debian/changelog

@@ -9,6 +9,9 @@ lefse (1.0.8-3) UNRELEASED; urgency=medium
   * debhelper-compat 12
   * Standards-Version: 4.4.0
   * Secure URI in copyright format
+  * Fix installation of lefse.py
+  * Depends: python3-rpy2, r-cran-coin
+  * Add manpages
 
  -- Shayan Doust <hello@shayandoust.me>  Mon, 09 Sep 2019 21:01:50 +0200
 

debian/control

@@ -14,7 +14,9 @@ Homepage: https://bitbucket.org/biobakery/biobakery/wiki/lefse
 Package: lefse
 Architecture: all
 Depends: ${python3:Depends},
-         ${misc:Depends}
+         ${misc:Depends},
+         python3-rpy2,
+         r-cran-coin
 Description: determine features of organisms, clades, taxonomic units, genes
  LEfSe (Linear discriminant analysis Effect Size) determines the features
  (organisms, clades, operational taxonomic units, genes, or functions)

debian/createmanpages

+#!/bin/sh
+MANDIR=debian/mans
+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\nThis manpage was written by $DEBFULLNAME for the Debian distribution and
+can be used for any other usage of the program.
+"
+
+progname=format_input
+help2man --no-info --no-discard-stderr --help-option="-h" \
+         --name="$NAME" \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=lefse2circlader
+help2man --no-info --no-discard-stderr --help-option="-h" \
+         --name="$NAME" \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=plot_cladogram
+help2man --no-info --no-discard-stderr --help-option="-h" \
+         --name="$NAME" \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=plot_features
+help2man --no-info --no-discard-stderr --help-option="-h" \
+         --name="$NAME" \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=plot_res
+help2man --no-info --no-discard-stderr --help-option="-h" \
+         --name="$NAME" \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=qiime2lefse
+help2man --no-info --no-discard-stderr --help-option="-h" \
+         --name="$NAME" \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=run_lefse
+help2man --no-info --no-discard-stderr --help-option="-h" \
+         --name="$NAME" \
+            --version-string="$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

+debian/mans/*.1

debian/mans/format_input.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.11.
+.TH FORMAT_INPUT "1" "September 2019" "format_input 1.0.8" "User Commands"
+.SH NAME
+format_input \- determine features of organisms, clades, taxonomic units, genes
+.SH SYNOPSIS
+.B format_input
+[\-h] [\-\-output_table OUTPUT_TABLE] [\-f {c,r}]
+[\-c [1..n_feats]] [\-s [1..n_feats]] [\-o float]
+[\-u [1..n_feats]] [\-m {f,s}] [\-n int] [\-biom_c BIOM_CLASS]
+[\-biom_s BIOM_SUBCLASS]
+INPUT_FILE OUTPUT_FILE
+.SH DESCRIPTION
+LEfSe formatting modules
+.SH OPTIONS
+.SS "positional arguments:"
+.TP
+INPUT_FILE
+the input file, feature hierarchical level can be
+specified with | or . and those symbols must not be
+present for other reasons in the input file.
+.TP
+OUTPUT_FILE
+the output file containing the data for LEfSe
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-\-output_table\fR OUTPUT_TABLE
+the formatted table in txt format
+.TP
+\fB\-f\fR {c,r}
+set whether the features are on rows (default) or on
+columns
+.TP
+\fB\-c\fR [1..n_feats]
+set which feature use as class (default 1)
+.TP
+\fB\-s\fR [1..n_feats]
+set which feature use as subclass (default \fB\-1\fR meaning
+no subclass)
+.TP
+\fB\-o\fR float
+set the normalization value (default \fB\-1\fR.0 meaning no
+normalization)
+.TP
+\fB\-u\fR [1..n_feats]
+set which feature use as subject (default \fB\-1\fR meaning
+no subject)
+.TP
+\fB\-m\fR {f,s}
+set the policy to adopt with missin values: f removes
+the features with missing values, s removes samples
+with missing values (default f)
+.TP
+\fB\-n\fR int
+set the minimum cardinality of each subclass
+(subclasses with low cardinalities will be grouped
+together, if the cardinality is still low, no pairwise
+comparison will be performed with them)
+.TP
+\fB\-biom_c\fR BIOM_CLASS
+For biom input files: Set which feature use as class
+.TP
+\fB\-biom_s\fR BIOM_SUBCLASS
+For biom input files: set which feature use as
+subclass
+.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/mans/lefse2circlader.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.11.
