[med-svn] [Git][med-team/pycoqc][master] 3 commits: Override false positives about compressed JS in example output
Andreas Tille
gitlab at salsa.debian.org
Wed Apr 22 11:00:22 BST 2020
Andreas Tille pushed to branch master at Debian Med / pycoqc
Commits:
41d92f77 by Andreas Tille at 2020-04-22T11:26:33+02:00
Override false positives about compressed JS in example output
- - - - -
bbf3bbe1 by Andreas Tille at 2020-04-22T11:59:19+02:00
Fix dependencies
- - - - -
2a7e7f6f by Andreas Tille at 2020-04-22T11:59:43+02:00
Add manpages
- - - - -
9 changed files:
- + debian/Barcode_split.1
- + debian/Fast5_to_seq_summary.1
- debian/control
- + debian/createmanpages
- + debian/manpages
- + debian/patches/series
- + debian/patches/unversioned_depends_tqdm.patch
- + debian/pycoQC.1
- + debian/source/lintian-overrides
Changes:
=====================================
debian/Barcode_split.1
=====================================
@@ -0,0 +1,56 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.13.
+.TH BARCODE_SPLIT "1" "April 2020" "Barcode_split 2.5.0.21" "User Commands"
+.SH NAME
+Barcode_split \- simple tool to split sequencing summary report in per barcodes
+.SH DESCRIPTION
+usage: Barcode_split [\-h] [\-\-version] \fB\-\-summary_file\fR
+.TP
+[SUMMARY_FILE [SUMMARY_FILE ...]]
+[\-\-barcode_file [BARCODE_FILE [BARCODE_FILE ...]]]
+[\-\-output_dir OUTPUT_DIR] [\-\-output_unclassified]
+[\-\-min_barcode_percent MIN_BARCODE_PERCENT] [\-v | \fB\-q]\fR
+.PP
+Barcode_split is a simple tool to split sequencing summary report in per
+barcodes
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-\-version\fR
+show program's version number and exit
+.TP
+\fB\-\-summary_file\fR [SUMMARY_FILE [SUMMARY_FILE ...]], \fB\-f\fR [SUMMARY_FILE [SUMMARY_FILE ...]]
+Path to a sequencing_summary generated by Albacore
+1.0.0 + (read_fast5_basecaller.py) / Guppy 2.1.3+
+(guppy_basecaller). One can also pass multiple space
+separated file paths or a UNIX style regex matching
+multiple files
+.TP
+\fB\-\-barcode_file\fR [BARCODE_FILE [BARCODE_FILE ...]], \fB\-b\fR [BARCODE_FILE [BARCODE_FILE ...]]
+Path to the barcode_file generated by Guppy 2.1.3+
+(guppy_barcoder) or Deepbinner 0.2.0+. One can also
+pass multiple space separated file paths or a UNIX
+style regex matching multiple files
+.TP
+\fB\-\-output_dir\fR OUTPUT_DIR, \fB\-o\fR OUTPUT_DIR
+Folder where to output split barcode data (default:
+current dir
+.TP
+\fB\-\-output_unclassified\fR, \fB\-u\fR
+If given, unclassified barcodes are also written in a
+file. By default they are skiped
+.TP
+\fB\-\-min_barcode_percent\fR MIN_BARCODE_PERCENT, \fB\-p\fR MIN_BARCODE_PERCENT
+Minimal percent of total reads to retain barcode
+label. If below, the barcode value is set as
+`unclassified` (default: 0.1)
+.TP
+\fB\-v\fR, \fB\-\-verbose\fR
+Increase verbosity
+.TP
+\fB\-q\fR, \fB\-\-quiet\fR
+Reduce verbosity
+.SH AUTHOR
+ This manpage was written by Andreas Tille for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/Fast5_to_seq_summary.1
=====================================
@@ -0,0 +1,64 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.13.
