removing plotCov option - and with it a bunch of dependencies - so that groot can get back into conda. Also bumps version patch

Author: will-rowe

cmd/report.go

@@ -21,7 +21,6 @@
 package cmd
 
 import (
-	"errors"
 	"fmt"
 	"log"
 	"os"
@@ -37,7 +36,6 @@ import (
 var (
 	bamFile   *string  // a BAM file to generate report from
 	covCutoff *float64 // breadth of coverage theshold
-	plotCov   *bool    // keeps the coverage plots for each annotated gene
 	lowCov    *bool    // reports ARGs which don't have 5' or 3' coverage
 )
 
@@ -49,9 +47,7 @@ var reportCmd = &cobra.Command{
 
 	This will report gene, read count, gene length, coverage cigar to STDOUT as tab separated values.
 
-	Coverage cigar is present to help debug and indicates if the reference gene is covered (M) or not (D).
-
-	This command also prints a coverage plot for each gene (--plotCov flag)`,
+	Coverage cigar is present to help debug and indicates if the reference gene is covered (M) or not (D).`,
 	Run: func(cmd *cobra.Command, args []string) {
 		runReport()
 	},
@@ -64,7 +60,6 @@ func init() {
 	RootCmd.AddCommand(reportCmd)
 	bamFile = reportCmd.Flags().String("bamFile", "", "BAM file generated by groot alignment (will use STDIN if not provided)")
 	covCutoff = reportCmd.Flags().Float64P("covCutoff", "c", 0.97, "coverage cutoff for reporting ARGs")
-	plotCov = reportCmd.Flags().Bool("plotCov", false, "plots coverage of each reported ARG (saves to ./groot-plots/)")
 	lowCov = reportCmd.Flags().Bool("lowCov", false, "reports ARGs which don't have 5' or 3' coverage (overrides -c option)")
 }
 
@@ -118,15 +113,6 @@ func runReport() {
 	log.Printf("\tcoverage cutoff: %.2f", *covCutoff)
 	log.Printf("\tprocessors: %d", *proc)
 	bamReader := reporting.NewBAMreader()
-	if *plotCov == true {
-		bamReader.Plot = true
-		// setup the plot dir
-		if _, err := os.Stat("./groot-plots"); os.IsNotExist(err) {
-			if err := os.MkdirAll("./groot-plots", 0700); err != nil {
-				log.Fatal(errors.New("can't create a ./groot-plots directory"))
-			}
-		}
-	}
 	if *bamFile != "" {
 		bamReader.InputFile = *bamFile
 	}

docs/conf.py

@@ -32,7 +32,7 @@
 # The short X.Y version
 version = '1.0'
 # The full version, including alpha/beta/rc tags
-release = '1.0.0'
+release = '1.0.2'
 
 
 # -- General configuration ---------------------------------------------------

docs/tutorial.md

@@ -205,6 +205,8 @@ ls *.bam | parallel --gnu "groot report --bamFile {} -c 1 --plotCov > {/.}.repor
 - `-c 1` tells groot to only report ARGs that have been entirely covered by reads, I.E. a full-length,100% identity match
 - `--plotCov` tells groot to generate coverage plots for each ARG it reports
 
