Mercurial > repos > iuc > fasta_stats
changeset 3:56022eb50bbd draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit ecd37d0702cbe5cf9fa244c129a008b039d5e164"
| author | iuc |
|---|---|
| date | Mon, 05 Jul 2021 13:36:26 +0000 |
| parents | cd0874854f51 |
| children | 0dbb995c7d35 |
| files | fasta-stats.pl fasta-stats.xml test-data/ng50_out.txt test-data/test_out.txt |
| diffstat | 4 files changed, 13 insertions(+), 5 deletions(-) [+] |
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--- 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) {
--- a/fasta-stats.xml Mon Apr 26 10:01:43 2021 +0000 +++ b/fasta-stats.xml Mon Jul 05 13:36:26 2021 +0000 @@ -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>
--- 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 @@ -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