FunVIP 0.3.22.2__tar.gz → 0.3.23__tar.gz

{funvip-0.3.22.2 → funvip-0.3.23}/FunVIP.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: FunVIP
-Version: 0.3.22.2
+Version: 0.3.23
 Summary: Fungal Validation & Identification Pipeline
 Author-email: Changwan Seo <wan101010@snu.ac.kr>
 License: GPL-3.0

{funvip-0.3.22.2 → funvip-0.3.23}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: FunVIP
-Version: 0.3.22.2
+Version: 0.3.23
 Summary: Fungal Validation & Identification Pipeline
 Author-email: Changwan Seo <wan101010@snu.ac.kr>
 License: GPL-3.0

{funvip-0.3.22.2 → funvip-0.3.23}/funvip/external/BLAST_Windows/bin/cleanup-blastdb-volumes.py

@@ -1,162 +1,162 @@
-#!/usr/bin/env python3
-"""
-# $Id: cleanup-blastdb-volumes.py 590894 2019-08-07 14:59:53Z camacho $
-# ===========================================================================
-# 
-#                            PUBLIC DOMAIN NOTICE
-#               National Center for Biotechnology Information
-# 
-#  This software/database is a "United States Government Work" under the
-#  terms of the United States Copyright Act.  It was written as part of
-#  the author's official duties as a United States Government employee and
-#  thus cannot be copyrighted.  This software/database is freely available
-#  to the public for use. The National Library of Medicine and the U.S.
-#  Government have not placed any restriction on its use or reproduction.
-# 
-#  Although all reasonable efforts have been taken to ensure the accuracy
-#  and reliability of the software and data, the NLM and the U.S.
-#  Government do not and cannot warrant the performance or results that
-#  may be obtained by using this software or data. The NLM and the U.S.
-#  Government disclaim all warranties, express or implied, including
-#  warranties of performance, merchantability or fitness for any particular
-#  purpose.
-# 
-#  Please cite the author in any work or product based on this material.
-# 
-# ===========================================================================
-# 
-# Author:  Christiam Camacho
-# 
-# File Description:
-#   Script to remove needless BLAST database files.
-# 
-# ===========================================================================
-"""
-import argparse, os, configparser
-import unittest, tempfile
-from pathlib import Path
-from glob import glob
-
-VERSION = '1.0'
-DESC = r""" Remove needless BLAST database volumes.  """
-
-
-class Tester(unittest.TestCase):
-    """ Testing class for this script. """
-
-    def test_blastdb_config_invalid(self):
-        rv = get_blastdb_from_ncbi_config("/dev/null")
-        self.assertIsNone(rv)
-
-    def test_blastdb_config(self):
-        config = configparser.ConfigParser()
-        expected = "/blast/db/blast"
-        config['BLAST'] = {'BLASTDB': expected}
-        tf = tempfile.NamedTemporaryFile(mode="wt")
-        config.write(tf)
-        tf.flush()
-        rv = get_blastdb_from_ncbi_config(tf.name)
-        self.assertEqual(expected, rv)
-
-    def test_blastdb_finder(self):
-        tal = tempfile.NamedTemporaryFile(suffix=".pin")
-        dbname = find_blastdb(tal.name[:-4], True)
-        self.assertEqual(dbname, tal.name[:-4])
-
-
-def find_blastdb(name: str, is_prot: bool) -> str:
-    """ Returns full path to BLAST database or None. """
-    alias_file = "{}.{}al".format(name, "p" if is_prot else "n")
-    index_file = "{}.{}in".format(name, "p" if is_prot else "n")
-    if os.path.exists(alias_file) or os.path.exists(index_file):
-        return name
-
-    if "BLASTDB" in os.environ:
-        alf = os.path.join(os.environ["BLASTDB"], alias_file)
-        idxf = os.path.join(os.environ["BLASTDB"], index_file)
-        if os.path.exists(alf) or os.path.exists(idxf):
-            return os.path.join(os.environ["BLASTDB"], name)
-
-    paths = [ os.getcwd(), str(Path.home()) ]
-    if "NCBI" in os.environ:
-        paths.append(os.path.join(os.environ["NCBI"]))
-
-    for path in paths:
-        for fname in [ ".ncbirc", "ncbi.ini" ]:
-            ncbirc = os.path.join(path, fname)
-            if os.path.exists(ncbirc):
-                blastdb = get_blastdb_from_ncbi_config(ncbirc)
-                if blastdb is not None:
-                    alf = os.path.join(blastdb, alias_file)
-                    idxf = os.path.join(blastdb, index_file)
-                    if os.path.exists(alf) or os.path.exists(idxf):
-                        return os.path.join(blastdb, name)
-
-
-def get_blastdb_from_ncbi_config(config_file: str) -> str:
-    """ Return the BLASTDB setting from the NCBI configuration file or None. """
-    config = configparser.ConfigParser()
-    config.read(config_file)
-    if 'BLAST' in config and 'BLASTDB' in config['BLAST']:
-        return config['BLAST']['BLASTDB']
-
-
-def main():
-    """ Entry point into this program. """
-    parser = create_arg_parser()
-    args = parser.parse_args()
-
-    ext = args.dbtype[0]
-    db = find_blastdb(args.db, ext == 'p')
-    if db == None:
-        print("Cannot find {} {} BLAST database".