+.TH LEFSE2CIRCLADER "1" "September 2019" "lefse2circlader 1.0.8" "User Commands"
+.SH NAME
+lefse2circlader \- determine features of organisms, clades, taxonomic units, genes
+.SH SYNOPSIS
+.B lefse2circlader
+[\-h] [\-l levels with label] [INPUT_FILE] [OUTPUT_FILE]
+.SH DESCRIPTION
+Convert LEfSe output to Circlader input
+.SH OPTIONS
+.SS "positional arguments:"
+.TP
+INPUT_FILE
+the input file [stdin if not present]
+.TP
+OUTPUT_FILE
+the output file [stdout if not present]
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.HP
+\fB\-l\fR levels with label
+.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/mans/plot_cladogram.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.11.
+.TH PLOT_CLADOGRAM "1" "September 2019" "plot_cladogram 1.0.8" "User Commands"
+.SH NAME
+plot_cladogram \- determine features of organisms, clades, taxonomic units, genes
+.SH SYNOPSIS
+.B plot_cladogram
+[\-h] [\-\-clade_sep CLADE_SEP] [\-\-max_lev MAX_LEV]
+[\-\-max_point_size MAX_POINT_SIZE]
+[\-\-min_point_size MIN_POINT_SIZE]
+[\-\-point_edge_width MARKEREDGEWIDTH]
+[\-\-siblings_connector_width SIBLINGS_CONNECTOR_WIDTH]
+[\-\-parents_connector_width PARENTS_CONNECTOR_WIDTH]
+[\-\-radial_start_lev RADIAL_START_LEV]
+[\-\-labeled_start_lev LABELED_START_LEV]
+[\-\-labeled_stop_lev LABELED_STOP_LEV]
+[\-\-abrv_start_lev ABRV_START_LEV]
+[\-\-abrv_stop_lev ABRV_STOP_LEV]
+[\-\-expand_void_lev EXPAND_VOID_LEV]
+[\-\-class_legend_vis CLASS_LEGEND_VIS]
+[\-\-colored_connector COLORED_CONNECTORS] [\-\-alpha ALPHA]
+[\-\-title TITLE] [\-\-sub_clade SUB_CLADE]
+[\-\-title_font_size TITLE_FONT_SIZE]
+[\-\-right_space_prop R_PROP] [\-\-left_space_prop L_PROP]
+[\-\-label_font_size LABEL_FONT_SIZE]
+[\-\-background_color {k,w}] [\-\-colored_labels {0,1}]
+[\-\-class_legend_font_size CLASS_LEGEND_FONT_SIZE]
+[\-\-dpi DPI] [\-\-format {png,svg,pdf}]
+[\-\-all_feats ALL_FEATS]
+INPUT_FILE OUTPUT_FILE
+.SH DESCRIPTION
+Cladoplot
+.SH OPTIONS
+.SS "positional arguments:"
+.TP
+INPUT_FILE
+tab delimited input file
+.TP
+OUTPUT_FILE
+the file for the output image
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.HP
+\fB\-\-clade_sep\fR CLADE_SEP
+.HP
+\fB\-\-max_lev\fR MAX_LEV
+.HP
+\fB\-\-max_point_size\fR MAX_POINT_SIZE
+.HP
+\fB\-\-min_point_size\fR MIN_POINT_SIZE
+.HP
+\fB\-\-point_edge_width\fR MARKEREDGEWIDTH
+.HP
+\fB\-\-siblings_connector_width\fR SIBLINGS_CONNECTOR_WIDTH
+.HP
+\fB\-\-parents_connector_width\fR PARENTS_CONNECTOR_WIDTH
+.HP
+\fB\-\-radial_start_lev\fR RADIAL_START_LEV
+.HP
+\fB\-\-labeled_start_lev\fR LABELED_START_LEV
+.HP
+\fB\-\-labeled_stop_lev\fR LABELED_STOP_LEV
+.HP
+\fB\-\-abrv_start_lev\fR ABRV_START_LEV
+.HP
+\fB\-\-abrv_stop_lev\fR ABRV_STOP_LEV
+.HP
