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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,225 @@ | ||
| // Copyright © 2016 Wei Shen <shenwei356@gmail.com> | ||
| // | ||
| // Permission is hereby granted, free of charge, to any person obtaining a copy | ||
| // of this software and associated documentation files (the "Software"), to deal | ||
| // in the Software without restriction, including without limitation the rights | ||
| // to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | ||
| // copies of the Software, and to permit persons to whom the Software is | ||
| // furnished to do so, subject to the following conditions: | ||
| // | ||
| // The above copyright notice and this permission notice shall be included in | ||
| // all copies or substantial portions of the Software. | ||
| // | ||
| // THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | ||
| // IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | ||
| // FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | ||
| // AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | ||
| // LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | ||
| // OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN | ||
| // THE SOFTWARE. | ||
|
|
||
| package cmd | ||
|
|
||
| import ( | ||
| "fmt" | ||
| "regexp" | ||
| "runtime" | ||
| "strconv" | ||
| "sort" | ||
|
|
||
| "github.com/brentp/xopen" | ||
| "github.com/spf13/cobra" | ||
| "github.com/gonum/floats" | ||
| "github.com/tatsushid/go-prettytable" | ||
| "github.com/dustin/go-humanize" | ||
| "github.com/gonum/stat" | ||
| "github.com/shenwei356/util/math" | ||
| ) | ||
|
|
||
| // stat2Cmd represents the seq command | ||
| var stat2Cmd = &cobra.Command{ | ||
| Use: "stat2", | ||
| Short: "summary of selected number fields", | ||
| Long: `summary of selected number fields: num, sum, min, max, mean, stdev | ||
| `, | ||
| Run: func(cmd *cobra.Command, args []string) { | ||
| config := getConfigs(cmd) | ||
| files := getFileList(args) | ||
| if len(files) > 1 { | ||
| checkError(fmt.Errorf("no more than one file should be given")) | ||
| } | ||
| runtime.GOMAXPROCS(config.NumCPUs) | ||
|
|
||
| fieldStr := getFlagString(cmd, "fields") | ||
| if fieldStr == "" { | ||
| checkError(fmt.Errorf("flag -f (--field) needed")) | ||
| } | ||
|
|
||
| fuzzyFields := getFlagBool(cmd, "fuzzy-fields") | ||
| fields, colnames, negativeFields, needParseHeaderRow := parseFields(cmd, fieldStr, config.NoHeaderRow) | ||
| var fieldsMap map[int]struct{} | ||
| if len(fields) > 0 { | ||
| fields2 := make([]int, len(fields)) | ||
| fieldsMap = make(map[int]struct{}, len(fields)) | ||
| for i, f := range fields { | ||
| if negativeFields { | ||
| fieldsMap[f*-1] = struct{}{} | ||
| fields2[i] = f * -1 | ||
| } else { | ||
| fieldsMap[f] = struct{}{} | ||
| fields2[i] = f | ||
| } | ||
| } | ||
| fields = fields2 | ||
| } | ||
|
|
||
| outfh, err := xopen.Wopen(config.OutFile) | ||
| checkError(err) | ||
| defer outfh.Close() | ||
|
|
||
|
|
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| file := files[0] | ||
| csvReader, err := newCSVReaderByConfig(config, file) | ||
| checkError(err) | ||
| csvReader.Run() | ||
|
|
||
| parseHeaderRow := needParseHeaderRow // parsing header row | ||
| var colnames2fileds map[string]int // column name -> field | ||
| var colnamesMap map[string]*regexp.Regexp | ||
| var HeaderRow []string | ||
| var isHeaderRow bool | ||
|
|
||
| checkFields := true | ||
|
|
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| data := make(map[int][]float64) | ||
|
|
||
| for chunk := range csvReader.Ch { | ||
| checkError(chunk.Err) | ||
|
|
||