-              format("protein" if ext == 'p' else "nucleotide", args.db),
-              file=sys.stderr)
-        return 1
-
-    alias_file = "{}.{}al".format(db, ext)
-    if not os.path.exists(alias_file):
-        return 1
-
-    with open(alias_file, "rt") as al:
-        for line in al:
-            if not line.startswith("DBLIST"):
-                continue
-            vols = list(map(lambda x: x.replace('"', ''), line.split()[1:]))
-            for existing_vols in sorted(glob("{}.*.{}in".format(db, ext))):
-                vol_name = os.path.basename(existing_vols)[:-4]
-                if vol_name in vols:
-                    continue
-                if args.dry_run:
-                    print("Will remove extra volume {}".format(existing_vols[:-4]))
-                to_rm = glob("{}??".format(existing_vols[:-2]))
-                to_rm += glob("{}.tar.gz.md5".format(existing_vols[:-4]))
-                for f in to_rm:
-                    if not args.dry_run:
-                        os.unlink(f)
-                        print("Removed {}".format(f))
-                    elif args.verbose > 0:
-                        print("Will remove {}".format(f))
-
-    return 0
-
-
-def create_arg_parser():
-    """ Create the command line options parser object for this script. """
-    parser = argparse.ArgumentParser(description=DESC)
-    parser.add_argument("-db", required=True, help="BLAST database name")
-    parser.add_argument("-dbtype", help="Molecule type", required=True,
-                        choices=["prot", "nucl"])
-    parser.add_argument("-dry-run", action='store_true',
-                        help="Do not delete any files, just list them")
-    parser.add_argument('-version', action='version',
-                        version='%(prog)s ' + VERSION)
-    parser.add_argument("-verbose", action="count", default=0,
-                        help="Increase output verbosity")
-    return parser
-
-
-if __name__ == "__main__":
-    import sys
-    sys.exit(main())
-
+#!/usr/bin/env python3
+"""
+# $Id: cleanup-blastdb-volumes.py 590894 2019-08-07 14:59:53Z camacho $
+# ===========================================================================
+# 
+#                            PUBLIC DOMAIN NOTICE
+#               National Center for Biotechnology Information
+# 
+#  This software/database is a "United States Government Work" under the
+#  terms of the United States Copyright Act.  It was written as part of
+#  the author's official duties as a United States Government employee and
+#  thus cannot be copyrighted.  This software/database is freely available
+#  to the public for use. The National Library of Medicine and the U.S.
+#  Government have not placed any restriction on its use or reproduction.
+# 
+#  Although all reasonable efforts have been taken to ensure the accuracy
+#  and reliability of the software and data, the NLM and the U.S.
+#  Government do not and cannot warrant the performance or results that
+#  may be obtained by using this software or data. The NLM and the U.S.
+#  Government disclaim all warranties, express or implied, including
+#  warranties of performance, merchantability or fitness for any particular
+#  purpose.
+# 
+#  Please cite the author in any work or product based on this material.