+.TH FAST5_TO_SEQ_SUMMARY "1" "April 2020" "Fast5_to_seq_summary 2.5.0.21" "User Commands"
+.SH NAME
+Fast5_to_seq_summary \- generate a sequencing summary like file from a directory containing Fast5 files
+.SH DESCRIPTION
+usage: Fast5_to_seq_summary [\-h] [\-\-version] \fB\-\-fast5_dir\fR FAST5_DIR
+.TP
+\fB\-\-seq_summary_fn\fR SEQ_SUMMARY_FN
+[\-\-max_fast5 MAX_FAST5] [\-\-threads THREADS]
+[\-\-basecall_id BASECALL_ID]
+[\-\-fields FIELDS [FIELDS ...]] [\-\-include_path]
+[\-\-verbose_level VERBOSE_LEVEL]
+.PP
+Fast5_to_seq_summary generate a sequencing summary like file from a directory
+containing Fast5 files
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-\-version\fR, \fB\-v\fR
+show program's version number and exit
+.TP
+\fB\-\-fast5_dir\fR FAST5_DIR, \fB\-f\fR FAST5_DIR
+Directory containing fast5 files. Can contain multiple
+subdirectories
+.TP
+\fB\-\-seq_summary_fn\fR SEQ_SUMMARY_FN, \fB\-s\fR SEQ_SUMMARY_FN
+path of the summary sequencing file where to write the
+data extracted from the fast5 files
+.TP
+\fB\-\-max_fast5\fR MAX_FAST5
+Maximum number of file to try to parse. 0 to
+deactivate (default: 0)
+.TP
+\fB\-\-threads\fR THREADS, \fB\-t\fR THREADS
+Total number of threads to use. 1 thread is used for
+the reader and 1 for the writer. Minimum 3 (default:
+4)
+.TP
+\fB\-\-basecall_id\fR BASECALL_ID
+id of the basecalling group. By default leave to 0,
+but if you perfome multiple basecalling on the same
+fast5 files, this can be used to indicate the
+corresponding group (1, 2 ...) (default: 0)
+.TP
+\fB\-\-fields\fR FIELDS [FIELDS ...]
+list of field names corresponding to attributes to try
+to fetch from the fast5 files (default: ['read_id',
+\&'run_id', 'channel', 'start_time',
+\&'sequence_length_template', 'mean_qscore_template',
+\&'calibration_strand_genome_template',
+\&'barcode_arrangement'])
+.TP
+\fB\-\-include_path\fR
+If given, the absolute path to the corresponding file
+is added in an extra column (default: False)
+.TP
+\fB\-\-verbose_level\fR VERBOSE_LEVEL
+Level of verbosity, from 2 (Chatty) to 0 (Nothing)
+(default: 0)
+.SH AUTHOR
+ This manpage was written by Andreas Tille for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/control
=====================================
@@ -15,7 +15,15 @@ Homepage: https://github.com/a-slide/pycoQC
Package: pycoqc
Architecture: all
Depends: ${python3:Depends},
- ${misc:Depends}
+ ${misc:Depends},
+ python3-numpy,
+ python3-scipy,
+ python3-pandas,
+ python3-plotly (>= 4.1.0),
+ python3-jinja2,
+ python3-h5py,
+ python3-tqdm,
+ python3-pysam
Description: computes metrics and generates Interactive QC plots
PycoQC computes metrics and generates interactive QC plots for Oxford
Nanopore technologies sequencing data
=====================================
debian/createmanpages
=====================================
@@ -0,0 +1,41 @@
+#!/bin/sh
+MANDIR=debian
+mkdir -p $MANDIR
+
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
+NAME=`grep "^Description:" debian/control | sed 's/^Description: *//' | head -n1`
+PROGNAME=`grep "^Package:" debian/control | sed 's/^Package: *//' | head -n1`
+
+AUTHOR=".SH AUTHOR\n \
+This manpage was written by $DEBFULLNAME for the Debian distribution and\n \
+can be used for any other usage of the program.\
+"
+
+# If program name is different from package name or title should be
+# different from package short description change this here
+progname=pycoQC
