Actualiser README.md

better check of format

Dockerfile

@@ -0,0 +1,102 @@
+FROM python:2.7.17-alpine AS builder
+
+RUN apk add --no-cache \
+    bash flex build-base curl openssl-dev bzip2-dev readline-dev sqlite-dev zlib-dev xz-dev tk-dev libffi-dev make ncurses-dev git
+
+RUN pip install Cython==0.29
+
+RUN mkdir -p /app
+WORKDIR /app
+COPY src .
+
+RUN gcc -o littlebigman littlebigman.c
+RUN python setup.py build_ext --inplace
+RUN python setup.py install
+RUN ./install.sh
+
+WORKDIR /app
+RUN git clone https://forge.metabarcoding.org/obitools/ecopcr.git
+WORKDIR /app/ecopcr/src
+RUN make clean && make \
+    && cp ecoPCR ecofind ecogrep /usr/local/bin
+
+WORKDIR /app
+RUN git clone https://forge.metabarcoding.org/obitools/ecoprimers.git
+WORKDIR /app/ecoprimers/src
+RUN make clean && make \
+    && cp ecoPrimers /usr/local/bin \
+    && cp ../tools/ecoPCRFormat.py /usr/local/bin/ecoPCRFormat \
+    && chmod +x /usr/local/bin/ecoPCRFormat
+
+WORKDIR /app
+RUN git clone --recurse-submodules https://forge.metabarcoding.org/obitools/sumatra.git
+WORKDIR /app/sumatra
+RUN make clean && make \
+    && cp sumatra /usr/local/bin 
+
+WORKDIR /app
+RUN git clone --recurse-submodules https://forge.metabarcoding.org/obitools/sumaclust.git
+WORKDIR /app/sumaclust
+RUN make clean && make \
+    && cp sumaclust /usr/local/bin 
+
+RUN find /usr/local/bin /usr/local/python2/bin /usr/local/python2/lib -type f -exec file {} \; | \
+    grep -E 'ELF (32-bit|64-bit) (executable|shared object)' | \
+    cut -d: -f1 | \
+    xargs -r strip --strip-unneeded || true
+
+RUN pip install "virtualenv<20" && \
+    virtualenv --system-site-packages /obitools-doc 
+    
+ENV PATH="/obitools-doc/bin:${PATH}"
+RUN pip install "sphinx==1.8.5"
+
+COPY doc /obitools-doc/doc
+
+RUN echo "/doc" > /obitools-doc/doc/sphinx/build_dir.txt
+
+ENV PYTHONPATH="/app"
+
+WORKDIR /obitools-doc/doc/sphinx
+RUN make html
+RUN cp /app/docserver.sh /usr/local/bin/docserver
+RUN chmod +x /usr/local/bin/docserver
+
+
+#--- Image finale minimaliste ---
+FROM python:2.7.17-alpine
+LABEL org.opencontainers.image.title="OBITools2 (legacy)"
+LABEL org.opencontainers.image.description="Legacy OBITools2 environment for compatibility with older pipelines and benchmarks. Includes OBITools2, ecoPCR, ecoPrimers, sumatra, and sumaclust. Python 2-based software stack. Full documentation embedded in the image."
+LABEL org.opencontainers.image.version="latest"
+LABEL org.opencontainers.image.authors="Eric Coissac <eric.coissac@metabarcoding.org>"
+LABEL org.opencontainers.image.url="https://registry.metabarcoding.org/image/obitools%2Fobitools2"
+LABEL org.opencontainers.image.documentation="https://metabarcoding.org/en/obitools/obitools2"
+LABEL org.opencontainers.image.source="https://forge.metabarcoding.org/obitools/obitools"
+
+# Dépendances runtime seulement (exemple)
+RUN apk add --no-cache \
+    openssl \
+    zlib \
+    libgomp
+
+# Copier Python compilé et libs depuis le builder
+COPY --from=builder /usr/local/lib/python2.7/site-packages /usr/local/lib/python2.7/site-packages
+COPY --from=builder /usr/local/bin /usr/local/bin
+COPY --from=builder /obitools-doc/doc/sphinx/build/html /doc
+
+RUN rm -rf /usr/local/share /usr/local/include /usr/local/lib/pkgconfig /usr/local/lib/python2.7/test && \
+    find /usr/local/bin /usr/local/python2/bin /usr/local/python2/lib -type f -exec file {} \; | \
+    grep -E 'ELF (32-bit|64-bit) (executable|shared object)' | \
+    cut -d: -f1 | \
+    xargs -r strip --strip-unneeded || true
+
+RUN mkdir -p /data 
+
+ENV LD_LIBRARY_PATH=/usr/local/lib
+ENV PATH="/usr/local/bin:${PATH}"
+
+VOLUME ["/data"]
+
+WORKDIR /data
+
+CMD ["ash"]

