initial commit

.gitignore

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+_STARtmp
+Log.out
+.*/Log.out
+*.log
+_download
+vendor
+.DS_Store
+go.sum
+_log

LICENSE

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+Copyright (c) 2019 Jianfeng Li
+
+Licensed under the Academic Free License version 3.0
+
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+
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+    Rosen. Permission is granted to copy, distribute, or communicate this 
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+    modify this License as applied to the Original Work or to Derivative 
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+    distribute or communicate your modified version (the "Modified 
+    License") and apply it to other original works of authorship subject to 
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+    notice "Licensed under <insert your license name here>" or with a notice 
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+Other images and documentation are licensed under the Creative Commons Attribution 3.0 (CC BY 3.0) License.   See 
+
+http://creativecommons.org/licenses/by/3.0/

Makefile

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+install:
+	go install .
+

README.md

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+<img src="https://img.shields.io/badge/lifecycle-experimental-orange.svg" alt="Life cycle: experimental"> <a href="https://godoc.org/github.com/openbiox/bioextr"><img src="https://godoc.org/github.com/openbiox/bioextr?status.svg" alt="GoDoc"></a>
+
+## bioextr
+
+[bioextr](https://github.com/openbiox/bioextr) is a simple command line tool to extract information from text or json files.
+
+## Installation
+
+```bash
+# windows
+wget https://github.com/openbiox/bioextr/releases/download/v0.1.0/bioextr.exe
+
+# osx
+wget https://github.com/openbiox/bioextr/releases/download/v0.1.0/bioextr_osx
+mv bioextr_osx bioextr
+chmod a+x bioextr
+
+# linux
+wget https://github.com/openbiox/bioextr/releases/download/v0.1.0/bioextr_linux64
+mv bioextr_linux64 bioextr
+chmod a+x bioextr
+
+# get latest version
+go get -u github.com/openbiox/bioextr
+```
+
+## Usage
+
+### Text mining
+
+- support calculate correlations between any keywords at the sentence level (PubMed)
+- support extract URLs from PubMed and SRA abstract
+
+## Maintainer
+
+- [@Jianfeng](https://github.com/Miachol)
+
+## License
+
+Academic Free License version 3.0
+

cmd/parse.go

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+package cmd
+
+import (
+	"bufio"
+	"encoding/json"
+	"fmt"
+	"io/ioutil"
+	"os"
+	"strings"
+	"sync"
+
+	"github.com/openbiox/ligo/extract"
+	"github.com/openbiox/ligo/flag"
+	"github.com/openbiox/ligo/parse"
+	"github.com/spf13/cobra"
+)
+
+var stdin []byte
+var sraFields []*extract.SraFields
+var pubMedFields []*extract.PubmedFields
+
+func parseStdin(cmd *cobra.Command) []string {
+	cleanArgs := []string{}
+	var err error
+	hasStdin := false
+	if cleanArgs, hasStdin = flag.CheckStdInFlag(cmd); hasStdin {
+		reader := bufio.NewReader(os.Stdin)
+		stdin, err = ioutil.ReadAll(reader)
+		if err != nil {
+			log.Fatal(err)
+		}
+	}
+	return cleanArgs
+}
+
+func simpleExtr(cmd *cobra.Command, args []string) {
+	cleanArgs := parseStdin(cmd)
+	var wg sync.WaitGroup
+	sem := make(chan struct{}, RootClis.Thread)
+
+	if len(stdin) > 0 {
+		wg.Add(1)
+		go func() {
+			defer wg.Done()
+			sem <- struct{}{}        // 获取信号
+			defer func() { <-sem }() // 释放信号
+			parseJSON(stdin)
+		}()
+		RootClis.HelpFlags = false
+	}
+	if len(cleanArgs) > 0 {
+		for _, v := range cleanArgs {
+			wg.Add(1)
+			go func(v string) {
+				defer wg.Done()
+				sem <- struct{}{} // 获取信号
+				var input []byte
+				var con *os.File
+				var err error
+				if con, err = os.Open(v); err != nil {
+					log.Warnln(err)
+					return
+				}
+				if input, err = ioutil.ReadAll(con); err != nil {
+					log.Warnln(err)
+					return
+				}
+				parseJSON(input)
+				defer func() { <-sem }() // 释放信号
+			}(v)
+		}
+		RootClis.HelpFlags = false
+	}
+	wg.Wait()
+}
+
+func parseJSON(dat []byte) {
+	var pubmedJson []parse.PubmedArticleJSON
+	var sraJson []parse.ExperimentPkgJSON
+	keyWords := []string{}
+	if strings.Contains(RootClis.Keywords, " ,") {
+		keyWords = strings.Split(RootClis.Keywords, " ,")
+	} else {
+		keyWords = strings.Split(RootClis.Keywords, ",")
+	}
+	if RootClis.Mode == "pubmed" && len(dat) > 0 {
+		json.Unmarshal(stdin, &pubmedJson)
+		for _, v := range pubmedJson {
+			pubMedFields = append(pubMedFields, extract.GetSimplePubmedFields(&keyWords, &v, RootClis.CallCor))
+		}
+		dat, _ := json.MarshalIndent(pubMedFields, "", "    ")
+		fmt.Println(string(dat))
+	} else if RootClis.Mode == "sra" && len(dat) > 0 {
+		json.Unmarshal(stdin, &sraJson)
+		done := make(map[string]int)
+		for _, v := range sraJson {
+			sraFields = append(sraFields, extract.GetSimpleSraFields(&keyWords, &v, RootClis.CallCor, done))
+			done[v.EXPERIMENT.TITLE+v.STUDY.DESCRIPTOR.STUDYTITLE] = 1
+		}
+		dat, _ := json.MarshalIndent(sraFields, "", "    ")
+		fmt.Println(string(dat))
+	}
+}
+
+func init() {
+	RootCmd.Flags().StringVarP(&RootClis.Keywords, "keywords", "w", "algorithm, tool, model, pipleline, method, database, workflow, dataset, bioinformatics, sequencing, http, github.com, gitlab.com, bitbucket.org", "Keywords to extracted from abstract.")
+	RootCmd.Flags().BoolVarP(&RootClis.CallCor, "call-cor", "", false, "Wheather to calculate the corelated keywords, and return the sentence contains >=2 keywords.")
+	RootCmd.Flags().StringVarP(&RootClis.Mode, "mode", "", "", "mode to extract information (pubmed, sra).")
+}