update pfam links (#64)

README.md

@@ -1,20 +1,21 @@
 # lollipops
 
 **Please cite this work as**
-* Jay JJ, Brouwer C (2016) Lollipops in the Clinic: Information Dense Mutation Plots for Precision Medicine. PLoS ONE 11(8): e0160519. doi: [10.1371/journal.pone.0160519](http://dx.doi.org/10.1371/journal.pone.0160519).
+
+- Jay JJ, Brouwer C (2016) Lollipops in the Clinic: Information Dense Mutation Plots for Precision Medicine. PLoS ONE 11(8): e0160519. doi: [10.1371/journal.pone.0160519](http://dx.doi.org/10.1371/journal.pone.0160519).
 
 A simple 'lollipop' mutation diagram generator that tries to make things
 simple and easy by automating as much as possible. It uses the
 [UniProt REST API](http://www.uniprot.org/uploadlists/) and/or
-[Pfam API](http://pfam.xfam.org/help#tabview=tab9) to automate translation
+[Pfam API](http://pfam-legacy.xfam.org/help#tabview=tab9) to automate translation
 of Gene Symbols and lookup domain/motif features for display. If
 variant changes are provided, it will also annotate them to the diagram
 using the "lollipops" markers that give the tool it's name.
 
 ## Example
 
-Basic usage is just the gene symbol (ex: ``TP53``) and a list of
-mutations (ex: ``R273C R175H T125 R248Q``)
+Basic usage is just the gene symbol (ex: `TP53`) and a list of
+mutations (ex: `R273C R175H T125 R248Q`)
 
     ./lollipops TP53 R273C R175H T125 R248Q
 
@@ -24,17 +25,17 @@ More advanced usage allows for per-mutation color (e.g. sample type) and
 size specification (e.g. denoting number of samples), along with text
 labels, a legend for abbreviated domains, and more:
 
-		./lollipops -legend -labels TP53 R248Q#7f3333@131 R273C R175H T125@5
+    	./lollipops -legend -labels TP53 R248Q#7f3333@131 R273C R175H T125@5
 
 ![TP53 Lollipop diagram with 5 customized mutations](tp53_more.png?raw=true)
 
 ## Usage
 
-Usage: ``lollipops [options] {-U UNIPROT_ID | GENE_SYMBOL} [PROTEIN CHANGES ...]``
+Usage: `lollipops [options] {-U UNIPROT_ID | GENE_SYMBOL} [PROTEIN CHANGES ...]`
 
 Where **GENE_SYMBOL** is the official human HGNC gene symbol. This will use the
 official API to lookup the **UNIPROT_ID**. To skip the lookup or use other species,
-specify the UniProt ID with -U (e.g. ``-U P04637`` for TP53)
+specify the UniProt ID with -U (e.g. `-U P04637` for TP53)
 
 #### Protein changes
 
@@ -84,7 +85,7 @@ the area is exponentially proportional to the count indicated. Examples:
   -uniprot                use UniprotKB as an alternative to Pfam for
                           fetching domain/motif information
   -l=filename.json        use local file instead of Pfam API for graphic data
-                            see: http://pfam.xfam.org/help#tabview=tab9
+                            see: http://pfam-legacy.xfam.org/help#tabview=tab9
 ```
 
 ## Installation
@@ -93,7 +94,7 @@ Head over to the [Releases](https://github.com/joiningdata/lollipops/releases) t
 download the latest version for your system in a simple command-line executable.
 
 If you already have Go installed and want the bleeding edge, just
-``go get -u github.com/joiningdata/lollipops`` to download the latest version.
+`go get -u github.com/joiningdata/lollipops` to download the latest version.
 
 ## Embedding
 

data/data.go

@@ -24,7 +24,7 @@ import (
 )
 
 // MotifNames has human-readable names
-//  - mostly from http://pfam.xfam.org/help#tabview=tab9
+//  - mostly from http://pfam-legacy.xfam.org/help#tabview=tab9
 var MotifNames = map[string]string{
 	"disorder":       "Disordered region",
 	"low_complexity": "Low complexity region",
@@ -66,13 +66,13 @@ func GetLocalGraphicData(filename string) (*GraphicResponse, error) {
 	f.Close()
 	for i, x := range pf.Motifs {
 		if x.Link != "" && !strings.Contains(x.Link, "://") {
-			x.Link = "http://pfam.xfam.org" + x.Link
+			x.Link = "http://pfam-legacy.xfam.org" + x.Link
 			pf.Motifs[i] = x
 		}
 	}
 	for i, x := range pf.Regions {
 		if x.Link != "" && !strings.Contains(x.Link, "://") {
-			x.Link = "http://pfam.xfam.org" + x.Link
+			x.Link = "http://pfam-legacy.xfam.org" + x.Link
 			pf.Regions[i] = x
 		}
 	}

data/pfam.go

@@ -25,7 +25,7 @@ import (
 	"os"
 )
 
-const PfamGraphicURL = "https://pfam.xfam.org/protein/%s/graphic"
+const PfamGraphicURL = "https://pfam-legacy.xfam.org/protein/%s/graphic"
 
 func GetPfamGraphicData(accession string) (*GraphicResponse, error) {
 	queryURL := fmt.Sprintf(PfamGraphicURL, accession)
@@ -56,13 +56,13 @@ func GetPfamGraphicData(accession string) (*GraphicResponse, error) {
 	r := data[0]
 	for i, x := range r.Motifs {
 		if x.Link != "" {
-			x.Link = "https://pfam.xfam.org" + x.Link
+			x.Link = "https://pfam-legacy.xfam.org" + x.Link
 			r.Motifs[i] = x
 		}
 	}
 	for i, x := range r.Regions {
 		if x.Link != "" {
-			x.Link = "https://pfam.xfam.org" + x.Link
+			x.Link = "https://pfam-legacy.xfam.org" + x.Link
 			r.Regions[i] = x
 		}
 	}

main.go

@@ -116,7 +116,7 @@ Alternative input sources:
   -uniprot                use UniprotKB as an alternative to Pfam for
                           fetching domain/motif information
   -l=filename.json        use local file instead of Pfam API for graphic data
-                            see: http://pfam.xfam.org/help#tabview=tab9
+                            see: http://pfam-legacy.xfam.org/help#tabview=tab9
 
 `)
 	}

workflow/lollipops.cwl

@@ -128,7 +128,7 @@ inputs:
       prefix: "-uniprot"
   localDomainFile:
     doc: "get domain info from a file"
-    ## see: http://pfam.xfam.org/help#tabview=tab9
+    ## see: http://pfam-legacy.xfam.org/help#tabview=tab9
     type: File?
     inputBinding:
       prefix: "-l="