+\fB\-\-expand_void_lev\fR EXPAND_VOID_LEV
+.HP
+\fB\-\-class_legend_vis\fR CLASS_LEGEND_VIS
+.HP
+\fB\-\-colored_connector\fR COLORED_CONNECTORS
+.HP
+\fB\-\-alpha\fR ALPHA
+.HP
+\fB\-\-title\fR TITLE
+.HP
+\fB\-\-sub_clade\fR SUB_CLADE
+.HP
+\fB\-\-title_font_size\fR TITLE_FONT_SIZE
+.HP
+\fB\-\-right_space_prop\fR R_PROP
+.HP
+\fB\-\-left_space_prop\fR L_PROP
+.HP
+\fB\-\-label_font_size\fR LABEL_FONT_SIZE
+.TP
+\fB\-\-background_color\fR {k,w}
+set the color of the background
+.TP
+\fB\-\-colored_labels\fR {0,1}
+draw the label with class color (1) or in black (0)
+.HP
+\fB\-\-class_legend_font_size\fR CLASS_LEGEND_FONT_SIZE
+.HP
+\fB\-\-dpi\fR DPI
+.TP
+\fB\-\-format\fR {png,svg,pdf}
+the format for the output file
+.HP
+\fB\-\-all_feats\fR ALL_FEATS
+.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/mans/plot_features.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.11.
+.TH PLOT_FEATURES "1" "September 2019" "plot_features 1.0.8" "User Commands"
+.SH NAME
+plot_features \- determine features of organisms, clades, taxonomic units, genes
+.SH SYNOPSIS
+.B plot_features
+[\-h] [\-\-width WIDTH] [\-\-height HEIGHT] [\-\-top TOP]
+[\-\-bot BOT] [\-\-title_font_size TITLE_FONT_SIZE]
+[\-\-class_font_size CLASS_FONT_SIZE]
+[\-\-class_label_pos {up,down}] [\-\-subcl_mean {y,n}]
+[\-\-subcl_median {y,n}] [\-\-font_size FONT_SIZE] [\-n flt]
+[\-\-format {png,pdf,svg}] [\-f {all,diff,one}]
+[\-\-feature_name FEATURE_NAME] [\-\-feature_num FEATURE_NUM]
+[\-\-archive {zip,none}] [\-\-background_color {k,w}]
+[\-\-dpi DPI]
+INPUT_FILE INPUT_FILE OUTPUT_FILE
+.SH DESCRIPTION
+Cladoplot
+.SH OPTIONS
+.SS "positional arguments:"
+.TP
+INPUT_FILE
+dataset files
+.TP
+INPUT_FILE
+LEfSe output file
+.TP
+OUTPUT_FILE
+the file for the output (the zip file if an archive is
+required, the output directory otherwise)
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.HP
+\fB\-\-width\fR WIDTH
+.HP
+\fB\-\-height\fR HEIGHT
+.TP
+\fB\-\-top\fR TOP
+set maximum y limit (\fB\-1\fR.0 means automatic limit)
+.TP
+\fB\-\-bot\fR BOT
+set minimum y limit (default 0.0, \fB\-1\fR.0 means automatic
+limit)
+.HP
+\fB\-\-title_font_size\fR TITLE_FONT_SIZE
+.HP
+\fB\-\-class_font_size\fR CLASS_FONT_SIZE
+.HP
+\fB\-\-class_label_pos\fR {up,down}
+.HP
+\fB\-\-subcl_mean\fR {y,n}
+.HP
+\fB\-\-subcl_median\fR {y,n}
+.HP
+\fB\-\-font_size\fR FONT_SIZE
+.TP
+\fB\-n\fR flt
+unused
+.TP
+\fB\-\-format\fR {png,pdf,svg}
+the format for the output file
+.TP
+\fB\-f\fR {all,diff,one}
+wheter to plot all features (all), only those
+differentially abundant according to LEfSe or only one
+(the one given with \fB\-\-feature_name\fR)
+.TP
+\fB\-\-feature_name\fR FEATURE_NAME
+The name of the feature to plot (levels separated by
+\&.)
