readme.renumf90
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| readme.renumf90 [2012/05/29 11:42] – ignacio | readme.renumf90 [2012/05/29 12:09] – [Fields in the parameter file] ignacio | ||
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| Line 25: | Line 25: | ||
| The parameter file contains keywords in capital followed by specifications | The parameter file contains keywords in capital followed by specifications | ||
| - | of a given effect/data item. The keywords need to be typed exactly. Specific | + | of a given effect/data item.\\ The keywords need to be typed exactly.\\ Specific |
| keywords need to occur sequentially, | keywords need to occur sequentially, | ||
| Line 42: | Line 42: | ||
| Lines with # are treated as comments | Lines with # are treated as comments | ||
| | | ||
| - | < | + | < |
| DATAFILE | DATAFILE | ||
| f1 | f1 | ||
| Line 48: | Line 48: | ||
| The data file is f1 | The data file is f1 | ||
| - | < | + | < |
| TRAITS | TRAITS | ||
| t1 t2 .. tn | t1 t2 .. tn | ||
| Line 57: | Line 57: | ||
| FIELDS_PASSED TO OUTPUT | FIELDS_PASSED TO OUTPUT | ||
| p1 p2 .. pm | p1 p2 .. pm | ||
| - | < | + | </file> |
| fields p1-pn are passed to output without changes; can be empty | fields p1-pn are passed to output without changes; can be empty | ||
| Line 66: | Line 66: | ||
| w is position of weight if present; can be empty | w is position of weight if present; can be empty | ||
| - | < | + | < |
| RESIDUAL_VARIANCE | RESIDUAL_VARIANCE | ||
| r | r | ||
| Line 97: | Line 97: | ||
| rtype is ' | rtype is ' | ||
| - | < | + | < |
| OPTIONAL | OPTIONAL | ||
| o1 o2.. oq | o1 o2.. oq | ||
| - | < | + | </file> |
| causes extra effects appended to the animal effect; current options include | causes extra effects appended to the animal effect; current options include | ||
| ' | ' | ||
| permanent environment | permanent environment | ||
| - | < | + | < |
| FILE | FILE | ||
| fped | fped | ||
| Line 125: | Line 125: | ||
| dam. | dam. | ||
| - | < | + | < |
| SNP_FILE | SNP_FILE | ||
| fsnp | fsnp | ||
| Line 136: | Line 136: | ||
| include digits 0, 1, 2 and 5; ID and SNP info need to be separated by | include digits 0, 1, 2 and 5; ID and SNP info need to be separated by | ||
| at leats one space; see info for program PreGSf90 | at leats one space; see info for program PreGSf90 | ||
| - | < | + | |
| + | < | ||
| PED_DEPTH | PED_DEPTH | ||
| p | p | ||
| Line 144: | Line 145: | ||
| the default is 3; all pedigrees are loaded if p=0. | the default is 3; all pedigrees are loaded if p=0. | ||
| - | < | + | < |
| GEN_INT | GEN_INT | ||
| min avg max | min avg max | ||
| Line 153: | Line 154: | ||
| pedigree. | pedigree. | ||
| - | < | + | < |
| REC_SEX | REC_SEX | ||
| i | i | ||
| Line 160: | Line 161: | ||
| pedigree checks. | pedigree checks. | ||
| - | < | + | < |
| UPG_TYPE | UPG_TYPE | ||
| t | t | ||
| Line 176: | Line 177: | ||
| custom_upg(year_of_birth, | custom_upg(year_of_birth, | ||
| - | < | + | < |
| RANDOM_REGRESSION | RANDOM_REGRESSION | ||
| r_type | r_type | ||
| Line 186: | Line 187: | ||
| to be generated from a single data variable; not yet implemented | to be generated from a single data variable; not yet implemented | ||
| - | < | + | < |
| RR_POSITION | RR_POSITION | ||
| r1 .. rq | r1 .. rq | ||
| Line 195: | Line 196: | ||
| </ | </ | ||
| - | < | + | < |
| (CO)VARIANCES | (CO)VARIANCES | ||
| g | g | ||
| Line 203: | Line 204: | ||
| account for the maternal effect if present | account for the maternal effect if present | ||
| - | < | + | < |
| (CO)VARIANCES_PE | (CO)VARIANCES_PE | ||
| gpe | gpe | ||
| Line 209: | Line 210: | ||
| //gpe// are (co)variances for the PE effect if present | //gpe// are (co)variances for the PE effect if present | ||
| - | < | + | < |
| (CO)VARIANCES_MPE | (CO)VARIANCES_MPE | ||
| gmpe | gmpe | ||
| Line 215: | Line 216: | ||
| //gmpe// are (co)variances for the MPE effect if present | //gmpe// are (co)variances for the MPE effect if present | ||
| + | |||
| + | ---- | ||
| Sections starting from EFFECTS can be repeated any number of types. | Sections starting from EFFECTS can be repeated any number of types. | ||
| Line 227: | Line 230: | ||
| skipped. Keywords out of order may not be recognized. | skipped. Keywords out of order may not be recognized. | ||
| + | =====OPTIONS===== | ||
| The following options can added at the end of the parameter file to redefine | The following options can added at the end of the parameter file to redefine | ||
| parameter used to read the input file: | parameter used to read the input file: | ||
| - the default size of character fields | - the default size of character fields | ||
| + | < | ||
| OPTION alpha size nn | OPTION alpha size nn | ||
| + | </ | ||
| where nn is the new size. | where nn is the new size. | ||