README.md

@@ -0,0 +1,11 @@
+# Legacy OBITools status
+
+Legacy OBITools is 20 years old. It was developed using Python 2, a language that is no longer supported. Therefore, maintaining this code is impossible. It has now been superseded by OBITools4, the latest version in the OBITools lineage.
+
+In order to enable users to continue using Legacy OBITools, a Docker image has been created and made available on the [metabarcoding.org registry](https://registry.metabarcoding.org). While we discourage using this old version for new projects, being able to run it can still be useful for reproducibility purposes.
+
+You can find more information about using this Docker image on the [relevant page](https://metabarcoding.org/en/obitools/obitools2) of the [new metabarcoding website](https://metabarcoding.org).
+
+All the best,
+
+Eric Coissac

doc/sphinx/source/welcome.rst

@@ -35,115 +35,6 @@ and all the sources can be downloaded from our subversion server
 Prerequisites
 .............
 
-To install the ``OBITools``, you need that these softwares are installed on your 
-system:
-
-* Python 2.7 (installed by default on most ``Unix`` systems, available from 
-  `the Python website <http://www.python.org/>`_)
-* ``gcc`` (installed by default on most ``Unix`` systems, available from the 
-  GNU sites dedicated to `GCC <https://www.gnu.org/software/gcc/>`_ and 
-  `GMake <https://www.gnu.org/software/make/>`_)
-  
-On a linux system 
-^^^^^^^^^^^^^^^^^
-
-You have to take care that the Python-dev packages are installed.
-
-On MacOSX
-^^^^^^^^^
-
-The C compiler and all the other compilation tools are included in the `XCode <https://itunes.apple.com/fr/app/xcode/id497799835?mt=12>`_
-application not installed by default. The Python included in the system is not
-suitable for running the ``OBITools``. You have to install a complete distribution
-of Python that you can download as a `MacOSX package from the Python website <https://www.python.org/downloads/>`_.
-  
-Downloading and installing the ``OBITools``
-...........................................
-
-The ``OBITools`` are downloaded and installed using the :download:`get-obitools.py <../../../get_obitools/get-obitools.py>` script.
-This is a user level installation that does not need administrator privilege.
-
-Once downloaded, move the file :download:`get-obitools.py <../../../get_obitools/get-obitools.py>` in the directory where you want to install
-the ``OBITools``. From a Unix terminal you must now run the command :
-
-  .. code-block:: bash
-
-      > python get-obitools.py
-      
-The script will create a new directory at the place you are running it in which all the
-``OBITools`` will be installed. No system privilege are required, and you system will not
-be altered in any way by the obitools installation.
-
-The newly created directory is named OBITools-VERSION where version is substituted by the
-latest version number available.
-
-Inside the newly created directory all the ``OBITools`` are installed. Close to this directory
-there is a shell script named ``obitools``. Running this script activate the ``OBITools``
-by reconfiguring your Unix environment. 
-
-  .. code-block:: bash
-
-	> ./obitools
-
-Once activated you can desactivate the ``OBITools`` byt typing the command ``exit``.
-
-  .. code-block:: bash
-
-	> exit
-	
-	OBITools are no more activated, Bye...
-	======================================
-	
-
-System level installation
-.........................
-
-To install the ``OBITools`` at the system level you can follow two options :
-
-	- copy the ``obitools`` script in a usual directory for installing program like ``/usr/local/bin``
-	  but never move the ``OBITools`` directory itself after the installation by the 
-	  :download:`get-obitools.py <../../../get_obitools/get-obitools.py>`.
-	  
-	- The other solution is to add the ``export/bin`` directory located in the ``OBITools`` directory
-	  to the ``PATH``environment variable.
-	  
-Retrieving the sources of the OBITools
-......................................
-
-If you want to compile by yourself the ``OBITools``, you will need to install the same
-prerequisite:
-
-  .. code-block:: bash
-  
-	> pip install -U virtualenv
-	
-	> pip install -U sphinx
-	
-	> pip install -U cython
-	
-moreover you need to install any subversion client (a list of clients is available from `Wikipedia <http://en.wikipedia.org/wiki/Comparison_of_Subversion_clients>`_)
-
-Then you can download the 
-
-  .. code-block:: bash
-
-      > svn co http://www.grenoble.prabi.fr/public-svn/OBISofts/OBITools/branches/OBITools-1.00/ OBITools
-
-This command will create a new directory called ``OBITools``.
-
-Compiling and installing the ``OBITools``
-.........................................
-
-From the directory where you retrieved the sources, execute the following commands:
- 
-  .. code-block:: bash
-
-      > cd OBITools
-
-      > python setup.py --serenity install
-      
-Once installed, you can test your installation by running the commands of the 
-:doc:`tutorials <./tutorials>`.
 