+# 
+# ===========================================================================
+# 
+# Author:  Christiam Camacho
+# 
+# File Description:
+#   Script to remove needless BLAST database files.
+# 
+# ===========================================================================
+"""
+import argparse, os, configparser
+import unittest, tempfile
+from pathlib import Path
+from glob import glob
+
+VERSION = '1.0'
+DESC = r""" Remove needless BLAST database volumes.  """
+
+
+class Tester(unittest.TestCase):
+    """ Testing class for this script. """
+
+    def test_blastdb_config_invalid(self):
+        rv = get_blastdb_from_ncbi_config("/dev/null")
+        self.assertIsNone(rv)
+
+    def test_blastdb_config(self):
+        config = configparser.ConfigParser()
+        expected = "/blast/db/blast"
+        config['BLAST'] = {'BLASTDB': expected}
+        tf = tempfile.NamedTemporaryFile(mode="wt")
+        config.write(tf)
+        tf.flush()
+        rv = get_blastdb_from_ncbi_config(tf.name)
+        self.assertEqual(expected, rv)
+
+    def test_blastdb_finder(self):
+        tal = tempfile.NamedTemporaryFile(suffix=".pin")
+        dbname = find_blastdb(tal.name[:-4], True)
+        self.assertEqual(dbname, tal.name[:-4])
+
+
+def find_blastdb(name: str, is_prot: bool) -> str:
+    """ Returns full path to BLAST database or None. """
+    alias_file = "{}.{}al".format(name, "p" if is_prot else "n")
+    index_file = "{}.{}in".format(name, "p" if is_prot else "n")
+    if os.path.exists(alias_file) or os.path.exists(index_file):
+        return name
+
+    if "BLASTDB" in os.environ:
+        alf = os.path.join(os.environ["BLASTDB"], alias_file)
+        idxf = os.path.join(os.environ["BLASTDB"], index_file)
+        if os.path.exists(alf) or os.path.exists(idxf):
+            return os.path.join(os.environ["BLASTDB"], name)
+
+    paths = [ os.getcwd(), str(Path.home()) ]
+    if "NCBI" in os.environ:
+        paths.append(os.path.join(os.environ["NCBI"]))
+
+    for path in paths:
+        for fname in [ ".ncbirc", "ncbi.ini" ]:
+            ncbirc = os.path.join(path, fname)
+            if os.path.exists(ncbirc):
+                blastdb = get_blastdb_from_ncbi_config(ncbirc)
+                if blastdb is not None:
+                    alf = os.path.join(blastdb, alias_file)
+                    idxf = os.path.join(blastdb, index_file)
+                    if os.path.exists(alf) or os.path.exists(idxf):
+                        return os.path.join(blastdb, name)
+
+
+def get_blastdb_from_ncbi_config(config_file: str) -> str:
+    """ Return the BLASTDB setting from the NCBI configuration file or None. """
+    config = configparser.ConfigParser()
+    config.read(config_file)
+    if 'BLAST' in config and 'BLASTDB' in config['BLAST']:
+        return config['BLAST']['BLASTDB']
+
+
+def main():
+    """ Entry point into this program. """
+    parser = create_arg_parser()
+    args = parser.parse_args()
+
+    ext = args.dbtype[0]
+    db = find_blastdb(args.db, ext == 'p')
+    if db == None:
+        print("Cannot find {} {} BLAST database".