+> NOTE: `--plotCov` was removed after v.1.0.0 as it relied on a library that could not be packaged for conda. Hopefully I can add it back in soon.
+
 We have now generated a resistome profile for each sample, using only full-length ARG sequences (present in the ARG-ANNOT database). We can sum rural/urban resistome profiles with a little bash loop to combine reports:
 
 ```bash

docs/using-groot.md

@@ -135,4 +135,3 @@ Flags explained:
 Some more flags that can be used:
 
 - `--lowCov`: overrides `c` option and will report ARGs which may not be covered at the 5'/3' ends
-- `--plotCov`: outputs coverage plot for each ARG reported

go.mod

@@ -3,7 +3,6 @@ module github.com/will-rowe/groot
 go 1.14
 
 require (
-	github.com/adam-hanna/arrayOperations v0.2.6
 	github.com/biogo/biogo v1.0.2
 	github.com/biogo/hts v1.1.0
 	github.com/dgryski/go-minhash v0.0.0-20190315135803-ad340ca03076 // indirect
@@ -15,5 +14,4 @@ require (
 	github.com/spf13/pflag v1.0.5
 	github.com/will-rowe/gfa v0.0.0-20190502084819-05c93955478b
 	github.com/will-rowe/ntHash v0.0.0-20190624153018-541592fc7931
-	gonum.org/v1/plot v0.7.0
 )

go.sum

@@ -3,10 +3,6 @@ dmitri.shuralyov.com/gpu/mtl v0.0.0-20190408044501-666a987793e9/go.mod h1:H6x//7
 github.com/BurntSushi/toml v0.3.1/go.mod h1:xHWCNGjB5oqiDr8zfno3MHue2Ht5sIBksp03qcyfWMU=
 github.com/BurntSushi/xgb v0.0.0-20160522181843-27f122750802/go.mod h1:IVnqGOEym/WlBOVXweHU+Q+/VP0lqqI8lqeDx9IjBqo=
 github.com/OneOfOne/xxhash v1.2.2/go.mod h1:HSdplMjZKSmBqAxg5vPj2TmRDmfkzw+cTzAElWljhcU=
-github.com/adam-hanna/arrayOperations v0.2.6 h1:QZC99xC8MgUawXnav7bFMejs/dm7YySnDpMx3oZzz2Y=
-github.com/adam-hanna/arrayOperations v0.2.6/go.mod h1:iIzkSjP91FnE66cUFNAjjUJVmjyAwCH0SXnWsx2nbdk=
-github.com/ajstarks/svgo v0.0.0-20180226025133-644b8db467af h1:wVe6/Ea46ZMeNkQjjBW6xcqyQA/j5e0D6GytH95g0gQ=
-github.com/ajstarks/svgo v0.0.0-20180226025133-644b8db467af/go.mod h1:K08gAheRH3/J6wwsYMMT4xOr94bZjxIelGM0+d/wbFw=
 github.com/alecthomas/template v0.0.0-20160405071501-a0175ee3bccc/go.mod h1:LOuyumcjzFXgccqObfd/Ljyb9UuFJ6TxHnclSeseNhc=
 github.com/alecthomas/units v0.0.0-20151022065526-2efee857e7cf/go.mod h1:ybxpYRFXyAe+OPACYpWeL0wqObRcbAqCMya13uyzqw0=
 github.com/armon/consul-api v0.0.0-20180202201655-eb2c6b5be1b6/go.mod h1:grANhF5doyWs3UAsr3K4I6qtAmlQcZDesFNEHPZAzj8=
@@ -35,8 +31,6 @@ github.com/dgryski/go-minhash v0.0.0-20190315135803-ad340ca03076/go.mod h1:VBi0X
 github.com/dgryski/go-sip13 v0.0.0-20181026042036-e10d5fee7954/go.mod h1:vAd38F8PWV+bWy6jNmig1y/TA+kYO4g3RSRF0IAv0no=
 github.com/ekzhu/lshensemble v1.1.0 h1:qxuckiF7m1ARGe8zxyqmzWFgpNVAsORbatF5XIj/oYc=
