIMULATION FACTOR SUBUNIT 1   PTHR44133.SF2.pir
-POLYA_MACHINERY CstF    CstF3/CstF77    PTHR19980.mag.mod       RNA CLEAVAGE STIMULATION FACTOR
+POLYA_MACHINERY CstF    CstF2/CstF64    PTHR45735.mag.mod       CLEAVAGE STIMULATION FACTOR SUBUNIT 2   PTHR45735.orig.30.pir
-POLYA_MACHINERY CstF    CstF3/CstF77    PTHR19980.SF0.mod       CLEAVAGE STIMULATION FACTOR SUBUNIT 3
+POLYA_MACHINERY CstF    CstF2/CstF64    PTHR45735.SF6.mod       CLEAVAGE STIMULATION FACTOR SUBUNIT 2   PTHR45735.SF6.pir
-POLYA_MACHINERY other   Fip1    PTHR13484.mag.mod       FIP1-LIKE 1 PROTEIN
+POLYA_MACHINERY CstF    CstF3/CstF77    PTHR19980.mag.mod       RNA CLEAVAGE STIMULATION FACTOR PTHR19980.orig.30.pir
-POLYA_MACHINERY other   Fip1    PTHR13484.SF9.mod       PRE-MRNA 3'-END-PROCESSING FACTOR FIP1
+POLYA_MACHINERY CstF    CstF3/CstF77    PTHR19980.SF0.mod       CLEAVAGE STIMULATION FACTOR SUBUNIT 3   PTHR19980.SF0.pir
-POLYA_MACHINERY other   WDR33   PTHR22836.mag.mod       WD40 REPEAT PROTEIN
+POLYA_MACHINERY other   Fip1    PTHR13484.mag.mod       FIP1-LIKE 1 PROTEIN     PTHR13484.orig.30.pir
-POLYA_MACHINERY other   WDR33   PTHR22836.SF0.mod       PRE-MRNA 3' END PROCESSING PROTEIN WDR33
+POLYA_MACHINERY other   Fip1    PTHR13484.SF9.mod       PRE-MRNA 3'-END-PROCESSING FACTOR FIP1  PTHR13484.SF9.pir
+POLYA_MACHINERY other   WDR33   PTHR22836.mag.mod       WD40 REPEAT PROTEIN     PTHR22836.orig.30.pir
+POLYA_MACHINERY other   WDR33   PTHR22836.SF0.mod       PRE-MRNA 3' END PROCESSING PROTEIN WDR33        PTHR22836.SF0.pir
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