[med-svn] r22631 - in trunk/packages/metaphlan2/trunk/debian: . patches
Andreas Tille
tille at moszumanska.debian.org
Mon Jul 25 14:46:31 UTC 2016
Author: tille
Date: 2016-07-25 14:46:30 +0000 (Mon, 25 Jul 2016)
New Revision: 22631
Added:
trunk/packages/metaphlan2/trunk/debian/patches/spelling.patch
Modified:
trunk/packages/metaphlan2/trunk/debian/metaphlan2.1
trunk/packages/metaphlan2/trunk/debian/patches/series
Log:
Spelling fixes
Modified: trunk/packages/metaphlan2/trunk/debian/metaphlan2.1
===================================================================
--- trunk/packages/metaphlan2/trunk/debian/metaphlan2.1 2016-07-25 14:40:21 UTC (rev 22630)
+++ trunk/packages/metaphlan2/trunk/debian/metaphlan2.1 2016-07-25 14:46:30 UTC (rev 22631)
@@ -44,7 +44,7 @@
You can also provide an externally BowTie2\-mapped SAM if you specify this format with
\fB\-\-input_type\fR. Two steps: first apply BowTie2 and then feed MetaPhlAn2 with the obtained sam:
.IP
-bowtie2 \fB\-\-sam\-no\-hd\fR \fB\-\-sam\-no\-sq\fR \fB\-\-no\-unal\fR \fB\-\-very\-sensitive\fR \fB\-S\fR metagenome.sam \fB\-x\fR ${mpa_dir}/db_v20/mpa_v20_m200 \fB\-U\fR metagenome.fastq
+bowtie2 \fB\-\-sam\-no\-hd\fR \fB\-\-sam\-no\-sq\fR \fB\-\-no\-unal\fR \fB\-\-very\-sensitive\fR \fB\-S\fR metagenome.sam \fB\-x\fR /usr/share/metaphlan2/db_v20/mpa_v20_m200 \fB\-U\fR metagenome.fastq
metaphlan2 metagenome.sam \fB\-\-input_type\fR sam > profiled_metagenome.txt
.IP *
Multiple alternative ways to pass the input are also available:
Modified: trunk/packages/metaphlan2/trunk/debian/patches/series
===================================================================
--- trunk/packages/metaphlan2/trunk/debian/patches/series 2016-07-25 14:40:21 UTC (rev 22630)
+++ trunk/packages/metaphlan2/trunk/debian/patches/series 2016-07-25 14:46:30 UTC (rev 22631)
@@ -1,2 +1,3 @@
fix_sequence.patch
mpa_dir-is-usr_share_metaphlan2.patch
+spelling.patch
Added: trunk/packages/metaphlan2/trunk/debian/patches/spelling.patch
===================================================================
--- trunk/packages/metaphlan2/trunk/debian/patches/spelling.patch (rev 0)
+++ trunk/packages/metaphlan2/trunk/debian/patches/spelling.patch 2016-07-25 14:46:30 UTC (rev 22631)
@@ -0,0 +1,64 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Mon, 23 May 2016 16:09:13 +0200
+Description: Spelling
+
+--- a/README.md
++++ b/README.md
+@@ -247,7 +247,7 @@ positional arguments:
+ Required arguments:
+ --mpa_pkl MPA_PKL the metadata pickled MetaPhlAn file
+ --input_type {fastq,fasta,multifasta,multifastq,bowtie2out,sam}
+- set wheter the input is the multifasta file of metagenomic reads or
++ set whether the input is the multifasta file of metagenomic reads or
+ the SAM file of the mapping of the reads against the MetaPhlAn db.
+ [default 'automatic', i.e. the script will try to guess the input format]
+
+@@ -315,7 +315,7 @@ Post-mapping arguments:
+ Additional analysis types and arguments:
+ -t ANALYSIS TYPE Type of analysis to perform:
+ * rel_ab: profiling a metagenomes in terms of relative abundances
+- * rel_ab_w_read_stats: profiling a metagenomes in terms of relative abundances and estimate the number of reads comming from each clade.