 
 Introduction

src/docserver.sh

@@ -0,0 +1,10 @@
+#!/bin/ash
+
+# Par défaut : /doc
+DOC_DIR="${1:-/doc}"
+PORT="${2:-8080}"
+
+echo "Serving documentation from $DOC_DIR on port $PORT..."
+cd "$DOC_DIR" || { echo "Directory not found: $DOC_DIR"; exit 1; }
+
+python -m SimpleHTTPServer "$PORT"

src/install.sh

@@ -0,0 +1,30 @@
+#!/bin/ash
+
+set -e
+
+SRC_DIR="/app"
+DEST_DIR="/usr/local/bin"
+PYTHON_INTERPRETER="$DEST_DIR/python2"
+
+mkdir -p "$DEST_DIR"
+
+for f in "$SRC_DIR"/*.py; do
+    [ -e "$f" ] || continue  # skip if no .py files
+
+    # skip setup.py explicitly
+    case "$(basename "$f")" in
+        setup.py) continue ;;
+    esac
+
+    base=$(basename "$f" .py)
+    dest="$DEST_DIR/$base"
+
+    # rewrite shebang line
+    {
+        echo "#!$PYTHON_INTERPRETER"
+        tail -n +2 "$f"
+    } > "$dest"
+
+    chmod +x "$dest"
+    echo "Installed script: $dest"
+done

src/littlebigman.c

@@ -0,0 +1,24 @@
+/*
+ * littlebigman.c
+ *
+ *  Created on: 11 juil. 2012
+ *      Author: coissac
+ */
+
+#include<stdio.h>
+
+int main(int argc, char *argv[])
+{
+    union { int entier;
+            char caractere[4] ;
+    } test;
+
+    test.entier=0x01020304;
+
+    if (test.caractere[3] == 1)
+       printf("-DLITTLE_END");
+    else
+        printf("-DBIG_END");
+
+	return 0;
+}

src/obiaddtaxids.py

@@ -348,6 +348,8 @@ if __name__=='__main__':
         entryIterator = SILVAIterator
         entries = entryIterator(entries, tax)
         options.tagname = 'species_name'
+    else:
+        raise Exception("Invalid database format (see --format option)")
 
     openFiles(options)
     
@@ -395,7 +397,7 @@ if __name__=='__main__':
 
     elif ((options.db_type =='UNITE_FULL') or (options.db_type =='UNITE_GENERAL')) :
         
-        restricting_ancestor = tax.findTaxonByName('Fungi')[0][0]
+        restricting_ancestor = None
                 
         for s in entries :
             

src/obitools/word/_readindex.ext.1.c

@@ -156,11 +156,9 @@
  * a data set that will trigger the worst case is nonexistent.  Heapsort's
  * only advantage over quicksort is that it requires little additional memory.
  */
-int
-heapsort(vbase, nmemb, size, compar)
-	void *vbase;
-	size_t nmemb, size;
-	int (*compar) __P((const void *, const void *));
+
+int heapsort(void *vbase, size_t nmemb, size_t size,
+             int (*compar)(const void *, const void *)) 
 {
 	register int cnt, i, j, l;
 	register char tmp, *tmp1, *tmp2;

