fix fragment based design

README.md

@@ -35,7 +35,7 @@ See [the docs](https://jjtimmons.github.io/repp/) or use `--help` on any command
 
 To design a plasmid based on its expected sequence save it to a FASTA or Genbank file. For example:
 
-```
+```txt
 >2ndVal_mScarlet-I
 CAACCTTACCAGAGGGCGCCCCAGCTGGCAATTCCGACGTCTAAGAAACCATTATTATCA...
 ```
@@ -46,6 +46,31 @@ Then call `repp make sequence` to design it. The following example uses Addgene
 repp make sequence --in "./2ndVal_mScarlet-I.fa" --addgene --dbs "parts_library.fa"
 ```
 
+### Features
+
+To design a plasmid based on the features it should contain, specify the features by name. By default, these should refer to features that are in REPP's feature database (`~/.repp/features.tsv`). Features can also refer to fragments, as in the following example where a plasmid is specified by its constituent list of iGEM parts:
+
+```bash
+repp make features "BBa_R0062,BBa_B0034,BBa_C0040,BBa_B0010,BBa_B0012" --backbone pSB1C3 --enzymes "EcoRI,PstI" --igem
+```
+
+### Fragments
+
+To design a plasmid from its constiuent fragments, save them to a multi-FASTA.
+
+```txt
+>GFP
+ATGAGTAAAGGAGAAGAACTTTTCACTGGAGTTGTCCCAATTCTTGTTGAATTAGATGG...
+>backbone
+TACTAGTAGCGGCCGCTGCAGTCCGGCAAAAAAGGGCAAGGTGTCACCACCCTGCCCTT...
+```
+
+And call the file from `repp make fragments`:
+
+```bash
+repp make fragments --in "./fragments.fa" --out "plasmid.json"
+```
+
 ### Databases
 
 `REPP` includes three embedded databases from large public repositories: [Addgene](https://www.addgene.org/), [iGEM](http://parts.igem.org/Main_Page), and [DNASU](https://dnasu.org/DNASU/Home.do). Each embedded database and its file path after installation are as follows:

internal/repp/fragments.go

@@ -33,7 +33,6 @@ func FragmentsCmd(cmd *cobra.Command, args []string) {
 	flags, conf := parseCmdFlags(cmd, args, true)
 
 	// read in the constituent fragments
-	var frags []*Frag
 	frags, err := read(flags.in, false)
 	if err != nil {
 		stderr.Fatalln(err)
@@ -44,12 +43,17 @@ func FragmentsCmd(cmd *cobra.Command, args []string) {
 		frags = append([]*Frag{flags.backbone}, frags...)
 	}
 
+	// set the conf property on each frag
+	for _, f := range frags {
+		f.conf = conf
+	}
+
 	target, solution := fragments(frags, conf)
 
 	// write the single list of fragments as a possible solution to the output file
 	writeJSON(
 		flags.out,
-		target.ID,
+		flags.in,
 		target.Seq,
 		[][]*Frag{solution},
 		len(target.Seq),

internal/repp/input.go

@@ -88,13 +88,14 @@ func NewFlags(
 // parseCmdFlags gathers the in path, out path, etc from a cobra cmd object
 // returns Flags and a Config struct for repp.Plasmid or repp.Fragments.
 func parseCmdFlags(cmd *cobra.Command, args []string, strict bool) (*Flags, *config.Config) {
+	cmdName := strings.ToLower(cmd.Name())
+
 	var err error
 	fs := &Flags{} // parsed flags
 	p := inputParser{}
 	c := config.New()
 
 	if fs.in, err = cmd.Flags().GetString("in"); fs.in == "" || err != nil {
-		cmdName := strings.ToLower(cmd.Name())
 		if cmdName == "features" {
 			fs.in = p.parseFeatureInput(args)
 		} else if cmdName == "sequence" && len(args) > 0 {
@@ -143,7 +144,7 @@ func parseCmdFlags(cmd *cobra.Command, args []string, strict bool) (*Flags, *con
 	}
 
 	filters, err := cmd.Flags().GetString("exclude")
-	if strict && err != nil {
+	if strict && err != nil && cmdName != "fragments" {
 		cmd.Help()
 		stderr.Fatalf("failed to parse filters: %v", err)
 	}