++ * rel_ab_w_read_stats: profiling a metagenomes in terms of relative abundances and estimate the number of reads coming from each clade.
+ * reads_map: mapping from reads to clades (only reads hitting a marker)
+ * clade_profiles: normalized marker counts for clades with at least a non-null marker
+ * marker_ab_table: normalized marker counts (only when > 0.0 and normalized by metagenome size if --nreads is specified)
+@@ -705,7 +705,7 @@ python ../metaphlan2_strainer.py -h
+ The default setting can be stringent for some cases where you have very few samples left in the phylogenetic tree. You can relax some parameters to add more samples back:
+
+ 1. *marker_in_clade*: In each sample, the clades with the percentage of present markers less than this threshold are removed. Default "0.8". You can set this parameter to "0.5" to add some more samples.
+-2. *sample_in_marker*: If the percentage of samples that a marker present in is less than this threhold, that marker is removed. Default "0.8". You can set this parameter to "0.5" to add some more samples.
++2. *sample_in_marker*: If the percentage of samples that a marker present in is less than this threshold, that marker is removed. Default "0.8". You can set this parameter to "0.5" to add some more samples.
+ 3. *N_in_marker*: The consensus markers with the percentage of N nucleotides greater than this threshold are removed. Default "0.2". You can set this parameter to "0.5" to add some more samples.
+ 4. *gap_in_sample*: The samples with full sequences concatenated from all markers and having the percentage of gaps greater than this threshold will be removed. Default 0.2. You can set this parameter to "0.5" to add some more samples.
+ 5. *relaxed_parameters*: use this option to automatically set the above parameters to add some more samples by accepting some more gaps, Ns, etc. This option is equivalent to set: marker_in_clade=0.5, sample_in_marker=0.5, N_in_marker=0.5, gap_in_sample=0.5. Default "False".
+--- a/metaphlan2.py
++++ b/metaphlan2.py
+@@ -459,7 +459,7 @@ def read_params(args):
+ arg = g.add_argument
+ input_type_choices = ['fastq','fasta','multifasta','multifastq','bowtie2out','sam'] # !!!!
+ arg( '--input_type', choices=input_type_choices, required = 'True', help =
+- "set wheter the input is the multifasta file of metagenomic reads or \n"
++ "set whether the input is the multifasta file of metagenomic reads or \n"
+ "the SAM file of the mapping of the reads against the MetaPhlAn db.\n"
+ "[default 'automatic', i.e. the script will try to guess the input format]\n" )
+
+@@ -556,7 +556,7 @@ def read_params(args):
+ default='rel_ab', help =
+ "Type of analysis to perform: \n"
+ " * rel_ab: profiling a metagenomes in terms of relative abundances\n"
+- " * rel_ab_w_read_stats: profiling a metagenomes in terms of relative abundances and estimate the number of reads comming from each clade.\n"
++ " * rel_ab_w_read_stats: profiling a metagenomes in terms of relative abundances and estimate the number of reads coming from each clade.\n"
+ " * reads_map: mapping from reads to clades (only reads hitting a marker)\n"
+ " * clade_profiles: normalized marker counts for clades with at least a non-null marker\n"
+ " * marker_ab_table: normalized marker counts (only when > 0.0 and normalized by metagenome size if --nreads is specified)\n"
+--- a/metaphlan2_strainer.py
++++ b/metaphlan2_strainer.py
+@@ -154,7 +154,7 @@ def read_params():
+ default=0.8,
+ type=float,
+ help='If the percentage of samples that a marker present in is '\
+- 'less than this threhold, that marker is removed. Default 0.8.')
++ 'less than this threshold, that marker is removed. Default 0.8.')
+ p.add_argument(
+ '--gap_in_trailing_col',
+ required=False,
More information about the debian-med-commit
mailing list