src/pidname.c

@@ -0,0 +1,35 @@
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <errno.h>
+#include <unistd.h>
+#include <limits.h>
+
+int main(int argc, char* argv[])
+{
+    if (argc < 2) {
+        fprintf(stderr, "Usage: %s <pid>\n", argv[0]);
+        return 1;
+    }
+
+    pid_t pid = (pid_t)atoi(argv[1]);
+    char pathbuf[PATH_MAX];
+    char proc_path[64];
+
+    // Construire le chemin vers le lien symbolique de l'exécutable
+    snprintf(proc_path, sizeof(proc_path), "/proc/%d/exe", pid);
+
+    // Lire le chemin via le lien symbolique
+    ssize_t len = readlink(proc_path, pathbuf, sizeof(pathbuf) - 1);
+    
+    if (len == -1) {
+        fprintf(stderr, "PID %d: readlink() failed\n", pid);
+        fprintf(stderr, "    %s\n", strerror(errno));
+        return 1;
+    }
+
+    // Terminer la chaîne correctement
+    pathbuf[len] = '\0';
+    printf("proc %d: %s\n", pid, pathbuf);
+    return 0;
+}

src/setup.py

@@ -0,0 +1,117 @@
+# -*- coding: utf-8 -*-
+import os
+import glob
+import subprocess
+from setuptools import setup, Extension, find_packages
+from Cython.Build import cythonize
+
+def find_cython_modules(base_dir):
+    """
+    Find Cython modules recursively in `base_dir`, following these rules:
+    - For each _toto.pyx file:
+      * Include _toto*.c files except _toto.c
+      * Parse _toto.lnk to compile listed .c files into .o if not yet compiled
+      * Include .o files from the .lnk file
+      * Include include_dirs listed in _toto.cfiles
+    Returns a list of setuptools.Extension instances.
+    """
+    extensions = []
+
+    for dirpath, _, filenames in os.walk(base_dir):
+        for filename in filenames:
+            if not filename.endswith(".pyx"):
+                continue
+
+            pyx_path = os.path.join(dirpath, filename)
+            prefix = pyx_path[:-4]  # remove ".pyx"
+
+            # Find all _toto*.c except _toto.c itself
+            c_files = sorted([
+                f for f in glob.glob(prefix + "*.c")
+                if f != prefix + ".c"
+            ])
+
+            # Read include directories from _toto.cfiles if exists
+            cfiles_path = prefix + ".cfiles"
+            include_dirs = []
+            if os.path.isfile(cfiles_path):
+                with open(cfiles_path) as f:
+                    include_dirs = [line.strip() for line in f if line.strip()]
+
+            # Read .lnk file listing additional source .c files to compile into .o
+            lnk_path = prefix + ".lnk"
+            o_files = []
+            if os.path.isfile(lnk_path):
+                with open(lnk_path) as f:
+                    for line in f:
+                        line = line.strip()
+                        if not line:
+                            continue
+                        # If line ends with .c, compile it to .o if needed
+                        if line.endswith(".c"):
+                            c_file = line
+                            # If relative path, resolve relative to pyx_path dir
+                            if not os.path.isabs(c_file):
+                                c_file = os.path.join(dirpath, c_file)
+                            o_file = os.path.splitext(c_file)[0] + ".o"
+                            if not os.path.isfile(o_file):
+                                print("Compiling to object:", c_file)
+                                cmd = ["gcc", "-c", "-fPIC", "-O2", c_file, "-o", o_file]
+                                for inc in include_dirs:
+                                    cmd.extend(["-I", inc])
+                                subprocess.check_call(cmd)
+                            o_files.append(o_file)
+                        else:
+                            # For non-.c lines in .lnk, ignore or raise? 
+                            # Here just ignore
+                            pass
+
+            # Module name relative to base_dir, convert path to dotted module name
+            relpath = os.path.relpath(pyx_path, ".")  # <-- par rapport à la racine du projet
+            modname = os.path.splitext(relpath)[0].replace(os.sep, ".")
+
+            assert modname.startswith("obitools."), "Module name should start with 'obitools.'"
+
+            print("Extension module name:", modname)
+            print("Expected output path:", modname.replace('.', os.sep) + ".so")
+            
+            print("Building extension:", modname)
+            print("  Sources:")
+            for s in [pyx_path] + c_files + o_files:
+                print("    -", s)
+            print("  Include dirs:")
+            for inc in include_dirs:
+                print("    -", inc)
+
+            ext = Extension(
+                modname,
+                sources=[pyx_path] + c_files + o_files,
+                include_dirs=include_dirs,
+            )
+            extensions.append(ext)
+
+    print("Cython modules:", extensions)
+
+    return extensions
+
+print("Packages found:", find_packages())
+
+
+setup(
+    name="obitools",
+    version="2.0.0",
+    description="OBITools metabarcoding toolkit",
+    author="Eric Coissac <eric.coissac@metabarcoding.org>",
+    packages=find_packages(),
+    # package_dir option can be removed if obitools/ is in current dir
+    ext_modules=cythonize(
+        find_cython_modules("obitools"),
+        compiler_directives={'embedsignature': True},
+        language_level=2,
+        include_path=["obitools"]
+    ),
+    # Remove ext_package here!
+    zip_safe=False,
+    include_package_data=True,
+    options={'build_ext': {'force': True}},
+)