 github.com/ekzhu/lshensemble v1.1.0/go.mod h1:9O+7M8zbVXy2WMyTT0zgia+rsQXrX0gB9CihuFwwRK8=
-github.com/fogleman/gg v1.3.0 h1:/7zJX8F6AaYQc57WQCyN9cAIz+4bCJGO9B+dyW29am8=
-github.com/fogleman/gg v1.3.0/go.mod h1:R/bRT+9gY/C5z7JzPU0zXsXHKM4/ayA+zqcVNZzPa1k=
 github.com/fsnotify/fsnotify v1.4.7/go.mod h1:jwhsz4b93w/PPRr/qN1Yymfu8t87LnFCMoQvtojpjFo=
 github.com/ghodss/yaml v1.0.0/go.mod h1:4dBDuWmgqj2HViK6kFavaiC9ZROes6MMH2rRYeMEF04=
 github.com/go-gl/glfw/v3.3/glfw v0.0.0-20191125211704-12ad95a8df72/go.mod h1:tQ2UAYgL5IevRw8kRxooKSPJfGvJ9fJQFa0TUsXzTg8=
@@ -46,8 +40,6 @@ github.com/go-logfmt/logfmt v0.4.0/go.mod h1:3RMwSq7FuexP4Kalkev3ejPJsZTpXXBr9+V
 github.com/go-stack/stack v1.8.0/go.mod h1:v0f6uXyyMGvRgIKkXu+yp6POWl0qKG85gN/melR3HDY=
 github.com/gogo/protobuf v1.1.1/go.mod h1:r8qH/GZQm5c6nD/R0oafs1akxWv10x8SbQlK7atdtwQ=
 github.com/gogo/protobuf v1.2.1/go.mod h1:hp+jE20tsWTFYpLwKvXlhS1hjn+gTNwPg2I6zVXpSg4=
-github.com/golang/freetype v0.0.0-20170609003504-e2365dfdc4a0 h1:DACJavvAHhabrF08vX0COfcOBJRhZ8lUbR+ZWIs0Y5g=
-github.com/golang/freetype v0.0.0-20170609003504-e2365dfdc4a0/go.mod h1:E/TSTwGwJL78qG/PmXZO1EjYhfJinVAhrmmHX6Z8B9k=
 github.com/golang/glog v0.0.0-20160126235308-23def4e6c14b/go.mod h1:SBH7ygxi8pfUlaOkMMuAQtPIUF8ecWP5IEl/CR7VP2Q=
 github.com/golang/groupcache v0.0.0-20190129154638-5b532d6fd5ef/go.mod h1:cIg4eruTrX1D+g88fzRXU5OdNfaM+9IcxsU14FzY7Hc=
 github.com/golang/mock v1.1.1/go.mod h1:oTYuIxOrZwtPieC+H1uAHpcLFnEyAGVDL/k47Jfbm0A=
@@ -69,12 +61,9 @@ github.com/grpc-ecosystem/go-grpc-middleware v1.0.0/go.mod h1:FiyG127CGDf3tlThmg
 github.com/grpc-ecosystem/go-grpc-prometheus v1.2.0/go.mod h1:8NvIoxWQoOIhqOTXgfV/d3M/q6VIi02HzZEHgUlZvzk=
 github.com/grpc-ecosystem/grpc-gateway v1.9.0/go.mod h1:vNeuVxBJEsws4ogUvrchl83t/GYV9WGTSLVdBhOQFDY=
 github.com/hashicorp/hcl v1.0.0/go.mod h1:E5yfLk+7swimpb2L/Alb/PJmXilQ/rhwaUYs4T20WEQ=
-github.com/inconshreveable/mousetrap v1.0.0 h1:Z8tu5sraLXCXIcARxBp/8cbvlwVa7Z1NHg9XEKhtSvM=
 github.com/inconshreveable/mousetrap v1.0.0/go.mod h1:PxqpIevigyE2G7u3NXJIT2ANytuPF1OarO4DADm73n8=
 github.com/jonboulle/clockwork v0.1.0/go.mod h1:Ii8DK3G1RaLaWxj9trq07+26W01tbo22gdxWY5EU2bo=
 github.com/julienschmidt/httprouter v1.2.0/go.mod h1:SYymIcj16QtmaHHD7aYtjjsJG7VTCxuUUipMqKk8s4w=
-github.com/jung-kurt/gofpdf v1.0.3-0.20190309125859-24315acbbda5 h1:PJr+ZMXIecYc1Ey2zucXdR73SMBtgjPgwa31099IMv0=
-github.com/jung-kurt/gofpdf v1.0.3-0.20190309125859-24315acbbda5/go.mod h1:7Id9E/uU8ce6rXgefFLlgrJj/GYY22cpxn+r32jIOes=
 github.com/kisielk/errcheck v1.1.0/go.mod h1:EZBBE59ingxPouuu3KfxchcWSUPOHkagtvWXihfKN4Q=
 github.com/kisielk/gotool v1.0.0/go.mod h1:XhKaO+MFFWcvkIS/tQcRk01m1F5IRFswLeQ+oQHNcck=