+help2man --no-info --no-discard-stderr --help-option=" --help" \
+ --name="computes metrics and generates interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies basecallers" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=Fast5_to_seq_summary
+help2man --no-info --no-discard-stderr --help-option=" --help" \
+ --name="generate a sequencing summary like file from a directory containing Fast5 files" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=Barcode_split
+help2man --no-info --no-discard-stderr --help-option=" --help" \
+ --name="simple tool to split sequencing summary report in per barcodes" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+
+echo "$MANDIR/*.1" > debian/manpages
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+ http://liw.fi/manpages/
+EOT
=====================================
debian/manpages
=====================================
@@ -0,0 +1 @@
+debian/*.1
=====================================
debian/patches/series
=====================================
@@ -0,0 +1 @@
+unversioned_depends_tqdm.patch
=====================================
debian/patches/unversioned_depends_tqdm.patch
=====================================
@@ -0,0 +1,15 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Wed, 22 Apr 2020 09:21:46 +0200
+Description: Do not check for absolute equality of tqdm
+
+--- a/setup.py
++++ b/setup.py
+@@ -34,7 +34,7 @@ setup(
+ 'plotly==4.1.0',
+ 'jinja2==2.10.1',
+ 'h5py==2.9.0',
+- 'tqdm==4.35.0',
++ 'tqdm>=4.35.0',
+ 'pysam==0.15.3'],
+ packages = [name],
+ package_dir = {name: name},
=====================================
debian/pycoQC.1
=====================================
@@ -0,0 +1,127 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.13.
+.TH PYCOQC "1" "April 2020" "pycoQC 2.5.0.21" "User Commands"
+.SH NAME
+pycoQC \- computes metrics and generates interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies basecallers
+.SH DESCRIPTION
+usage: pycoQC [\-h] [\-\-version]
+.IP
+[\-\-summary_file [SUMMARY_FILE [SUMMARY_FILE ...]]]
+[\-\-barcode_file [BARCODE_FILE [BARCODE_FILE ...]]]
+[\-\-bam_file [BAM_FILE [BAM_FILE ...]]]
+[\-\-html_outfile HTML_OUTFILE] [\-\-json_outfile JSON_OUTFILE]
+[\-\-min_pass_qual MIN_PASS_QUAL] [\-\-min_pass_len MIN_PASS_LEN]
+[\-\-filter_calibration] [\-\-filter_duplicated]
+[\-\-min_barcode_percent MIN_BARCODE_PERCENT]
+[\-\-report_title REPORT_TITLE] [\-\-template_file TEMPLATE_FILE]
+[\-\-config_file CONFIG_FILE] [\-\-sample SAMPLE] [\-\-default_config]
+[\-v | \fB\-q]\fR
+.PP
+pycoQC computes metrics and generates interactive QC plots from the sequencing summary
+report generated by Oxford Nanopore technologies basecallers
+.PP
+* Minimal usage
+.IP
+pycoQC \fB\-f\fR sequencing_summary.txt \fB\-o\fR pycoQC_output.html
+.PP
+* Including Guppy barcoding file + html output + json output
+.IP
+pycoQC \fB\-f\fR sequencing_summary.txt \fB\-b\fR barcoding_sequencing.txt \fB\-o\fR pycoQC_output.html \fB\-j\fR pycoQC_output.json
+.PP
+* Including Bam file + html output
+.IP
+pycoQC \fB\-f\fR sequencing_summary.txt \fB\-a\fR alignment.bam \fB\-o\fR pycoQC_output.html
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-\-version\fR
+show program's version number and exit
+.TP
+\fB\-v\fR, \fB\-\-verbose\fR
+Increase verbosity
+.TP
+\fB\-q\fR, \fB\-\-quiet\fR
+Reduce verbosity
+.SS "Input/output options:"
+.TP
+\fB\-\-summary_file\fR [SUMMARY_FILE [SUMMARY_FILE ...]], \fB\-f\fR [SUMMARY_FILE [SUMMARY_FILE ...]]