tree-maker/20250610123237629-tree.md

@@ -0,0 +1,278 @@
+```markdown
+/ 📂 app
+├── 📄 ali2consensus.py
+├── 📄 ecodbtaxstat.py
+├── 📄 ecotag.py
+├── 📄 ecotaxspecificity.py
+├── 📄 ecotaxstat.py
+├── 📄 extractreads.py
+├── 📄 extractreads2.py
+├── 📄 illuminapairedend.py
+├── 📄 ngsfilter.py
+├── 📄 obiaddtaxids.py
+├── 📄 obiannotate.py
+├── 📄 obiclean.py
+├── 📄 obicomplement.py
+├── 📄 obiconvert.py
+├── 📄 obicount.py
+├── 📄 obicut.py
+├── 📄 obidistribute.py
+├── 📄 obiextract.py
+├── 📄 obigrep.py
+├── 📄 obihead.py
+├── 📄 obijoinpairedend.py
+├── 📄 obipr2.py
+├── 📄 obisample.py
+├── 📄 obiselect.py
+├── 📄 obisilva.py
+├── 📄 obisort.py
+├── 📄 obisplit.py
+├── 📄 obistat.py
+├── 📄 obisubset.py
+├── 📄 obitab.py
+├── 📄 obitail.py
+├── 📄 obitaxonomy.py
+└── 📂 obitools/
+│  ├── 📄 SVGdraw.py
+│  ├── 📄 __init__.py
+│  ├── 📄 _obitools.h
+│  ├── 📄 _obitools.pxd
+│  ├── 📄 _obitools.pyx
+│  └── 📂 align/
+│    ├── 📄 __init__.py
+│    ├── 📄 _assemble.pxd
+│    ├── 📄 _assemble.pyx
+│    ├── 📄 _codonnws.pxd
+│    ├── 📄 _codonnws.pyx
+│    ├── 📄 _dynamic.pxd
+│    ├── 📄 _dynamic.pyx
+│    ├── 📄 _freeendgap.pxd
+│    ├── 📄 _freeendgap.pyx
+│    ├── 📄 _freeendgapfm.pxd
+│    ├── 📄 _freeendgapfm.pyx
+│    ├── 📄 _gprofilenws.pxd
+│    ├── 📄 _gprofilenws.pyx
+│    ├── 📄 _lcs.cfiles
+│    ├── 📄 _lcs.ext.1.c
+│    ├── 📄 _lcs.ext.2.c
+│    ├── 📄 _lcs.ext.3.c
+│    ├── 📄 _lcs.ext.4.c
+│    ├── 📄 _lcs.h
+│    ├── 📄 _lcs.lnk
+│    ├── 📄 _lcs.pxd
+│    ├── 📄 _lcs.pyx
+│    ├── 📄 _lcs_fast.h
+│    ├── 📄 _nws.pxd
+│    ├── 📄 _nws.pyx
+│    ├── 📄 _nwsdnabyprot.pxd
+│    ├── 📄 _nwsdnabyprot.pyx
+│    ├── 📄 _profilenws.pxd
+│    ├── 📄 _profilenws.pyx
+│    ├── 📄 _qsassemble.pyx
+│    ├── 📄 _qsrassemble.pyx
+│    ├── 📄 _rassemble.pxd
+│    ├── 📄 _rassemble.pyx
+│    ├── 📄 _sse.h
+│    ├── 📄 _upperbond.cfiles
+│    ├── 📄 _upperbond.ext.1.c
+│    ├── 📄 _upperbond.h
+│    ├── 📄 _upperbond.pxd
+│    ├── 📄 _upperbond.pyx
+│    ├── 📄 homopolymere.py
+│    ├── 📄 ssearch.py
+│  └── 📂 alignment/
+│    ├── 📄 __init__.py
+│    ├── 📄 ace.py
+│  └── 📂 barcodecoverage/
+│    ├── 📄 __init__.py
+│    ├── 📄 calcBc.py
+│    ├── 📄 drawBcTree.py
+│    ├── 📄 findErrors.py