+.TP
+\fB\-\-feature_num\fR FEATURE_NUM
+The number of the feature to plot
+.HP
+\fB\-\-archive\fR {zip,none}
+.TP
+\fB\-\-background_color\fR {k,w}
+set the color of the background
+.HP
+\fB\-\-dpi\fR DPI
+.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/mans/plot_res.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.11.
+.TH PLOT_RES "1" "September 2019" "plot_res 1.0.8" "User Commands"
+.SH NAME
+plot_res \- determine features of organisms, clades, taxonomic units, genes
+.SH SYNOPSIS
+.B plot_res
+[\-h] [\-\-feature_font_size FEATURE_FONT_SIZE]
+[\-\-format {png,svg,pdf}] [\-\-dpi DPI] [\-\-title TITLE]
+[\-\-title_font_size TITLE_FONT_SIZE]
+[\-\-class_legend_font_size CLASS_LEGEND_FONT_SIZE]
+[\-\-width WIDTH] [\-\-height HEIGHT] [\-\-left_space LS]
+[\-\-right_space RS] [\-\-orientation {h,v}] [\-\-autoscale {0,1}]
+[\-\-background_color {k,w}] [\-\-subclades N_SCL]
+[\-\-max_feature_len MAX_FEATURE_LEN] [\-\-all_feats ALL_FEATS]
+[\-\-otu_only] [\-\-report_features]
+INPUT_FILE OUTPUT_FILE
+.SH DESCRIPTION
+Plot results
+.SH OPTIONS
+.SS "positional arguments:"
+.TP
+INPUT_FILE
+tab delimited input file
+.TP
+OUTPUT_FILE
+the file for the output image
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-\-feature_font_size\fR FEATURE_FONT_SIZE
+the file for the output image
+.TP
+\fB\-\-format\fR {png,svg,pdf}
+the format for the output file
+.HP
+\fB\-\-dpi\fR DPI
+.HP
+\fB\-\-title\fR TITLE
+.HP
+\fB\-\-title_font_size\fR TITLE_FONT_SIZE
+.HP
+\fB\-\-class_legend_font_size\fR CLASS_LEGEND_FONT_SIZE
+.HP
+\fB\-\-width\fR WIDTH
+.TP
+\fB\-\-height\fR HEIGHT
+only for vertical histograms
+.HP
+\fB\-\-left_space\fR LS
+.HP
+\fB\-\-right_space\fR RS
+.HP
+\fB\-\-orientation\fR {h,v}
+.HP
+\fB\-\-autoscale\fR {0,1}
+.TP
+\fB\-\-background_color\fR {k,w}
+set the color of the background
+.TP
+\fB\-\-subclades\fR N_SCL
+number of label levels to be dislayed (starting from
+the leaves, \fB\-1\fR means all the levels, 1 is default )
+.TP
+\fB\-\-max_feature_len\fR MAX_FEATURE_LEN
+Maximum length of feature strings (def 60)
+.HP
+\fB\-\-all_feats\fR ALL_FEATS
+.TP
+\fB\-\-otu_only\fR
+Plot only species resolved OTUs (as opposed to all
+levels)
+.TP
+\fB\-\-report_features\fR
+Report important features to STDOUT
+.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/mans/qiime2lefse.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.11.