+Path to a sequencing_summary generated by Albacore
+1.0.0 + (read_fast5_basecaller.py) / Guppy 2.1.3+
+(guppy_basecaller). One can also pass multiple space
+separated file paths or a UNIX style regex matching
+multiple files (Required)
+.TP
+\fB\-\-barcode_file\fR [BARCODE_FILE [BARCODE_FILE ...]], \fB\-b\fR [BARCODE_FILE [BARCODE_FILE ...]]
+Path to the barcode_file generated by Guppy 2.1.3+
+(guppy_barcoder) or Deepbinner 0.2.0+. This is not a
+required file. One can also pass multiple space
+separated file paths or a UNIX style regex matching
+multiple files (optional)
+.TP
+\fB\-\-bam_file\fR [BAM_FILE [BAM_FILE ...]], \fB\-a\fR [BAM_FILE [BAM_FILE ...]]
+Path to a Bam file corresponding to reads in the
+summary_file. Preferably aligned with Minimap2 One can
+also pass multiple space separated file paths or a
+UNIX style regex matching multiple files (optional)
+.TP
+\fB\-\-html_outfile\fR HTML_OUTFILE, \fB\-o\fR HTML_OUTFILE
+Path to an output html file report (required if
+json_outfile not given)
+.TP
+\fB\-\-json_outfile\fR JSON_OUTFILE, \fB\-j\fR JSON_OUTFILE
+Path to an output json file report (required if
+html_outfile not given)
+.SS "Filtering options:"
+.TP
+\fB\-\-min_pass_qual\fR MIN_PASS_QUAL
+Minimum quality to consider a read as 'pass' (default:
+7)
+.TP
+\fB\-\-min_pass_len\fR MIN_PASS_LEN
+Minimum read length to consider a read as 'pass'
+(default: 0)
+.TP
+\fB\-\-filter_calibration\fR
+If given, reads flagged as calibration strand by the
+basecaller are removed (default: False)
+.TP
+\fB\-\-filter_duplicated\fR
+If given, duplicated read_ids are removed but the
+first occurence is kept (Guppy sometimes outputs the
+same read multiple times) (default: False)
+.TP
+\fB\-\-min_barcode_percent\fR MIN_BARCODE_PERCENT
+Minimal percent of total reads to retain barcode
+label. If below, the barcode value is set as
+`unclassified` (default: 0.1)
+.SS "HTML report options:"
+.TP
+\fB\-\-report_title\fR REPORT_TITLE
+Title to use in the html report (default: PycoQC
+report)
+.TP
+\fB\-\-template_file\fR TEMPLATE_FILE
+Jinja2 html template for the html report (default: )
+.TP
+\fB\-\-config_file\fR CONFIG_FILE
+Path to a JSON configuration file for the html report.
+If not provided, looks for it in ~/.pycoQC and
+~/.config/pycoQC/config. If it's still not found,
+falls back to default parameters. The first level keys
+are the names of the plots to be included. The second
+level keys are the parameters to pass to each plotting
+function (default: )")
+.SS "Other options:"
+.TP
+\fB\-\-sample\fR SAMPLE
+If not None a n number of reads will be randomly
+selected instead of the entire dataset for ploting
+function (deterministic sampling) (default: 100000)
+.TP
+\fB\-\-default_config\fR, \fB\-d\fR
+Print default configuration file. Can be used to
+generate a template JSON file (default: False)
+.SH AUTHOR
+ This manpage was written by Andreas Tille for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/source/lintian-overrides
=====================================
@@ -0,0 +1,2 @@
+# The rendered sample results are no JS without source
+pycoqc source: source-is-missing docs/pycoQC/results*
View it on GitLab: https://salsa.debian.org/med-team/pycoqc/-/compare/47825e4911720bef440d3fd13a595364d197d9e6...2a7e7f6f0b1643f2ae77b41ca1f8a953199df643
--
View it on GitLab: https://salsa.debian.org/med-team/pycoqc/-/compare/47825e4911720bef440d3fd13a595364d197d9e6...2a7e7f6f0b1643f2ae77b41ca1f8a953199df643
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