+│    ├── 📄 readFiles.py
+│    ├── 📄 writeBcTree.py
+│  └── 📂 blast/
+│    ├── 📄 __init__.py
+│  └── 📂 carto/
+│    ├── 📄 __init__.py
+│    ├── 📄 truc.svg
+│    ├── 📄 truc2.svg
+│  ├── 📄 collections.py
+│  ├── 📄 decorator.py
+│  └── 📂 distances/
+│    ├── 📄 __init__.py
+│    ├── 📄 observed.py
+│    ├── 📄 phylip.py
+│    ├── 📄 r.py
+│  └── 📂 dnahash/
+│    ├── 📄 __init__.py
+│  └── 📂 ecobarcode/
+│    ├── 📄 __init__.py
+│    ├── 📄 databases.py
+│    ├── 📄 ecotag.py
+│    ├── 📄 options.py
+│    ├── 📄 rawdata.py
+│    ├── 📄 taxonomy.py
+│  └── 📂 ecopcr/
+│    ├── 📄 __init__.py
+│    ├── 📄 annotation.py
+│    ├── 📄 options.py
+│    ├── 📄 sequence.py
+│    ├── 📄 taxonomy.py
+│  └── 📂 ecotag/
+│    ├── 📄 __init__.py
+│    ├── 📄 parser.py
+│  └── 📂 eutils/
+│    ├── 📄 __init__.py
+│  ├── 📄 fast.py
+│  └── 📂 fasta/
+│    ├── 📄 __init__.py
+│    ├── 📄 _fasta.pxd
+│    ├── 📄 _fasta.pyx
+│  └── 📂 fastq/
+│    ├── 📄 __init__.py
+│    ├── 📄 _fastq.pyx
+│  └── 📂 fnaqual/
+│    ├── 📄 __init__.py
+│    ├── 📄 fasta.py
+│    ├── 📄 quality.py
+│  └── 📂 format/
+│    ├── 📄 __init__.py
+│    ├── 📄 _format.pyx
+│    └── 📂 genericparser/
+│      ├── 📄 __init__.py
+│      ├── 📄 _genericparser.pyx
+│    └── 📂 ontology/
+│      ├── 📄 __init__.py
+│      ├── 📄 go_obo.py
+│    ├── 📄 options.py
+│    └── 📂 sequence/
+│      ├── 📄 __init__.py
+│      ├── 📄 embl.py
+│      ├── 📄 fasta.py
+│      ├── 📄 fastq.py
+│      ├── 📄 fnaqual.py
+│      ├── 📄 genbank.py
+│      ├── 📄 tagmatcher.py
+│  └── 📂 goa/
+│    ├── 📄 __init__.py
+│    ├── 📄 parser.py
+│  └── 📂 graph/
+│    ├── 📄 __init__.py
+│    └── 📂 algorithms/
+│      ├── 📄 __init__.py
+│      ├── 📄 clique.py
+│      ├── 📄 compact.py
+│      ├── 📄 component.py
+│    ├── 📄 dag.py
+│    └── 📂 layout/
+│      ├── 📄 __init__.py
+│      ├── 📄 radialtree.py
+│    ├── 📄 rootedtree.py
+│    ├── 📄 tree.py
+│  ├── 📄 gzip.py
+│  └── 📂 interactive/
+│    ├── 📄 __init__.py
+│  └── 📂 location/
+│    ├── 📄 __init__.py
+│    ├── 📄 feature.py
+│  └── 📂 metabarcoding/
+│    ├── 📄 __init__.py
+│    ├── 📄 options.py
+│  └── 📂 obischemas/
+│    ├── 📄 __init__.py
+│    └── 📂 kb/
+│      ├── 📄 __init__.py