test/input/fragments.fa

@@ -0,0 +1,4 @@
+>gfp
+ATGAGTAAAGGAGAAGAACTTTTCACTGGAGTTGTCCCAATTCTTGTTGAATTAGATGGTGATGTTAATGGGCACAAATTTTCTGTCAGTGGAGAGGGTGAAGGTGATGCAACATACGGAAAACTTACCCTTAAATTTATTTGCACTACTGGAAAACTACCTGTTCCATGGCCAACACTTGTCACTACTTTCTCTTATGGTGTTCAATGCTTTTCAAGATACCCAGATCATATGAAACGGCATGACTTTTTCAAGAGTGCCATGCCCGAAGGTTATGTACAGGAAAGAACTATATTTTTCAAAGATGACGGGAACTACAAGACACGTGCTGAAGTCAAGTTTGAAGGTGATACCCTTGTTAATAGAATCGAGTTAAAAGGTATTGATTTTAAAGAAGATGGAAACATTCTTGGACACAAATTGGAATACAACTATAACTCACACAATGTATACATCATGGCAGACAAACAAAAGAATGGAATCAAAGTTAACTTCAAAATTAGACACAACATTGAAGATGGAAGCGTTCAACTAGCAGACCATTATCAACAAAATACTCCAATTGGCGATGGCCCTGTCCTTTTACCAGACAACCATTACCTGTCCACACAATCTGCCCTTTCGAAAGATCCCAACGAAAAGAGAGACCACATGGTCCTTCTTGAGTTTGTAACAGCTGCTGGGATTACACATGGCATGGATGAACTATACAAATAG
+>backbone
+TACTAGTAGCGGCCGCTGCAGTCCGGCAAAAAAGGGCAAGGTGTCACCACCCTGCCCTTTTTCTTTAAAACCGAAAAGATTACTTCGCGTTATGCAGGCTTCCTCGCTCACTGACTCGCTGCGCTCGGTCGTTCGGCTGCGGCGAGCGGTATCAGCTCACTCAAAGGCGGTAATACGGTTATCCACAGAATCAGGGGATAACGCAGGAAAGAACATGTGAGCAAAAGGCCAGCAAAAGGCCAGGAACCGTAAAAAGGCCGCGTTGCTGGCGTTTTTCCACAGGCTCCGCCCCCCTGACGAGCATCACAAAAATCGACGCTCAAGTCAGAGGTGGCGAAACCCGACAGGACTATAAAGATACCAGGCGTTTCCCCCTGGAAGCTCCCTCGTGCGCTCTCCTGTTCCGACCCTGCCGCTTACCGGATACCTGTCCGCCTTTCTCCCTTCGGGAAGCGTGGCGCTTTCTCATAGCTCACGCTGTAGGTATCTCAGTTCGGTGTAGGTCGTTCGCTCCAAGCTGGGCTGTGTGCACGAACCCCCCGTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCAACCCGGTAAGACACGACTTATCGCCACTGGCAGCAGCCACTGGTAACAGGATTAGCAGAGCGAGGTATGTAGGCGGTGCTACAGAGTTCTTGAAGTGGTGGCCTAACTACGGCTACACTAGAAGAACAGTATTTGGTATCTGCGCTCTGCTGAAGCCAGTTACCTTCGGAAAAAGAGTTGGTAGCTCTTGATCCGGCAAACAAACCACCGCTGGTAGCGGTGGTTTTTTTGTTTGCAAGCAGCAGATTACGCGCAGAAAAAAAGGATCTCAAGAAGATCCTTTGATCTTTTCTACGGGGTCTGACGCTCAGTGGAACGAAAACTCACGTTAAGGGATTTTGGTCATGAGATTATCAAAAAGGATCTTCACCTAGATCCTTTTAAATTAAAAATGAAGTTTTAAATCAATCTAAAGTATATATGAGTAAACTTGGTCTGACAGCTCGAGGCTTGGATTCTCACCAATAAAAAACGCCCGGCGGCAACCGAGCGTTCTGAACAAATCCAGATGGAGTTCTGAGGTCATTACTGGATCTATCAACAGGAGTCCAAGCGAGCTCGATATCAAATTACGCCCCGCCCTGCCACTCATCGCAGTACTGTTGTAATTCATTAAGCATTCTGCCGACATGGAAGCCATCACAAACGGCATGATGAACCTGAATCGCCAGCGGCATCAGCACCTTGTCGCCTTGCGTATAATATTTGCCCATGGTGAAAACGGGGGCGAAGAAGTTGTCCATATTGGCCACGTTTAAATCAAAACTGGTGAAACTCACCCAGGGATTGGCTGAGACGAAAAACATATTCTCAATAAACCCTTTAGGGAAATAGGCCAGGTTTTCACCGTAACACGCCACATCTTGCGAATATATGTGTAGAAACTGCCGGAAATCGTCGTGGTATTCACTCCAGAGCGATGAAAACGTTTCAGTTTGCTCATGGAAAACGGTGTAACAAGGGTGAACACTATCCCATATCACCAGCTCACCGTCTTTCATTGCCATACGAAATTCCGGATGAGCATTCATCAGGCGGGCAAGAATGTGAATAAAGGCCGGATAAAACTTGTGCTTATTTTTCTTTACGGTCTTTAAAAAGGCCGTAATATCCAGCTGAACGGTCTGGTTATAGGTACATTGAGCAACTGACTGAAATGCCTCAAAATGTTCTTTACGATGCCATTGGGATATATCAACGGTGGTATATCCAGTGATTTTTTTCTCCATTTTAGCTTCCTTAGCTCCTGAAAATCTCGATAACTCAAAAAATACGCCCGGTAGTGATCTTATTTCATTATGGTGAAAGTTGGAACCTCTTACGTGCCCGATCAACTCGAGTGCCACCTGACGTCTAAGAAACCATTATTATCATGACATTAACCTATAAAAATAGGCGTATCACGAGGCAGAATTTCAGATAAAAAAAATCCTTAGCTTTCGCTAAGGATGATTTCTGGAATTCGCGGCCGCTTCTAGAG