| Previous changeset 2:cd0874854f51 (2021-04-26) Next changeset 4:0dbb995c7d35 (2021-11-18) |
|
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit ecd37d0702cbe5cf9fa244c129a008b039d5e164" |
|
modified:
fasta-stats.pl fasta-stats.xml test-data/ng50_out.txt test-data/test_out.txt |
| b |
| diff -r cd0874854f51 -r 56022eb50bbd fasta-stats.pl --- a/fasta-stats.pl Mon Apr 26 10:01:43 2021 +0000 +++ b/fasta-stats.pl Mon Jul 05 13:36:26 2021 +0000 |
| [ |
| @@ -55,14 +55,18 @@ if (@len) { $stat{'num_bp'} = sum(@len); - $stat{'len_min'} = $len[0]; - $stat{'len_max'} = $len[-1]; + $stat{'len_min'} = $len[-1]; + $stat{'len_max'} = $len[0]; $stat{'len_median'} = $len[int(@len/2)]; $stat{'len_mean'} = int( $stat{'num_bp'} / $stat{'num_seq'} ); # calculate n50 my $thresh = int 0.5 * $stat{'num_bp'}; ($stat{'len_N50'}, $stat{'L50'}) = &calc_x50(\@len, $thresh); + + #calculate n90 + my $thresh = int 0.9 * $stat{'num_bp'}; + ($stat{'len_N90'}, $stat{'L90'}) = &calc_x50(\@len, $thresh); #calculate NG50 if ($calc_ng50) { |
| b |
| diff -r cd0874854f51 -r 56022eb50bbd fasta-stats.xml --- a/fasta-stats.xml Mon Apr 26 10:01:43 2021 +0000 +++ b/fasta-stats.xml Mon Jul 05 13:36:26 2021 +0000 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="fasta-stats" name="Fasta Statistics" version="1.0.2"> +<tool id="fasta-stats" name="Fasta Statistics" version="1.0.3"> <description>Display summary statistics for a fasta file.</description> <requirements> <requirement type="package" version="5.26">perl</requirement> |
| b |
| diff -r cd0874854f51 -r 56022eb50bbd test-data/ng50_out.txt --- a/test-data/ng50_out.txt Mon Apr 26 10:01:43 2021 +0000 +++ b/test-data/ng50_out.txt Mon Jul 05 13:36:26 2021 +0000 |
| b |
| @@ -1,12 +1,14 @@ GC_content 51.1 L50 2 +L90 7 LG50 2 len_N50 604 +len_N90 140 len_NG50 604 -len_max 30 +len_max 1501 len_mean 324 len_median 182 -len_min 1501 +len_min 30 num_A 895 num_C 940 num_G 807 |
| b |
| diff -r cd0874854f51 -r 56022eb50bbd test-data/test_out.txt --- a/test-data/test_out.txt Mon Apr 26 10:01:43 2021 +0000 +++ b/test-data/test_out.txt Mon Jul 05 13:36:26 2021 +0000 |
| b |
| @@ -1,6 +1,8 @@ GC_content 52.0 L50 1 +L90 1 len_N50 194780 +len_N90 194780 len_max 194780 len_mean 194780 len_median 194780 |