+│      ├── 📄 extern.py
+│    ├── 📄 options.py
+│  └── 📂 obo/
+│    ├── 📄 __init__.py
+│    └── 📂 go/
+│      ├── 📄 __init__.py
+│      ├── 📄 parser.py
+│    ├── 📄 parser.py
+│  └── 📂 options/
+│    ├── 📄 __init__.py
+│    ├── 📄 _bioseqfilter.pyx
+│    ├── 📄 _options.pyx
+│    ├── 📄 bioseqcutter.py
+│    ├── 📄 bioseqedittag.py
+│    ├── 📄 bioseqfilter.py
+│    ├── 📄 taxonomyfilter.py
+│  └── 📂 parallel/
+│    ├── 📄 __init__.py
+│    ├── 📄 jobqueue.py
+│  └── 📂 phylogeny/
+│    ├── 📄 __init__.py
+│    ├── 📄 newick.py
+│  └── 📂 profile/
+│    ├── 📄 __init__.py
+│    ├── 📄 _profile.pxd
+│    ├── 📄 _profile.pyx
+│  ├── 📄 sample.py
+│  └── 📂 seqdb/
+│    ├── 📄 __init__.py
+│    └── 📂 blastdb/
+│      ├── 📄 __init__.py
+│    ├── 📄 dnaparser.py
+│    └── 📂 embl/
+│      ├── 📄 __init__.py
+│      ├── 📄 parser.py
+│    └── 📂 genbank/
+│      ├── 📄 __init__.py
+│      ├── 📄 ncbi.py
+│      ├── 📄 parser.py
+│  └── 📂 sequenceencoder/
+│    ├── 📄 __init__.py
+│  └── 📂 solexa/
+│    ├── 📄 __init__.py
+│  ├── 📄 solexaPairEnd.py
+│  └── 📂 statistics/
+│    ├── 📄 __init__.py
+│    ├── 📄 hypergeometric.py
+│    ├── 📄 noncentralhypergeo.py
+│  ├── 📄 svg.py
+│  └── 📂 table/
+│    ├── 📄 __init__.py
+│    ├── 📄 csv.py
+│  └── 📂 tagmatcher/
+│    ├── 📄 __init__.py
+│    ├── 📄 options.py
+│    ├── 📄 parser.py
+│  └── 📂 thermo/
+│    ├── 📄 __init__.py
+│  └── 📂 tools/
+│    ├── 📄 __init__.py
+│    ├── 📄 _solexapairend.pyx
+│    ├── 📄 solexapairend.py
+│  └── 📂 tree/
+│    ├── 📄 __init__.py
+│    ├── 📄 dot.py
+│    ├── 📄 layout.py
+│    ├── 📄 newick.py
+│    ├── 📄 svg.py
+│    ├── 📄 unrooted.py
+│  └── 📂 unit/
+│    ├── 📄 __init__.py
+│    └── 📂 obitools/
+│      ├── 📄 __init__.py
+│  └── 📂 utils/
+│    ├── 📄 __init__.py
+│    ├── 📄 _utils.pxd
+│    ├── 📄 _utils.pyx
+│    ├── 📄 bioseq.py
+│    ├── 📄 crc64.py
+│    ├── 📄 iterator.py
+│  ├── 📄 version.py
+│  └── 📂 word/
+│    ├── 📄 __init__.py
+│    ├── 📄 _binary.pyx
+│    ├── 📄 _readindex.cfiles
+│    ├── 📄 _readindex.ext.1.c
+│    ├── 📄 _readindex.h
+│    ├── 📄 _readindex.pyx
+│    ├── 📄 options.py
+│    ├── 📄 predicate.py
+│  ├── 📄 zipfile.py
+├── 📄 obiuniq.py
+└── 📄 oligotag.py
+```