| for _, record := range chunk.Data { | ||
| if parseHeaderRow { // parsing header row | ||
| colnames2fileds = make(map[string]int, len(record)) | ||
| for i, col := range record { | ||
| colnames2fileds[col] = i + 1 | ||
| } | ||
| colnamesMap = make(map[string]*regexp.Regexp, len(colnames)) | ||
| for _, col := range colnames { | ||
| if negativeFields { | ||
| colnamesMap[col[1:]] = fuzzyField2Regexp(col) | ||
| } else { | ||
| colnamesMap[col] = fuzzyField2Regexp(col) | ||
| } | ||
| } | ||
|
|
||
| if len(fields) == 0 { // user gives the colnames | ||
| fields = []int{} | ||
| for _, col := range record { | ||
| var ok bool | ||
| if fuzzyFields { | ||
| for _, re := range colnamesMap { | ||
| if re.MatchString(col) { | ||
| ok = true | ||
| break | ||
| } | ||
| } | ||
| } else { | ||
| _, ok = colnamesMap[col] | ||
| } | ||
| if (negativeFields && !ok) || (!negativeFields && ok) { | ||
| fields = append(fields, colnames2fileds[col]) | ||
| } | ||
| } | ||
| } | ||
|
|
||
| fieldsMap = make(map[int]struct{}, len(fields)) | ||
| for _, f := range fields { | ||
| fieldsMap[f] = struct{}{} | ||
| } | ||
|
|
||
| HeaderRow = record | ||
| parseHeaderRow = false | ||
| isHeaderRow = true | ||
| } | ||
| if checkFields { | ||
| fields2 := []int{} | ||
| for f := range record { | ||
| _, ok := fieldsMap[f+1] | ||
| if negativeFields { | ||
| if !ok { | ||
| fields2 = append(fields2, f+1) | ||
| } | ||
| } else { | ||
| if ok { | ||
| fields2 = append(fields2, f+1) | ||
| } | ||
| } | ||
| } | ||
| fields = fields2 | ||
| if len(fields) == 0 { | ||
| checkError(fmt.Errorf("no fields matched in file: %s", file)) | ||
| } | ||
|
|
||
| checkFields = false | ||
| } | ||
|
|
||
| if isHeaderRow { | ||
| isHeaderRow = false | ||
| continue | ||
| } | ||
| for _, f := range fields { | ||
| if !reDigitals.MatchString(record[f-1]) { | ||
| checkError(fmt.Errorf("column %d has non-number data: %s", f, record[f-1])) | ||
| } | ||
| v, e := strconv.ParseFloat(removeComma(record[f-1]), 64) | ||
| checkError(e) | ||
| if _, ok := data[f]; !ok { | ||
| data[f] = []float64{} | ||
| } | ||
| data[f] = append(data[f], v) | ||
| } | ||
| } | ||
| } | ||
| tbl, err := prettytable.NewTable([]prettytable.Column{ | ||
| {Header: "field"}, | ||
| {Header: "num", AlignRight: true}, | ||
| {Header: "sum", AlignRight: true}, | ||
| {Header: "min", AlignRight: true}, | ||
| {Header: "max", AlignRight: true}, | ||
| {Header: "mean", AlignRight: true}, | ||
| {Header: "stdev", AlignRight: true}}...) | ||
| checkError(err) | ||
| tbl.Separator = " " | ||
|
|
||
| fields = []int{} | ||
| for f := range data { | ||
| fields = append(fields, f) | ||
| } | ||
| sort.Ints(fields) | ||
|
|
||
| var fieldS string | ||
| for _, f := range fields { | ||
| if needParseHeaderRow { | ||
| fieldS = HeaderRow[f-1] | ||
| } else { | ||
| fieldS = fmt.Sprintf("%d", f) | ||
| } | ||
| mean, stdev := stat.MeanStdDev(data[f], nil) | ||
| tbl.AddRow( | ||
| fieldS, | ||
| humanize.Comma(int64(len(data[f]))), | ||
| humanize.Commaf(math.Round(floats.Sum(data[f]),2)), | ||
| humanize.Commaf(math.Round(floats.Min(data[f]),2)), | ||
| humanize.Commaf(math.Round(floats.Max(data[f]),2)), | ||
| humanize.Commaf(math.Round(mean,2)), | ||
| humanize.Commaf(math.Round(stdev,2))) | ||
| } | ||
| outfh.Write(tbl.Bytes()) | ||
| }, | ||
| } | ||
|
|
||
| func init() { | ||
| RootCmd.AddCommand(stat2Cmd) | ||
| stat2Cmd.Flags().StringP("fields", "f", "", `select only these fields. e.g -f 1,2 or -f columnA,columnB`) | ||
| stat2Cmd.Flags().BoolP("fuzzy-fields", "F", false, `using fuzzy fields, e.g. *name or id123*`) | ||
| } |
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