 github.com/konsorten/go-windows-terminal-sequences v1.0.1/go.mod h1:T0+1ngSBFLxvqU3pZ+m/2kptfBszLMUkC4ZK/EgS/cQ=
@@ -139,13 +128,9 @@ go.uber.org/zap v1.10.0/go.mod h1:vwi/ZaCAaUcBkycHslxD9B2zi4UTXhF60s6SWpuDF0Q=
 golang.org/x/crypto v0.0.0-20180904163835-0709b304e793/go.mod h1:6SG95UA2DQfeDnfUPMdvaQW0Q7yPrPDi9nlGo2tz2b4=
 golang.org/x/crypto v0.0.0-20190308221718-c2843e01d9a2/go.mod h1:djNgcEr1/C05ACkg1iLfiJU5Ep61QUkGW8qpdssI0+w=
 golang.org/x/crypto v0.0.0-20190510104115-cbcb75029529/go.mod h1:yigFU9vqHzYiE8UmvKecakEJjdnWj3jj499lnFckfCI=
-golang.org/x/exp v0.0.0-20180321215751-8460e604b9de/go.mod h1:CJ0aWSM057203Lf6IL+f9T1iT9GByDxfZKAQTCR3kQA=
-golang.org/x/exp v0.0.0-20180807140117-3d87b88a115f/go.mod h1:CJ0aWSM057203Lf6IL+f9T1iT9GByDxfZKAQTCR3kQA=
 golang.org/x/exp v0.0.0-20190306152737-a1d7652674e8/go.mod h1:CJ0aWSM057203Lf6IL+f9T1iT9GByDxfZKAQTCR3kQA=
 golang.org/x/exp v0.0.0-20200119233911-0405dc783f0a/go.mod h1:2RIsYlXP63K8oxa1u096TMicItID8zy7Y6sNkU49FU4=
-golang.org/x/image v0.0.0-20180708004352-c73c2afc3b81/go.mod h1:ux5Hcp/YLpHSI86hEcLt0YII63i6oz57MZXIpbrjZUs=
 golang.org/x/image v0.0.0-20190227222117-0694c2d4d067/go.mod h1:kZ7UVZpmo3dzQBMxlp+ypCbDeSB+sBbTgSJuh5dn5js=
-golang.org/x/image v0.0.0-20190802002840-cff245a6509b h1:+qEpEAPhDZ1o0x3tHzZTQDArnOixOzGD9HUJfcg0mb4=
 golang.org/x/image v0.0.0-20190802002840-cff245a6509b/go.mod h1:FeLwcggjj3mMvU+oOTbSwawSJRM1uh48EjtB4UJZlP0=
 golang.org/x/lint v0.0.0-20181026193005-c67002cb31c3/go.mod h1:UVdnD1Gm6xHRNCYTkRU2/jEulfH38KcIWyp/GAMgvoE=
 golang.org/x/lint v0.0.0-20190313153728-d0100b6bd8b3/go.mod h1:6SW0HCj/g11FgYtHlgUYUwCkIfeOF89ocIRzGO/8vkc=
@@ -173,15 +158,11 @@ golang.org/x/sys v0.0.0-20190412213103-97732733099d/go.mod h1:h1NjWce9XRLGQEsW7w
 golang.org/x/text v0.3.0/go.mod h1:NqM8EUOU14njkJ3fqMW+pc6Ldnwhi/IjpwHt7yyuwOQ=
 golang.org/x/time v0.0.0-20190308202827-9d24e82272b4/go.mod h1:tRJNPiyCQ0inRvYxbN9jk5I+vvW/OXSQhTDSoE431IQ=
 golang.org/x/tools v0.0.0-20180221164845-07fd8470d635/go.mod h1:n7NCudcB/nEzxVGmLbDWY5pfWTLqBcC2KZ6jyYvM4mQ=
-golang.org/x/tools v0.0.0-20180525024113-a5b4c53f6e8b/go.mod h1:n7NCudcB/nEzxVGmLbDWY5pfWTLqBcC2KZ6jyYvM4mQ=
 golang.org/x/tools v0.0.0-20190114222345-bf090417da8b/go.mod h1:n7NCudcB/nEzxVGmLbDWY5pfWTLqBcC2KZ6jyYvM4mQ=
 golang.org/x/tools v0.0.0-20190311212946-11955173bddd/go.mod h1:LCzVGOaR6xXOjkQ3onu1FJEFr0SW1gC7cKk1uF8kGRs=
 golang.org/x/tools v0.0.0-20191012152004-8de300cfc20a/go.mod h1:b+2E5dAYhXwXZwtnZ6UAqBI28+e2cm9otk0dWdXHAEo=
 golang.org/x/xerrors v0.0.0-20190717185122-a985d3407aa7/go.mod h1:I/5z698sn9Ka8TeJc9MKroUUfqBBauWjQqLJ2OPfmY0=
 golang.org/x/xerrors v0.0.0-20191204190536-9bdfabe68543/go.mod h1:I/5z698sn9Ka8TeJc9MKroUUfqBBauWjQqLJ2OPfmY0=
