[med-svn] [Git][med-team/fast5-research][master] Add manual pages for the scripts, remove lintian overrides and prevent sphinx...

Tue Aug 4 20:22:52 BST 2020


Shayan Doust pushed to branch master at Debian Med / fast5-research


Commits:
d514d956 by Shayan Doust at 2020-08-04T20:22:26+01:00
Add manual pages for the scripts, remove lintian overrides and prevent sphinx from generating the manpage

- - - - -


8 changed files:

- − debian/fast5-research.lintian-overrides
- debian/fast5-research.manpages
- + debian/mans/extract_reads.1
- + debian/mans/filter_from_bam.1
- + debian/mans/filter_reads.1
- + debian/mans/index_reads.1
- + debian/mans/read_summary.1
- debian/rules


Changes:

=====================================
debian/fast5-research.lintian-overrides deleted
=====================================
@@ -1,6 +0,0 @@
-# The following relevant binaries are documented within sphinx generated "man fast5_research"
-fast5-research: no-manual-page usr/bin/filter_from_bam
-fast5-research: no-manual-page usr/bin/filter_reads
-fast5-research: no-manual-page usr/bin/index_reads
-fast5-research: no-manual-page usr/bin/read_summary
-fast5-research: no-manual-page usr/bin/extract_reads


=====================================
debian/fast5-research.manpages
=====================================
@@ -1 +1 @@
-build/man/*
+debian/mans/*.1


=====================================
debian/mans/extract_reads.1
=====================================
@@ -0,0 +1,56 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.16.
+.TH EXTRACT_READS "1" "August 2020" "fast5-research" "User Commands"
+.SH NAME
+extract_reads \- extract reads from a bulk .fast5
+.SH DESCRIPTION
+Extracts reads from a bulk .fast5 to either single or multi-read .fast5
+.SH SYNOPSIS
+extract_reads [\-h] [\-\-multi | \fB\-\-single]\fR [\-\-flat] [\-\-by_id] [\-\-prefix PREFIX] [\-\-channel_range CHANNEL_RANGE CHANNEL_RANGE] [\-\-summary SUMMARY] [\-\-workers WORKERS] [\-\-limit LIMIT]
+input output
+.SS "positional arguments:"
+.TP
+input
+.br
+Bulk .fast5 file for input.
+.TP
+output
+.br
+Output folder.
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-\-multi\fR
+Output multi\-read files.
+.TP
+\fB\-\-single\fR
+Output single\-read files.
+.TP
+\fB\-\-flat\fR
+Create all .fast5 files in one directory
+.TP
+\fB\-\-by_id\fR
+Name single\-read .fast5 files by read_id.
+.TP
+\fB\-\-prefix\fR PREFIX
+Read file prefix.
+.TP
+\fB\-\-channel_range\fR CHANNEL_RANGE CHANNEL_RANGE
+Channel range (inclusive).
+.TP
+\fB\-\-summary\fR SUMMARY
+Strand summary file containing at least columns
+channel, start_time and duration).
+.TP
+\fB\-\-workers\fR WORKERS
+Number of worker processes.
+.TP
+\fB\-\-limit\fR LIMIT
+Limit reads per channel.
+.TP
+[\-\-prefix PREFIX]
+[\-\-channel_range CHANNEL_RANGE CHANNEL_RANGE]
+[\-\-summary SUMMARY] [\-\-workers WORKERS] [\-\-limit LIMIT]
+input output
+


=====================================
debian/mans/filter_from_bam.1
=====================================
@@ -0,0 +1,37 @@
+.TH FILTER_FROM_BAM "1" "August 2020" "fast5-research" "User Commands"
+.SH NAME
+filter_from_bam \- create filter file from BAM and sequencing summary
+.SH SYNOPSIS
+filter_from_bam [\-h] [\-\-seperator SEP] [\-\-id\-col READID_COL] [\-\-fname\-col FNAME_COL] [\-r REGION] [\-\-workers WORKERS] [\-p] BAM SUMMARY [SUMMARY ...]
+.SS "positional arguments:"
+.TP
+BAM
+.br
+Path to BAM file
+.TP
+SUMMARY
+.br
+Sequencing summary files
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-\-seperator\fR SEP
+Separator in sequencing summary files
+.TP
+\fB\-\-id\-col\fR READID_COL
+Column name for read_id in sequencing summary files
+.TP
+\fB\-\-fname\-col\fR FNAME_COL
+Column name for fast5 filename in sequencing summary
+files
+.TP
+\fB\-r\fR REGION, \fB\-\-region\fR REGION
+Print reads only from this region
+.TP
+\fB\-\-workers\fR WORKERS
+Number of worker processes.
+.TP
+\fB\-p\fR, \fB\-\-primary\-only\fR
+Ignore secondary and supplementary alignments


