Add some extensions for FASTA format.

chrovis · Dec 14, 2017 · 0eadbdd · 0eadbdd
1 parent 649204b
commit 0eadbdd
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Showing 3 changed files with 19 additions and 10 deletions.
diff --git a/src/cljam/io/fasta/core.clj b/src/cljam/io/fasta/core.clj
@@ -14,15 +14,16 @@
 
 (defn- fasta-index
   [fasta-path]
-  (if-let [fai-path (->> ["$1.fai" ".fai" "$1.FAI" ".FAI"]
-                         (eduction
-                          (comp
-                           (map #(cstr/replace fasta-path #"(?i)(\.fa(sta)?)$" %))
-                           (filter #(.isFile (cio/file %)))))
-                         first)]
-    (fai/reader fai-path)
-    (throw (FileNotFoundException.
-            (str "Could not find FASTA Index file for " fasta-path)))))
+  (let [fasta-exts #"(?i)(\.(fa|fasta|fas|fsa|seq|fna|faa|ffn|frn|mpfa)?)$"]
+    (if-let [fai-path (->> ["$1.fai" ".fai" "$1.FAI" ".FAI"]
+                           (eduction
+                            (comp
+                             (map #(cstr/replace fasta-path fasta-exts %))
+                             (filter #(.isFile (cio/file %)))))
+                           first)]
+      (fai/reader fai-path)
+      (throw (FileNotFoundException.
+              (str "Could not find FASTA Index file for " fasta-path))))))
 
 (defn ^FASTAReader reader
   [f]

diff --git a/src/cljam/io/util.clj b/src/cljam/io/util.clj
@@ -136,7 +136,7 @@
     #"(?i)\.bam$" :bam
     #"(?i)\.f(ast)?q" :fastq
     #"(?i)\.fai$" :fai
-    #"(?i)\.fa(sta)?" :fasta
+    #"(?i)\.(fa|fasta|fas|fsa|seq|fna|faa|ffn|frn|mpfa)" :fasta
     #"(?i)\.2bit$" :2bit
     #"(?i)\.vcf" :vcf
     #"(?i)\.bcf$" :bcf

diff --git a/test/cljam/io/util_test.clj b/test/cljam/io/util_test.clj
@@ -30,6 +30,14 @@
     "foo.FA.GZ" :fasta
     "foo.FASTA" :fasta
     "foo.FASTA.GZ" :fasta
+    "foo.fas" :fasta
+    "foo.fsa" :fasta
+    "foo.seq" :fasta
+    "foo.fna" :fasta
+    "foo.faa" :fasta
+    "foo.ffn" :fasta
+    "foo.frn" :fasta
+    "foo.mpfa" :fasta
     "foo.fai"  :fai
     "foo.fa.fai"  :fai
     "foo.2bit" :2bit