-gonum.org/v1/gonum v0.0.0-20180816165407-929014505bf4/go.mod h1:Y+Yx5eoAFn32cQvJDxZx5Dpnq+c3wtXuadVZAcxbbBo=
-gonum.org/v1/plot v0.7.0 h1:Otpxyvra6Ie07ft50OX5BrCfS/BWEMvhsCUHwPEJmLI=
-gonum.org/v1/plot v0.7.0/go.mod h1:2wtU6YrrdQAhAF9+MTd5tOQjrov/zF70b1i99Npjvgo=
 google.golang.org/appengine v1.1.0/go.mod h1:EbEs0AVv82hx2wNQdGPgUI5lhzA/G0D9YwlJXL52JkM=
 google.golang.org/genproto v0.0.0-20180817151627-c66870c02cf8/go.mod h1:JiN7NxoALGmiZfu7CAH4rXhgtRTLTxftemlI0sWmxmc=
 google.golang.org/grpc v1.19.0/go.mod h1:mqu4LbDTu4XGKhr4mRzUsmM4RtVoemTSY81AxZiDr8c=
@@ -201,4 +182,3 @@ gopkg.in/yaml.v2 v2.0.0-20170812160011-eb3733d160e7/go.mod h1:JAlM8MvJe8wmxCU4Bl
 gopkg.in/yaml.v2 v2.2.1/go.mod h1:hI93XBmqTisBFMUTm0b8Fm+jr3Dg1NNxqwp+5A1VGuI=
 gopkg.in/yaml.v2 v2.2.2/go.mod h1:hI93XBmqTisBFMUTm0b8Fm+jr3Dg1NNxqwp+5A1VGuI=
 honnef.co/go/tools v0.0.0-20190102054323-c2f93a96b099/go.mod h1:rf3lG4BRIbNafJWhAfAdb/ePZxsR/4RtNHQocxwk9r4=
-rsc.io/pdf v0.1.1/go.mod h1:n8OzWcQ6Sp37PL01nO98y4iUCRdTGarVfzxY20ICaU4=

src/reporting/reporting.go

@@ -6,30 +6,22 @@ import (
 	"log"
 	"os"
 	"strconv"
-	"strings"
 	"sync"
 
 	"github.com/biogo/hts/bam"
 	"github.com/biogo/hts/bgzf"
 	"github.com/biogo/hts/sam"
-
-	"gonum.org/v1/plot"
-	"gonum.org/v1/plot/plotter"
-	"gonum.org/v1/plot/plotutil"
-	"gonum.org/v1/plot/vg"
 )
 
 type annotation struct {
-	arg      string
-	count    int
-	length   int
-	coverage plotter.XYs
-	cigar    string
+	arg    string
+	count  int
+	length int
+	cigar  string
 }
 
 type BAMreader struct {
 	InputFile      string
-	Plot           bool
 	CoverageCutoff float64
 	LowCov         bool
 }
@@ -102,20 +94,25 @@ func (proc *BAMreader) Run() {
 			wg.Add(1)
 			go func(recs []*sam.Record, ref *sam.Reference, sendChan chan<- annotation) {
 				defer wg.Done()
+
 				// coverageCheck tells us if all bases in the reference have been covered by a read
 				coverageCheck := make(map[int]struct{})
+
 				// pileup contains coverage value for each base in the reference
 				pileup := make([]int, ref.Len())
+
 				// for each record, move along the alignment and update reference coverage info
 				for _, rec := range recs {
 					recStart := rec.Start()
 					recEnd := recStart + rec.Len()
+
 					// if the read goes beyond the reference, only go up to the last base of the ref
 					if recEnd > len(pileup)-1 {
 						recEnd = len(pileup) - 1
 					}
 
 					for i := recStart; i <= recEnd; i++ {
+
 						// if this is the first time the base has been covered, update coverageCheck
 						if _, ok := coverageCheck[i]; !ok {
 							coverageCheck[i] = struct{}{}
@@ -128,19 +125,19 @@ func (proc *BAMreader) Run() {