+              format("protein" if ext == 'p' else "nucleotide", args.db),
+              file=sys.stderr)
+        return 1
+
+    alias_file = "{}.{}al".format(db, ext)
+    if not os.path.exists(alias_file):
+        return 1
+
+    with open(alias_file, "rt") as al:
+        for line in al:
+            if not line.startswith("DBLIST"):
+                continue
+            vols = list(map(lambda x: x.replace('"', ''), line.split()[1:]))
+            for existing_vols in sorted(glob("{}.*.{}in".format(db, ext))):
+                vol_name = os.path.basename(existing_vols)[:-4]
+                if vol_name in vols:
+                    continue
+                if args.dry_run:
+                    print("Will remove extra volume {}".format(existing_vols[:-4]))
+                to_rm = glob("{}??".format(existing_vols[:-2]))
+                to_rm += glob("{}.tar.gz.md5".format(existing_vols[:-4]))
+                for f in to_rm:
+                    if not args.dry_run:
+                        os.unlink(f)
+                        print("Removed {}".format(f))
+                    elif args.verbose > 0:
+                        print("Will remove {}".format(f))
+
+    return 0
+
+
+def create_arg_parser():
+    """ Create the command line options parser object for this script. """
+    parser = argparse.ArgumentParser(description=DESC)
+    parser.add_argument("-db", required=True, help="BLAST database name")
+    parser.add_argument("-dbtype", help="Molecule type", required=True,
+                        choices=["prot", "nucl"])
+    parser.add_argument("-dry-run", action='store_true',
+                        help="Do not delete any files, just list them")
+    parser.add_argument('-version', action='version',
+                        version='%(prog)s ' + VERSION)
+    parser.add_argument("-verbose", action="count", default=0,
+                        help="Increase output verbosity")
+    return parser
+
+
+if __name__ == "__main__":
+    import sys
+    sys.exit(main())
+

{funvip-0.3.22.2 → funvip-0.3.23}/funvip/external/BLAST_Windows/bin/get_species_taxids.sh

@@ -1,152 +1,152 @@
-#!/bin/bash
-# $Id: get_species_taxids.sh 631039 2021-05-12 14:35:54Z fongah2 $
-# ===========================================================================
-#
-#                            PUBLIC DOMAIN NOTICE
-#               National Center for Biotechnology Information
-#
-#  This software/database is a "United States Government Work" under the
-#  terms of the United States Copyright Act.  It was written as part of
-#  the author's official duties as a United States Government employee and
-#  thus cannot be copyrighted.  This software/database is freely available
-#  to the public for use. The National Library of Medicine and the U.S.
-#  Government have not placed any restriction on its use or reproduction.
-#
-#  Although all reasonable efforts have been taken to ensure the accuracy
-#  and reliability of the software and data, the NLM and the U.S.
-#  Government do not and cannot warrant the performance or results that
-#  may be obtained by using this software or data. The NLM and the U.S.
-#  Government disclaim all warranties, express or implied, including
-#  warranties of performance, merchantability or fitness for any particular
-#  purpose.
-#
-#  Please cite the author in any work or product based on this material.
-#
-# ===========================================================================
-#
-# Author:  Amelia Fong
-#
-# File Description:
-#   Script to convert NCBI taxonomy IDs or text into taxonomy IDs suitable for
-#   filtering BLAST searches.
-#
-# N.B.: Depends on EDirect (https://www.ncbi.nlm.nih.gov/books/NBK179288/)
-#
-# ===========================================================================
-
-export PATH=/bin:/usr/bin:/am/ncbiapdata/bin:$HOME/edirect:$PATH
-set -uo pipefail
-
-TOO_MANY_MATCHES=500
-OUTPUT=`mktemp`
-TMP=`mktemp`
-trap " /bin/rm -fr $OUTPUT $TMP" INT QUIT EXIT HUP KILL ALRM
-
-usage() { 
-    echo "$0 usage:"; 
-    echo -e "\t-t <taxonomy ID>\n\t\tGet taxonomy IDs at or below input taxonomy ID level"; 
-    echo -e "\t-n <Scientific Name, Common Name or Keyword>\n\t\tGet taxonomy information for organism";
-    exit 0; 
-}
-
-error_exit() {
-    msg=$1
-    exit_code=${2:-1}
-    >&2 echo $msg;
-    exit $exit_code;
-}
-
-check_deps() {
-    for app in esearch efetch esummary; do 
-        command -v $app >/dev/null 2>&1 || error_exit "Cannot find Entrez EDirect $app tool, please see installation in https://www.ncbi.nlm.nih.gov/books/NBK179288/"
-    done
-}
-
-check_deps
-
-TAXID=""
-NAME=""
-while getopts  "ht::n::o::" OPT; do
-    case $OPT in
-        h)
-            usage
-            ;;
-        t)
-            TAXID=${OPTARG}
-            ;;
-        n)
-            NAME=${OPTARG}
-            ;;
-    esac
-done
-
-if [ -z "${TAXID}" ] && [ -z "${NAME}" ]; then
-    usage
-fi
-if [ ! -z "${TAXID}" ] && [ ! -z "${NAME}" ]; then
-    echo -e "Input Error: -t is incompatible with -n\n"
-    usage
-fi
-
-if  [ ! -z "${TAXID}" ]; then
-    esearch -db taxonomy -query "txid$TAXID[orgn]" > $OUTPUT 
-    if [ $? -ne 0 ]; then
-        error_exit  "esearch error" $?