| - the size of th record length | - the size of th record length | ||
| + | < | ||
| OPTION max_string_readline nn | OPTION max_string_readline nn | ||
| + | </ | ||
| where nn is the new size. | where nn is the new size. | ||
| - the maximun number of fields | - the maximun number of fields | ||
| + | < | ||
| OPTION max_field_readline nn | OPTION max_field_readline nn | ||
| + | </ | ||
| where nn is the number of fields. | where nn is the number of fields. | ||
| Line 248: | Line 258: | ||
| - | Combining fields or interactions | + | =====Combining fields or interactions====== |
| - | ================================ | + | |
| Several fields in the data file can be combined into one using a COMBINE keyword. | Several fields in the data file can be combined into one using a COMBINE keyword. | ||
| - | COMBINE a b c .... | + | < |
| + | COMBINE a b c .... | ||
| + | </ | ||
| catenates b c ... into c. Keywords COMBINE need to be on top of the parameter | catenates b c ... into c. Keywords COMBINE need to be on top of the parameter | ||
| file, but possibly after comments. There may be many combined fields. | file, but possibly after comments. There may be many combined fields. | ||
| For example: | For example: | ||
| - | COMBINE 7 2 3 4 | + | </ |
| + | COMBINE 7 2 3 4 | ||
| + | </ | ||
| combines content of fields 2 3 4 into field 7; the data file is not changed, | combines content of fields 2 3 4 into field 7; the data file is not changed, | ||
| only the program treats field 7 as fields 2 3 4 put together (without spaces). | only the program treats field 7 as fields 2 3 4 put together (without spaces). | ||
| Line 265: | Line 278: | ||
| - | Additive Pedigree File | + | =====Additive Pedigree File====== |
| - | ====================== | + | |
| The additive pedigree file(s) renadd* has the following structure: | The additive pedigree file(s) renadd* has the following structure: | ||
| Line 285: | Line 297: | ||
| - | Extensions | + | =====Extensions======= |
| - | ========== | + | |
| The program is being modified to support inbreeding, dominance, random | The program is being modified to support inbreeding, dominance, random | ||
| Line 292: | Line 303: | ||
| - | Example | + | =====Example====== |
| - | ======== | + | |
| - | data file - data.test | + | |
| - | --------------------- | + | **__data file__** |
| + | |||
| + | < | ||
| 1 aa 34.5 11 12 zz | 1 aa 34.5 11 12 zz | ||
| 3 bb 21.333 22 23 xx | 3 bb 21.333 22 23 xx | ||
| Line 303: | Line 315: | ||
| 3 aa 30 55 56 yy | 3 aa 30 55 56 yy | ||
| 5 bb 1234567.890 66 67 zz | 5 bb 1234567.890 66 67 zz | ||
| + | </ | ||
| - | pedigree file - test.ped | + | |
| - | ------------------------ | + | **__pedigree file__** |
| + | < | ||
| qq 0 0 | qq 0 0 | ||
| aa 0 0 | aa 0 0 | ||
| Line 311: | Line 325: | ||
| cc qq 0 | cc qq 0 | ||
| dd 0 aa | dd 0 aa | ||
| + | </ | ||
| - | parameter file - testpar1 | + | |
| - | ------------------------- | + | **__parameter file__** |
| + | < | ||
| # Parameter file for program renf90; it is translated to parameter | # Parameter file for program renf90; it is translated to parameter | ||
| # file for BLUPF90 family f programs. | # file for BLUPF90 family f programs. | ||
| Line 356: | Line 372: | ||
| RANDOM | RANDOM | ||
| diagonal | diagonal | ||
| + | </ | ||
| - | + | **__printout__** \\ | |
| - | printout | + | \\ |
| - | ------------------------------------------------------ | + | (temporary; the amount of details may change) |
| + | < | ||
| | | ||
| name of parameter file? testpar1 | name of parameter file? testpar1 | ||
| Line 448: | Line 466: | ||
| Wrote parameter file " | Wrote parameter file " | ||
| Wrote renumbered data " | Wrote renumbered data " | ||
| + | </ | ||
| - | + | **__new | |
| - | new parameter | + | < |
| - | ------------------------------- | + | |
| # BLUPF90 parameter file created by RENF90 | # BLUPF90 parameter file created by RENF90 | ||
| DATAFILE | DATAFILE | ||
| Line 512: | Line 530: | ||
| | | ||
| 0.1000 | 0.1000 | ||
| + | </ | ||
| - | data file - renf90.dat | + | **__data file__** |
| - | ---------------------- | + | < |
| 34.5 11 1 3 5 12 1 3 aa 1 | 34.5 11 1 3 5 12 1 3 aa 1 | ||
| | | ||
| Line 523: | Line 542: | ||
| 30 55 2 3 5 56 2 2 aa 3 | 30 55 2 3 5 56 2 2 aa 3 | ||
| | | ||
| + | </ | ||
| - | | + | |
| - | -------------------------------------------------------- | + | **__Pedigree file__** |
| + | < | ||
| 1 6 3 1 0 2 2 0 0 bb | 1 6 3 1 0 2 2 0 0 bb | ||
| 6 0 0 1 0 0 0 2 0 qq | 6 0 0 1 0 0 0 2 0 qq | ||
| Line 534: | Line 554: | ||
| 3 0 5 1 0 1 2 0 2 aa | 3 0 5 1 0 1 2 0 2 aa | ||
| 4 6 7 1 0 2 1 0 0 cc | 4 6 7 1 0 2 1 0 0 cc | ||
| + | </ | ||
| - | renumbering tables - renf90.tables | + | **'' |
| - | ---------------------------------- | + | < |
| | | ||
| | | ||
readme.renumf90.txt · Last modified: 2024/05/22 18:53 by dani