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compbiocore / qcdb

QC Database
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first version is ready #23

Closed aguang closed 5 years ago

aguang commented 5 years ago

This first version uses mysql and has parsers for the programs qckitfastq, fastqc, and picardTools (including only CollectInsertSizeMetrics, CollectAlignmentSummaryMetrics, and CollectGcBiastMetrics from picardTools). It contains a reference table for field names for each metric and program, a sample metadata table with SRS and SRX ids as well as library type, and metrics for each unique sample.

It does not have other sample metadata that would be taken from SRA. That is being worked on in #14, which will also include a script to populate thosefields post-hoc. Other than that it should be feature complete, and we can start populating it.

codecov[bot] commented 5 years ago

Codecov Report

:exclamation: No coverage uploaded for pull request base (master@b72505d). Click here to learn what that means. The diff coverage is 70.34%.

Impacted file tree graph

@@            Coverage Diff            @@
##             master      #23   +/-   ##
=========================================
  Coverage          ?   70.34%           
=========================================
  Files             ?       10           
  Lines             ?      499           
  Branches          ?        0           
=========================================
  Hits              ?      351           
  Misses            ?      148           
  Partials          ?        0
Impacted Files Coverage Δ
qcdb/db_create.py 0% <0%> (ø)
qcdb/db_load.py 30.23% <30.23%> (ø)
qcdb/connection.py 64.28% <64.28%> (ø)
qcdb/tables_create.py 65.71% <65.71%> (ø)
tests/test_connection.py 73.91% <73.91%> (ø)
qcdb/parsers/parse.py 82.52% <82.52%> (ø)
qcdb/parsers/picardtools_parse.py 85.71% <85.71%> (ø)
qcdb/parsers/qckitfastq_parse.py 87.5% <87.5%> (ø)
tests/test_db.py 95.06% <95.06%> (ø)
qcdb/parsers/fastqc_parse.py 95.55% <95.55%> (ø)

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aguang commented 5 years ago

to clarify, we provide 3 picardtools metrics currently: insertsize_metrics, alignment_summary_metrics, and summary_gcbias_metrics