Mercurial > repos > greg > vsnp_statistics
changeset 21:377c1a96aae9 draft
Uploaded
| author | greg |
|---|---|
| date | Tue, 24 Aug 2021 12:32:50 +0000 |
| parents | d4ef7003c539 |
| children | 61239720da38 |
| files | .shed.yml test-data/vsnp_statistics1.tabular test-data/vsnp_statistics2.tabular test-data/vsnp_statistics4.tabular vsnp_statistics.py |
| diffstat | 5 files changed, 19 insertions(+), 4 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/.shed.yml Tue Aug 24 12:32:50 2021 +0000 @@ -0,0 +1,13 @@ +name: vsnp_statistics +owner: greg +description: | + Contains a tool that produces an Excel spreadsheet containing statistics for samples and associated metrics files. +homepage_url: https://github.com/USDA-VS/vSNP +long_description: | + Contains a tool Accepts a single fastqsanger sample, a set of paired read samples, or a collections of samples + along with associated SAMtools idxstats and vSNP zero coverage metrics files and extracts information from them + to produce an Excel spreadsheet containing statistics for each sample. +remote_repository_url: https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_statistics +type: unrestricted +categories: + - Sequence Analysis
--- a/test-data/vsnp_statistics1.tabular Thu Aug 12 17:08:20 2021 +0000 +++ b/test-data/vsnp_statistics1.tabular Tue Aug 24 12:32:50 2021 +0000 @@ -1,2 +1,2 @@ -Reference FASTQ File Size Mean Read Length Mean Read Quality Reads Passing Q30 Total Reads All Mapped Reads Unmapped Reads Unmapped Reads Percentage of Total Reference with Coverage Average Depth of Coverage Good SNP Count +# Reference FASTQ File Size Mean Read Length Mean Read Quality Reads Passing Q30 Total Reads All Mapped Reads Unmapped Reads Unmapped Reads Percentage of Total Reference with Coverage Average Depth of Coverage Good SNP Count 89 Mcap_Deer_DE_SRR650221_fastq_gz 1.6 MB 121.0 29.7 0.53 4317 17063 223 0.05 8.27% 0.439436 36
--- a/test-data/vsnp_statistics2.tabular Thu Aug 12 17:08:20 2021 +0000 +++ b/test-data/vsnp_statistics2.tabular Tue Aug 24 12:32:50 2021 +0000 @@ -1,2 +1,2 @@ -Reference Read1 FASTQ File Size Reads Mean Read Length Mean Read Quality Reads Passing Q30 Read2 FASTQ File Size Reads Mean Read Length Mean Read Quality Reads Passing Q30 Total Reads All Mapped Reads Unmapped Reads Unmapped Reads Percentage of Total Reference with Coverage Average Depth of Coverage Good SNP Count +# Reference Read1 FASTQ File Size Reads Mean Read Length Mean Read Quality Reads Passing Q30 Read2 FASTQ File Size Reads Mean Read Length Mean Read Quality Reads Passing Q30 Total Reads All Mapped Reads Unmapped Reads Unmapped Reads Percentage of Total Reference with Coverage Average Depth of Coverage Good SNP Count 89 13-1941-6_S4_L001_R1_600000_fastq_gz 8.7 KB 25 100.0 65.7 1.00 13-1941-6_S4_L001_R2_600000_fastq_gz 8.5 KB 25 100.0 66.3 1.00 50 45 5 0.10 98.74% 10.338671 611
--- a/test-data/vsnp_statistics4.tabular Thu Aug 12 17:08:20 2021 +0000 +++ b/test-data/vsnp_statistics4.tabular Tue Aug 24 12:32:50 2021 +0000 @@ -1,2 +1,2 @@ -Reference Read1 FASTQ File Size Reads Mean Read Length Mean Read Quality Reads Passing Q30 Read2 FASTQ File Size Reads Mean Read Length Mean Read Quality Reads Passing Q30 Total Reads All Mapped Reads Unmapped Reads Unmapped Reads Percentage of Total Reference with Coverage Average Depth of Coverage Good SNP Count +# Reference Read1 FASTQ File Size Reads Mean Read Length Mean Read Quality Reads Passing Q30 Read2 FASTQ File Size Reads Mean Read Length Mean Read Quality Reads Passing Q30 Total Reads All Mapped Reads Unmapped Reads Unmapped Reads Percentage of Total Reference with Coverage Average Depth of Coverage Good SNP Count 89 Unnamed Collection_R1 8.7 KB 25 100.0 65.7 1.00 Unnamed Collection_R2 8.5 KB 25 100.0 66.3 1.00 50 46 4 0.08 0.16% 0.002146 0
--- a/vsnp_statistics.py Thu Aug 12 17:08:20 2021 +0000 +++ b/vsnp_statistics.py Tue Aug 24 12:32:50 2021 +0000 @@ -110,7 +110,9 @@ 'Total Reads', 'All Mapped Reads', 'Unmapped Reads', 'Unmapped Reads Percentage of Total', 'Reference with Coverage', 'Average Depth of Coverage', 'Good SNP Count'] with open(output_file, "w") as outfh: - outfh.write("%s\n" % "\t".join(columns)) + # Make sure the header starts with a # so + # MultiQC can properly handle the output. + outfh.write("# %s\n" % "\t".join(columns)) line_items = [] # Get the current stats and associated files. # Get and output the statistics.