Merged in mbhall88/snakemake-wrappers/pyfastaq-replace_bases (pull re…

…quest snakemake#92)

add pyfastaq replace_bases wrapper

bio/pyfastaq/replace_bases/environment.yaml

@@ -0,0 +1,4 @@
+channels:
+  - bioconda
+dependencies:
+  - pyfastaq ==3.17.0

bio/pyfastaq/replace_bases/meta.yaml

@@ -0,0 +1,4 @@
+name: pyfastaq replace_bases
+description: Replaces all occurrences of one letter with another.
+authors:
+  - Michael Hall

bio/pyfastaq/replace_bases/test/Snakefile

@@ -0,0 +1,12 @@
+rule replace_bases:
+    input:
+        "{sample}.rna.fa"
+    output:
+        "{sample}.dna.fa",
+    params:
+        old_base = "U",
+        new_base = "T",
+    log:
+        "logs/fastaq/replace_bases/test/{sample}.log"
+    wrapper:
+        "master/bio/pyfastaq/replace_bases"

bio/pyfastaq/replace_bases/test/sample1.rna.fa

@@ -0,0 +1,2 @@
+>sample1
+ACGU

bio/pyfastaq/replace_bases/wrapper.py

@@ -0,0 +1,19 @@
+__author__ = "Michael Hall"
+__copyright__ = "Copyright 2019, Michael Hall"
+__email__ = "[email protected]"
+__license__ = "MIT"
+
+
+from snakemake.shell import shell
+
+
+log = snakemake.log_fmt_shell(stdout=False, stderr=True)
+
+shell(
+    "fastaq replace_bases"
+    " {snakemake.input[0]}"
+    " {snakemake.output[0]}"
+    " {snakemake.params.old_base}"
+    " {snakemake.params.new_base}"
+    " {log}"
+)

test.py

@@ -285,6 +285,9 @@ def test_pindel_pindel2vcf_multi_input():
     run("bio/pindel/pindel2vcf",
         ["snakemake", "pindel/all.vcf", "--use-conda", "-F"])
 
+def test_pyfastaq_replace_bases():
+    run("bio/pyfastaq/replace_bases",
+        ["snakemake", "sample1.dna.fa", "--use-conda", "-F"])
 
 def test_samtools_mpileup():
      run("bio/samtools/mpileup",