 				// check we have a fully covered reference
 				pileupCoverage := float64(len(coverageCheck)) / float64(len(pileup))
 				if pileupCoverage >= proc.CoverageCutoff {
+
 					// get the reference name (remove asterisk from cluster representative if it is present)
 					refName := ref.Name()
 					if refName[0] == 42 {
 						refName = refName[1:]
 					}
+
 					// represent pileup as a CIGAR-ish string (so can see what bases aren't covered)
 					cigar := []string{}
+
 					// plot coverage for this gene using the pileup
-					coverage := make(plotter.XYs, len(pileup))
-					for i := range coverage {
-						coverage[i].X = float64(i)
-						coverage[i].Y = float64(pileup[i])
-						if pileup[i] == 0 {
+					for _, val := range pileup {
+						if val == 0 {
 							cigar = append(cigar, "D")
 						} else {
 							cigar = append(cigar, "M")
@@ -152,11 +149,10 @@ func (proc *BAMreader) Run() {
 					}
 					// create the annotation
 					anno := annotation{
-						arg:      refName,
-						count:    len(records),
-						length:   ref.Len(),
-						coverage: coverage,
-						cigar:    cleanCigar,
+						arg:    refName,
+						count:  len(records),
+						length: ref.Len(),
+						cigar:  cleanCigar,
 					}
 					// send annotation on
 					sendChan <- anno
@@ -173,30 +169,6 @@ func (proc *BAMreader) Run() {
 	for anno := range reportChan {
 		// print info to stdout
 		fmt.Printf("%v\t%d\t%d\t%v\n", anno.arg, anno.count, anno.length, anno.cigar)
-
-		// this will clean up the ARG name so that we can use it as a filename
-		var replacer = strings.NewReplacer("/", "__", "\t", "__")
-
-		// plot coverage for this gene
-		if proc.Plot == true {
-			covPlot, err := plot.New()
-			if err != nil {
-				panic(err)
-			}
-			covPlot.Title.Text = "coverage plot"
-			covPlot.X.Label.Text = "position in gene"
-			covPlot.Y.Label.Text = "coverage (number of reads at position)"
-			err = plotutil.AddLinePoints(covPlot, anno.arg, anno.coverage)
-			if err != nil {
-				panic(err)
-			}
-			// clean the ARG name
-			anno.arg = replacer.Replace(anno.arg)
-			fileName := fmt.Sprintf("./groot-plots/coverage-for-%v.png", anno.arg)
-			if err := covPlot.Save(8*vg.Inch, 8*vg.Inch, fileName); err != nil {
-				panic(err)
-			}
-		}
 	}
 }
 

src/version/version.go

@@ -9,9 +9,9 @@ const major = 1
 const minor = 0
 
 // patch is the patch version number
-const patch = 1
+const patch = 2
 
-// GetVersion() returns the full version string for the current GROOT software
+// GetVersion returns the full version string for the current GROOT software
 func GetVersion() string {
 	return fmt.Sprintf("%d.%d.%d", major, minor, patch)
 }