# HG changeset patch # User lz_hust # Date 1559385616 14400 # Node ID e0a6b2ba8bd37ccddb089d18281403539f1484e4 # Parent e504efcefa1444d5ce320c8c2fb11e992d9eb3a2 Deleted selected files diff -r e504efcefa14 -r e0a6b2ba8bd3 fasta-tool.pl --- a/fasta-tool.pl Sat Jun 01 06:40:01 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,960 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - fasta-tool/fasta-tool.pl at master · huster16/fasta-tool · GitHub - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- Skip to content -
- - - - - - - - -
- -
- - -
- -
- - - -
-
-
- - - - - - - - - - -
-
- - - -

- - /fasta-tool - - -

- -
- - - -
- -
- - -
-
-
- - - - - - - - Permalink - - - - - -
- - -
- - Branch: - master - - - - - - - -
- -
- - Find file - - - Copy path - -
- -

- fasta-tool/fasta-tool.pl -

- -
- - Find file - - - Copy path - -
-
- - - - -
-
- - - - - 1st - - - - 7bdf0b2 - May 31, 2019 - -
- -
-
- - 1 contributor - - -
- -

- Users who have contributed to this file -

-
- - -
-
-
- - - - - - -
- -
- -
- 24 lines (21 sloc) - - 470 Bytes -
- -
- -
- Raw - Blame - History -
- - -
- - - -
-
-
- - - -
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
#!/usr/bin/perl -w
-
# usage : perl toolExample.pl <FASTA file> <output file>
-
open (IN, "<$ARGV[0]");
open (OUT, ">$ARGV[1]");
while (<IN>) {
chop;
if (m/^>/) {
s/^>//;
if ($. > 1) {
print OUT sprintf("%.3f", $gc/$length) . "\n";
}
$gc = 0;
$length = 0;
} else {
++$gc while m/[gc]/ig;
$length += length $_;
}
}
print OUT sprintf("%.3f", $gc/$length) . "\n";
close( IN );
close( OUT );
- - - -
- -
- - - -
- - -
- - -
 -
- - - -
-
-
- -
-
- - -
- - - - - - -
- - - You can’t perform that action at this time. -
- - - - - - - - - - - - - - -
- - - - diff -r e504efcefa14 -r e0a6b2ba8bd3 fasta-tool.xml --- a/fasta-tool.xml Sat Jun 01 06:40:01 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,957 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - fasta-tool/fasta-tool.xml at master · huster16/fasta-tool · GitHub - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- Skip to content -
- - - - - - - - -
- -
- - -
- -
- - - -
-
-
- - - - - - - - - - -
-
- - - -

- - /fasta-tool - - -

- -
- - - -
- -
- - -
-
-
- - - - - - - - Permalink - - - - - -
- - -
- - Branch: - master - - - - - - - -
- -
- - Find file - - - Copy path - -
- -

- fasta-tool/fasta-tool.xml -

- -
- - Find file - - - Copy path - -
-
- - - - -
-
- - - - - 1st - - - - 7bdf0b2 - May 31, 2019 - -
- -
-
- - 1 contributor - - -
- -

- Users who have contributed to this file -

-
- - -
-
-
- - - - - - -
- -
- -
- 23 lines (19 sloc) - - 609 Bytes -
- -
- -
- Raw - Blame - History -
- - -
- - - -
-
-
- - - -
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
<tool id="fa_gc_content_1" name="Compute GC content" version="0.1.0">
<description>for each sequence in a file</description>
<command interpreter="perl">toolExample.pl $input $output</command>
<inputs>
<param format="fasta" name="input" type="data" label="Source file"/>
</inputs>
<outputs>
<data format="tabular" name="output" />
</outputs>
-
<tests>
<test>
<param name="input" value="fa_gc_content_input.fa"/>
<output name="out_file1" file="fa_gc_content_output.txt"/>
</test>
</tests>
-
<help>
This tool computes GC content from a FASTA file.
</help>
-
</tool>
- - - -
- -
- - - -
- - -
- - -
 -
- - - -
-
-
- -
-
- - -
- - - - - - -
- - - You can’t perform that action at this time. -
- - - - - - - - - - - - - - -
- - - -