From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Fri, 6 Aug 2010 08:59:16 +0000 (+0000)
Subject: added -o option and tests to analyze_vals
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=cba09ac68ac99668cfe9c802b91712b7c1a20fc2;p=biopieces.git

added -o option and tests to analyze_vals

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1037 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/bp_bin/analyze_vals b/bp_bin/analyze_vals
index d1d9ede..726c91c 100755
--- a/bp_bin/analyze_vals
+++ b/bp_bin/analyze_vals
@@ -36,12 +36,13 @@ use Data::Dumper;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $options, $in, $out, $record, $analysis, $key, $len, %skip_hash,
+my ( $options, $in, $out, $record, $analysis, $key, $len, %skip_hash, $data_out,
      %key_hash, $skip, $keys, $types, $counts, $mins, $maxs, $sums, $means );
 
 $options = Maasha::Biopieces::parse_options(
     [
         { long => 'no_stream', short => 'x', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+        { long => 'data_out',  short => 'o', type => 'file', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
         { long => 'keys',      short => 'k', type => 'list', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
         { long => 'no_keys',   short => 'K', type => 'list', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
     ]   
@@ -50,6 +51,9 @@ $options = Maasha::Biopieces::parse_options(
 $in  = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
 $out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
 
+$data_out = Maasha::Biopieces::write_stream( $options->{ "data_out" }, $options->{ "compress" } );
+$data_out ||= \*STDOUT;
+
 map { $skip_hash{ $_ } = 1 } @{ $options->{ "no_keys" } };
 map { $key_hash{ $_ } = 1; $skip = 1 } @{ $options->{ "keys" } };
 
@@ -122,13 +126,15 @@ foreach $key ( sort keys %{ $analysis } )
     $means  .= sprintf "% 15s", $analysis->{ $key }->{ "MEAN" };
 }
 
-print "$keys\n";
-print "$types\n";
-print "$counts\n";
-print "$mins\n";
-print "$maxs\n";
-print "$sums\n";
-print "$means\n";
+print $data_out "$keys\n";
+print $data_out "$types\n";
+print $data_out "$counts\n";
+print $data_out "$mins\n";
+print $data_out "$maxs\n";
+print $data_out "$sums\n";
+print $data_out "$means\n";
+
+close $data_out;
 
 Maasha::Biopieces::close_stream( $in );
 Maasha::Biopieces::close_stream( $out );
diff --git a/bp_test/in/analyze_vals.in b/bp_test/in/analyze_vals.in
new file mode 100644
index 0000000..0df90f2
--- /dev/null
+++ b/bp_test/in/analyze_vals.in
@@ -0,0 +1,9 @@
+V0: Human
+V1: 123
+---
+V0: Dog
+V1: 45
+---
+V0: Mouse
+V1: 6
+---
diff --git a/bp_test/out/analyze_vals.out.1 b/bp_test/out/analyze_vals.out.1
new file mode 100644
index 0000000..ea45064
--- /dev/null
+++ b/bp_test/out/analyze_vals.out.1
@@ -0,0 +1,7 @@
+KEY               V0             V1
+TYPE            alph            num
+COUNT              3              3
+MIN                3              6
+MAX                5            123
+SUM            13.00         174.00
+MEAN            4.33          58.00
diff --git a/bp_test/out/analyze_vals.out.2 b/bp_test/out/analyze_vals.out.2
new file mode 100644
index 0000000..7065732
--- /dev/null
+++ b/bp_test/out/analyze_vals.out.2
@@ -0,0 +1,7 @@
+KEY               V0
+TYPE            alph
+COUNT              3
+MIN                3
+MAX                5
+SUM            13.00
+MEAN            4.33
diff --git a/bp_test/out/analyze_vals.out.3 b/bp_test/out/analyze_vals.out.3
new file mode 100644
index 0000000..6726a07
--- /dev/null
+++ b/bp_test/out/analyze_vals.out.3
@@ -0,0 +1,7 @@
+KEY               V1
+TYPE             num
+COUNT              3
+MIN                6
+MAX              123
+SUM           174.00
+MEAN           58.00
diff --git a/bp_test/test/test_analyze_vals b/bp_test/test/test_analyze_vals
new file mode 100755
index 0000000..4fa0b2e
--- /dev/null
+++ b/bp_test/test/test_analyze_vals
@@ -0,0 +1,15 @@
+#!/bin/bash
+
+source "$BP_DIR/bp_test/lib/test.sh"
+
+run "$bp -I $in -o $tmp -x"
+assert_no_diff $tmp $out.1
+rm $tmp
+
+run "$bp -I $in -k V0 -o $tmp -x"
+assert_no_diff $tmp $out.2
+rm $tmp
+
+run "$bp -I $in -K V0 -o $tmp -x"
+assert_no_diff $tmp $out.3
+rm $tmp