+.TH QIIME2LEFSE "1" "September 2019" "qiime2lefse 1.0.8" "User Commands"
+.SH NAME
+qiime2lefse \- determine features of organisms, clades, taxonomic units, genes
+.SH SYNOPSIS
+.B qiime2lefse
+[\-h] [\-\-in [INPUT_FILE]] [\-\-md [METADATA_FILE]]
+[\-\-out [OUTPUT_FILE]] [\-c class attribute]
+[\-s subclass attribute] [\-u subject attribute]
+.SH DESCRIPTION
+Script will convert QIIME TSV BIOM table for use with lefse. It is imperative
+that this table has taxa metadata associated with it named 'Consensus
+Lineage', this can be down with e.g. the follow biom convert script: \fB\-\-\-\-\fR biom
+convert \fB\-i\fR otu.biom \fB\-o\fR otu.txt \fB\-\-to\-tsv\fR \fB\-\-header\-key\fR Taxonomy \fB\-\-outputmetadata\-id\fR 'Consensus Lineage'
+.SH OPTIONS
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-\-in\fR [INPUT_FILE]
+the Qiime OTU table file [ stdin if not present ]
+.TP
+\fB\-\-md\fR [METADATA_FILE]
+the Qiime OTU table file [ only OTU table without
+metadata if not present ]
+.TP
+\fB\-\-out\fR [OUTPUT_FILE]
+the output file [stdout if not present]
+.TP
+\fB\-c\fR class attribute
+the attribute to use as class
+.TP
+\fB\-s\fR subclass attribute
+the attribute to use as subclass
+.TP
+\fB\-u\fR subject attribute
+the attribute to use as subject
+.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/mans/run_lefse.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.11.
+.TH RUN_LEFSE "1" "September 2019" "run_lefse 1.0.8" "User Commands"
+.SH NAME
+run_lefse \- determine features of organisms, clades, taxonomic units, genes
+.SH SYNOPSIS
+.B run_lefse
+[\-h] [\-o str] [\-a float] [\-w float] [\-l float] [\-\-nlogs int]
+[\-\-verbose int] [\-\-wilc int] [\-r str] [\-\-svm_norm int]
+[\-b int] [\-e int] [\-c int] [\-f float] [\-s {0,1,2}]
+[\-\-min_c int] [\-t str] [\-y {0,1}]
+INPUT_FILE OUTPUT_FILE
+.SH DESCRIPTION
+LEfSe 1.0
+.SH OPTIONS
+.SS "positional arguments:"
+.TP
+INPUT_FILE
+the input file
+.TP
+OUTPUT_FILE
+the output file containing the data for the visualization
+module
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-o\fR str
+set the file for exporting the result (only concise textual
+form)
+.TP
+\fB\-a\fR float
+set the alpha value for the Anova test (default 0.05)
+.TP
+\fB\-w\fR float
+set the alpha value for the Wilcoxon test (default 0.05)
+.TP
+\fB\-l\fR float
+set the threshold on the absolute value of the logarithmic
+LDA score (default 2.0)
+.TP
+\fB\-\-nlogs\fR int
+max log ingluence of LDA coeff
+.TP
+\fB\-\-verbose\fR int
+verbose execution (default 0)
+.TP
+\fB\-\-wilc\fR int
+wheter to perform the Wicoxon step (default 1)
+.TP
+\fB\-r\fR str
+select LDA or SVM for effect size (default LDA)
+.TP
+\fB\-\-svm_norm\fR int
+whether to normalize the data in [0,1] for SVM feature
+waiting (default 1 strongly suggested)
+.TP
+\fB\-b\fR int
+set the number of bootstrap iteration for LDA (default 30)
+.TP
+\fB\-e\fR int
+set whether perform the wilcoxon test only among the
+subclasses with the same name (default 0)
+.TP
+\fB\-c\fR int
+set whether perform the wilcoxon test ing the Curtis's
+approach [BETA VERSION] (default 0)
+.TP
+\fB\-f\fR float
+set the subsampling fraction value for each bootstrap
+iteration (default 0.66666)
+.TP
+\fB\-s\fR {0,1,2}
+set the multiple testing correction options. 0 no correction
+(more strict, default), 1 correction for independent
+comparisons, 2 correction for independent comparison
+.TP
+\fB\-\-min_c\fR int
+minimum number of samples per subclass for performing
+wilcoxon test (default 10)
+.TP
+\fB\-t\fR str
+set the title of the analysis (default input file without
+extension)
+.TP
+\fB\-y\fR {0,1}
+(for multiclass tasks) set whether the test is performed in
+a one\-against\-one ( 1 \- more strict!) or in a one\-againstall setting ( 0 \- less strict) (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.