.hg_archival.txt

 repo: 092c2fe2278cb7f0b18d81faeb4aab98b89dc096
-node: b2f9b3286d4be376805e3b5c26cf141ed375c605
+node: cbd7880df400b453b8beb4e62b39e4a23b5523b6
 branch: default
-tag: 2.7.5
+tag: 2.7.6

.hgtags

@@ -11,3 +11,6 @@ e424931b4d94d50cf62381c79c335935415b33b9 2.5.0
 8963e486f79043c79a299f7a684e4550b0115c32 2.7.0
 d8ab9ca4244c09a7a4995042a99fbba1e3598ac0 2.7.1
 a1fe0d15320c04f69d56f1b7dd31cff972a7b8df 2.7.2
+b2f9b3286d4be376805e3b5c26cf141ed375c605 2.7.5
+847b250adbe97b9f4adc7e15f0d4bb5a66e782ec 2.7.4
+178d1aaf4ac76e5d5477833e8e614104dcd32088 2.7.3

debian/changelog

+metaphlan2 (2.7.6-1) UNRELEASED; urgency=medium
+
+  * New upstream version
+  * Point Vcs fields to salsa.debian.org
+  * Standards-Version: 4.1.4
+  * Avoid privacy breach by referencing remote files from README.html
+
+ -- Andreas Tille <tille@debian.org>  Mon, 28 May 2018 07:27:16 +0200
+
 metaphlan2 (2.7.5-1) unstable; urgency=medium
 
   * New upstream version (no data shiped with this archive any more)

debian/control

@@ -8,9 +8,9 @@ Build-Depends: debhelper (>= 11~),
                dh-python,
                pandoc,
                bowtie2
-Standards-Version: 4.1.3
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/metaphlan2.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/metaphlan2.git
+Standards-Version: 4.1.4
+Vcs-Browser: https://salsa.debian.org/med-team/metaphlan2
+Vcs-Git: https://salsa.debian.org/med-team/metaphlan2.git
 Homepage: https://bitbucket.org/biobakery/metaphlan2
 
 Package: metaphlan2
@@ -21,7 +21,8 @@ Depends: ${python:Depends},
          python-biom-format,
          python-msgpack,
          python-pandas,
-         bowtie2
+         bowtie2,
+         libjs-twitter-bootstrap
 Description: Metagenomic Phylogenetic Analysis
  MetaPhlAn is a computational tool for profiling the composition of
  microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from

debian/docs

 README.html
+debian/images
\ No newline at end of file

debian/images/get-pngs

+#!/bin/sh
+# fetch PNG images that are used in README.html and referenced at remote locations
+
+wget https://bitbucket.org/repo/rM969K/images/476974413-tree_alignment.png
+wget https://bitbucket.org/repo/rM969K/images/1771497600-snp_distance.png
+wget https://bitbucket.org/repo/rM969K/images/1574126761-RAxML_bestTree.s__Bacteroides_caccae.tree.metadata.png

debian/rules

@@ -7,12 +7,10 @@
 
 override_dh_auto_build:
 	dh_auto_build
-	pandoc -s --from markdown --to html README.md > README.html
+	pandoc -s --from markdown --to html README.md | \
+	    sed -e 's#"[^"]*//cdnjs.cloudflare.com/ajax/libs/html5shiv/.*/html5shiv-printshiv.min.js"#"file:///usr/share/twitter-bootstrap/files/html5shiv/html5shiv-printshiv.min.js"#' \
+	        -e 's#"https://bitbucket.org/repo/r[Mm]969[Kk]/images#"images#' \
+	    > README.html
 
 override_dh_installchangelogs:
 	dh_installchangelogs changeset.txt
-
-#override_dh_fixperms:
-#	dh_fixperms
-#	chmod +x debian/*/usr/share/metaphlan2/strainer_tutorial/*.sh
-#	chmod -x debian/*/usr/share/metaphlan2/strainer_src/*.ini

debian/source/include-binaries

+debian/images/1574126761-RAxML_bestTree.s__Bacteroides_caccae.tree.metadata.png
+debian/images/1771497600-snp_distance.png
+debian/images/476974413-tree_alignment.png

metaphlan2.py

@@ -16,8 +16,8 @@ from __future__ import with_statement
 __author__ = ('Nicola Segata (nicola.segata@unitn.it), '
               'Duy Tin Truong, '
               'Francesco Asnicar (f.asnicar@unitn.it)')
-__version__ = '2.7.5'
-__date__ = '6 February 2018'
+__version__ = '2.7.6'
+__date__ = '2 March 2018'
 
 
 import sys
@@ -433,7 +433,7 @@ def read_params(args):
             "\n------------------------------------------------------------------- \n \n\n"
 
 
-            "\n========== MetaPhlAn 2 strain tracking ============================ \n\n"
+            "\n========== Marker level analysis ============================ \n\n"
             "MetaPhlAn 2 introduces the capability of charachterizing organisms at the strain level using non\n"
             "aggregated marker information. Such capability comes with several slightly different flavours and \n"
             "are a way to perform strain tracking and comparison across multiple samples.\n"
@@ -499,18 +499,16 @@ def read_params(args):
     arg('--mpa_pkl', type=str, default=None,
         help="The metadata pickled MetaPhlAn file [deprecated]")
 
