Mercurial > repos > peterjc > sample_seqs

changeset 8:4231c585b6dd draft

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Uploaded v0.2.1, fixed missing test file, added more tests
author peterjc
date Mon, 16 Mar 2015 13:40:54 -0400
parents 4099383e0ac8
children a1141d5f1533
files tools/sample_seqs/README.rst tools/sample_seqs/sample_seqs.py tools/sample_seqs/sample_seqs.xml
diffstat 3 files changed, 38 insertions(+), 8 deletions(-) [+]
line wrap: on
line diff
--- a/tools/sample_seqs/README.rst	Fri Mar 06 05:02:33 2015 -0500
+++ b/tools/sample_seqs/README.rst	Mon Mar 16 13:40:54 2015 -0400
@@ -1,7 +1,7 @@
 Galaxy tool to sub-sample sequence files
 ========================================
 
-This tool is copyright 2014 by Peter Cock, The James Hutton Institute
+This tool is copyright 2014-2014 by Peter Cock, The James Hutton Institute
 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
 See the licence text below (MIT licence).
 
@@ -63,6 +63,9 @@
           This works by first counting all your sequences, then calculates
           the percentage required in order to sample them uniformly (evenly).
           This makes two passes through the input and is therefore slower. 
+v0.2.1  - Was missing a file for the functional tests.
+        - Included testing of stdout messages.
+        - Includes testing of failure modes.
 ======= ======================================================================
 
 
--- a/tools/sample_seqs/sample_seqs.py	Fri Mar 06 05:02:33 2015 -0500
+++ b/tools/sample_seqs/sample_seqs.py	Mon Mar 16 13:40:54 2015 -0400
@@ -64,7 +64,7 @@
 options, args = parser.parse_args()
 
 if options.version:
-    print("v0.2.0")
+    print("v0.2.1")
     sys.exit(0)
 
 in_file = options.input
@@ -172,7 +172,7 @@
     if N < 1:
         sys_exit("Bad -c count argument %r" % options.count)
     total = count_sequences(in_file, seq_format)
-    print("Input file has %i sequences" % total)
+    sys.stderr.write("Input file has %i sequences\n" % total)
     if interleaved:
         # Paired
         if total % 2:
--- a/tools/sample_seqs/sample_seqs.xml	Fri Mar 06 05:02:33 2015 -0500
+++ b/tools/sample_seqs/sample_seqs.xml	Mon Mar 16 13:40:54 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="sample_seqs" name="Sub-sample sequences files" version="0.2.0">
+<tool id="sample_seqs" name="Sub-sample sequences files" version="0.2.1">
     <description>e.g. to reduce coverage</description>
     <requirements>
         <requirement type="package" version="1.65">biopython</requirement>
@@ -122,25 +122,52 @@
             <param name="type" value="percentage" />
             <param name="percent" value="20.0" />
             <output name="output_file" file="MID4_GLZRM4E04_rnd30_frclip.sample_N5.sff" ftype="sff"/>
+            <assert_stderr>
+                <has_line line="Sampling 20.000% of sequences" />
+                <has_line line="Selected 5 records" />
+            </assert_stderr>
         </test>
         <test>
             <param name="input_file" value="MID4_GLZRM4E04_rnd30_frclip.sff" ftype="sff" />
             <param name="type" value="everyNth" />
-            <param name="percent" value="5" />
+            <param name="every_n" value="5" />
             <param name="interleaved" value="true" />
             <output name="output_file" file="MID4_GLZRM4E04_rnd30_frclip.pair_sample_N5.sff" ftype="sff"/>
+            <assert_stderr>
+                <has_line line="Sampling every 5th sequence" />
+                <has_line line="Selected 3 pairs" />
+            </assert_stderr>
         </test>
         <test>
-            <param name="input_file" value="MID4_GLZRM4E04_rnd30.sff" ftype="sff" />
+            <param name="input_file" value="MID4_GLZRM4E04_rnd30_frclip.sff" ftype="sff" />
             <param name="type" value="desired_count" />
-            <param name="count" value="30" />
-            <output name="output_file" file="MID4_GLZRM4E04_rnd30.sff" ftype="sff"/>
+            <param name="count" value="25" />
+            <output name="output_file" file="MID4_GLZRM4E04_rnd30_frclip.sff" ftype="sff"/>
+            <assert_stderr>
+                <has_line line="Input file has 25 sequences" />
+                <has_line line="Taking all the sequences" />
+                <has_line line="Selected 25 records" />
+            </assert_stderr>
         </test>
         <test>
             <param name="input_file" value="MID4_GLZRM4E04_rnd30_frclip.sff" ftype="sff" />
             <param name="type" value="desired_count" />
             <param name="count" value="1" />
             <output name="output_file" file="MID4_GLZRM4E04_rnd30_frclip.sample_C1.sff" ftype="sff"/>
+            <assert_stderr>
+                <has_line line="Input file has 25 sequences" />
+                <has_line line="Sampling just first sequence!" />
+                <has_line line="Selected 1 records" />
+            </assert_stderr>
+        </test>
+        <test expect_failure="true" expect_exit_code="1">
+            <param name="input_file" value="MID4_GLZRM4E04_rnd30_frclip.sff" ftype="sff" />
+            <param name="type" value="desired_count" />
+            <param name="count" value="30" />
+            <assert_stderr>
+                <has_line line="Input file has 25 sequences" />
+                <has_line line="Requested 30 sequences, but file only has 25." />
+            </assert_stderr>
         </test>
     </tests>
     <help>