=====================================
debian/mans/filter_reads.1
=====================================
@@ -0,0 +1,46 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.16.
+.TH FILTER_READS "1" "August 2020" "fast5-research" "User Commands"
+.SH NAME
+filter_reads \- extract reads from multi\-read .fast5 files 
+.SH SYNOPSIS
+filter_reads [\-h] [\-\-tsv_field TSV_FIELD] [\-\-prefix PREFIX] [\-\-recursive] [\-\-workers WORKERS] [\-\-multi | \fB\-\-single]\fR input output filter
+.PP
+Extract reads from multi\-read .fast5 files.
+.SS "positional arguments:"
+.TP
+input
+.br
+Path to input multi\-read .fast5 files (or list of
+files).
+.TP
+output
+.br
+Output folder.
+.TP
+filter
+.br
+A .tsv file with column `read_id` defining required
+reads. If a `filename` column is present, this will be
+used as the location of the read.
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-\-tsv_field\fR TSV_FIELD
+Field name from `filter` file to obtain read IDs.
+.TP
+\fB\-\-prefix\fR PREFIX
+Read file prefix.
+.TP
+\fB\-\-recursive\fR
+Search recursively under `input` for source files.
+.TP
+\fB\-\-workers\fR WORKERS
+Number of worker processes.
+.TP
+\fB\-\-multi\fR
+Output multi\-read files.
+.TP
+\fB\-\-single\fR
+Output single\-read files.


=====================================
debian/mans/index_reads.1
=====================================
@@ -0,0 +1,20 @@
+.TH INDEX_READS "1" "August 2020" "fast5-research" "User Commands"
+.SH NAME
+index_reads \- build index of reads within .fast5 files. Output to stdout.
+.SH DESCRIPTION
+index_reads [\-h] [\-\-recursive] [\-\-workers WORKERS] input
+.SS "positional arguments:"
+.TP
+input
+.br
+\&.fast5 directory
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-\-recursive\fR
+Search recursively under `input` for source files.
+.TP
+\fB\-\-workers\fR WORKERS
+Number of worker processes.


=====================================
debian/mans/read_summary.1
=====================================
@@ -0,0 +1,21 @@
+.TH READ_SUMMARY "1" "August 2020" "fast5-research" "User Commands"
+.SH NAME
+read_summary \- summarise reads stored in a bulk .fast5. 
+.SH DESCRIPTION
+read_summary [\-h] [\-\-channel_range CHANNEL_RANGE CHANNEL_RANGE] input output
+.SS "positional arguments:"
+.TP
+input
+.br
+Bulk .fast5 file for input.
+.TP
+output
+.br
+Output text file.
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-\-channel_range\fR CHANNEL_RANGE CHANNEL_RANGE
+Channel range (inclusive).


=====================================
debian/rules
=====================================
@@ -16,7 +16,6 @@ override_dh_auto_build: export https_proxy=127.0.0.1:9
 override_dh_auto_build:
 	dh_auto_build
 	PYTHONPATH=. python3 -m sphinx -N -bhtml docs/ build/html # HTML generator
-	PYTHONPATH=. python3 -m sphinx -N -bman docs/ build/man # Manpage generator
 
 override_dh_auto_test:
 ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))



View it on GitLab: https://salsa.debian.org/med-team/fast5-research/-/commit/d514d956031f678e5ad1d92240873ef4e47c8de0

-- 
View it on GitLab: https://salsa.debian.org/med-team/fast5-research/-/commit/d514d956031f678e5ad1d92240873ef4e47c8de0
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