-    arg('--bowtie2db', metavar="METAPHLAN_BOWTIE2_DB", type=str, default=None,
+    arg('--bowtie2db', metavar="METAPHLAN_BOWTIE2_DB", type=str, default=DEFAULT_DB_FOLDER,
         help=("The BowTie2 database file of the MetaPhlAn database. Used if "
-              "--input_type is fastq, fasta, multifasta, or multifastq "
-              "[deprecated]"))
+              "--input_type is fastq, fasta, multifasta, or multifastq [default "+DEFAULT_DB_FOLDER+"]\n"))
 
     arg('-x', '--index', type=str, default='v20_m200',
-        help=("Specify the id of the database version to use. If the database "
-              "files are not found on the local MetaPhlAn2 installation they "
-              "will be automatically downloaded"))
+        help=("Specify the id of the database version to use. If the database\n"
+              "files are not found on the local MetaPhlAn2 installation they\n"
+              "will be automatically downloaded\n"))
 
-    bt2ps = ['sensitive', 'very-sensitive', 'sensitive-local',
-             'very-sensitive-local']
+    bt2ps = ['sensitive', 'very-sensitive', 'sensitive-local', 'very-sensitive-local']
     arg('--bt2_ps', metavar="BowTie2 presets", default='very-sensitive',
         choices=bt2ps, help="Presets options for BowTie2 (applied only when a "
                             "multifasta file is provided)\n"
@@ -812,29 +810,32 @@ def download_unpack_tar(url, download_file_name, folder, bowtie2_build, nproc):
             sys.stderr.write("Fatal error running '{}'\nError message: '{}'\n\n".format(' '.join(bt2_cmd), e))
             sys.exit(1)
 
+    sys.stderr.write('Removing uncompress database {}\n'.format(fna_file))
+    os.remove(fna_file)
 
-def check_and_install_database(index, bowtie2_build, nproc):
+
+def check_and_install_database(index, bowtie2_db, bowtie2_build, nproc):
     """ Check if the database is installed, if not download and install """
 
-    if len(glob(os.path.join(DEFAULT_DB_FOLDER, "mpa_{}*".format(index)))) >= 7:
+    if len(glob(os.path.join(bowtie2_db, "mpa_{}*".format(index)))) >= 7:
         return
 
     # download the tar archive and decompress
     sys.stderr.write("\nDownloading MetaPhlAn2 database\nPlease note due to "
                      "the size this might take a few minutes\n")
-    download_unpack_tar(DATABASE_DOWNLOAD, index, DEFAULT_DB_FOLDER, bowtie2_build, nproc)
+    download_unpack_tar(DATABASE_DOWNLOAD, index, bowtie2_db, bowtie2_build, nproc)
     sys.stderr.write("\nDownload complete\n")
 
 
-def set_mapping_arguments(index):
+def set_mapping_arguments(index, bowtie2_db):
     mpa_pkl = 'mpa_pkl'
     bowtie2db = 'bowtie2db'
 
-    if os.path.isfile(os.path.join(DEFAULT_DB_FOLDER, "mpa_{}.pkl".format(index))):
-        mpa_pkl = os.path.join(DEFAULT_DB_FOLDER, "mpa_{}.pkl".format(index))
+    if os.path.isfile(os.path.join(bowtie2_db, "mpa_{}.pkl".format(index))):
+        mpa_pkl = os.path.join(bowtie2_db, "mpa_{}.pkl".format(index))
 
-    if glob(os.path.join(DEFAULT_DB_FOLDER, "mpa_{}*.bt2".format(index))):
-        bowtie2db = os.path.join(DEFAULT_DB_FOLDER, "mpa_{}".format(index))
+    if glob(os.path.join(bowtie2_db, "mpa_{}*.bt2".format(index))):
+        bowtie2db = os.path.join(bowtie2_db, "mpa_{}".format(index))
 
     return (mpa_pkl, bowtie2db)
 
@@ -1354,15 +1355,14 @@ def metaphlan2():
     pars = read_params(sys.argv)
 
     # check if the database is installed, if not then install
-    check_and_install_database(pars['index'], pars['bowtie2_build'],
-                               pars['nproc'])
+    check_and_install_database(pars['index'], pars['bowtie2db'], pars['bowtie2_build'], pars['nproc'])
 
     if pars['install']:
         sys.stderr.write('The database is installed\n')
         return
 
     # set correct map_pkl and bowtie2db variables
-    pars['mpa_pkl'], pars['bowtie2db'] = set_mapping_arguments(pars['index'])
+    pars['mpa_pkl'], pars['bowtie2db'] = set_mapping_arguments(pars['index'], pars['bowtie2db'])
 
     #if pars['inp'] is None and ( pars['input_type'] is None or  pars['input_type'] == 'automatic'):
     #    sys.stderr.write( "The --input_type parameter need top be specified when the "
@@ -1440,7 +1440,7 @@ def metaphlan2():
                             for p in ["1.bt2", "2.bt2", "3.bt2", "4.bt2", "rev.1.bt2", "rev.2.bt2"]]):
             sys.stderr.write("No MetaPhlAn BowTie2 database found (--index "
                              "option)!\nExpecting location {}\nExiting..."
-                             .format(DEFAULT_DB_FOLDER))
+                             .format(pars['bowtie2db']))
             sys.exit(1)
 
         if bow:

strainphlan_src/add_metadata_tree.py

@@ -11,7 +11,7 @@ import copy
 import ConfigParser
 import dendropy
 import numpy
-import ipdb
+# import ipdb
 
 
 def read_params():

utils/merge_metaphlan_tables.py

@@ -50,6 +50,9 @@ def merge( aaastrIn, astrLabels, iCol, ostm ):
             iLine = -1
             # For a line in the file
             for astrLine in iIn:
+                if astrLine[0].startswith('#'):
+                    continue
+
                 iLine += 1
 
                 # ID is from first column, data are everything else