-    fi
-
-    efetch -format uid < $OUTPUT > $TMP 
-    if [ $? -ne 0 ]; then
-        error_exit "efetch error" $?
-    fi
-
-    if [ ! -s $TMP ]; then
-        error_exit "Taxonomy ID not found"
-    fi
-
-    sort -n $TMP > $OUTPUT
-fi
-
-if [ ! -z "${NAME}" ]; then
-
-    esearch -db taxonomy -query "$NAME[All Names]" > $OUTPUT 
-    if [ $? -ne 0 ]; then
-        error_exit "esearch error" $?
-    fi
-
-    NUM_RESULTS=$(grep "<Count>" $OUTPUT | sed -e 's,.*<Count>\([^<]*\)</Count>.*,\1,g')
-
-    if [ $NUM_RESULTS -eq 0 ]; then
-        CORRECT_NAME=$(espell -db taxonomy -query "$NAME" | grep "<CorrectedQuery>" | sed -e 's,.*<CorrectedQuery>\([^<]*\)</CorrectedQuery>.*,\1,g')
-
-        if [ ! -z "${CORRECT_NAME}" ]; then
-            error_exit "No matches found for \"$NAME\". Did you mean \"$CORRECT_NAME\"?"
-        fi
-
-        esearch -db taxonomy -query "$NAME[Name Tokens]" > $OUTPUT 
-        if [ $? -ne 0 ]; then
-            error_exit "esearch error"
-        fi
-        NUM_RESULTS=$(grep "<Count>" $OUTPUT | sed -e 's,.*<Count>\([^<]*\)</Count>.*,\1,g')
-        if [ $NUM_RESULTS -gt $TOO_MANY_MATCHES ]; then
-            error_exit "More than $TOO_MANY_MATCHES matches found, please refine your search."
-        fi
-        if [ $NUM_RESULTS -eq 0 ]; then
-            error_exit "No matches for \"$NAME\"."
-        fi
-    fi
-
-    esummary -mode json < $OUTPUT > $TMP
-
-    if [ $? -ne 0 ]; then
-        error_exit "esummary error" $?
-    fi
-        
-    cat $TMP | tr ',|{' '\n' | \
-    grep 'uid\|rank\|division\|scientificname\|commonname' | \
-    grep -v "uids\|genbankdivision" | tr  '"\|,'  " " | tr -s ' ' | \
-    sed 's/ uid/Taxid/g;s/name/ name/g' | awk '/Taxid/{print ""}1' > $OUTPUT
-
-    echo -e "\n$NUM_RESULTS matche(s) found.\n" >> $OUTPUT
-fi
-
-cat $OUTPUT
+#!/bin/bash
+# $Id: get_species_taxids.sh 631039 2021-05-12 14:35:54Z fongah2 $
+# ===========================================================================
+#
+#                            PUBLIC DOMAIN NOTICE
+#               National Center for Biotechnology Information
+#
+#  This software/database is a "United States Government Work" under the
+#  terms of the United States Copyright Act.  It was written as part of
+#  the author's official duties as a United States Government employee and
+#  thus cannot be copyrighted.  This software/database is freely available
+#  to the public for use. The National Library of Medicine and the U.S.
+#  Government have not placed any restriction on its use or reproduction.
+#
+#  Although all reasonable efforts have been taken to ensure the accuracy
+#  and reliability of the software and data, the NLM and the U.S.
+#  Government do not and cannot warrant the performance or results that
+#  may be obtained by using this software or data. The NLM and the U.S.
+#  Government disclaim all warranties, express or implied, including
+#  warranties of performance, merchantability or fitness for any particular
+#  purpose.
+#
+#  Please cite the author in any work or product based on this material.
+#
+# ===========================================================================
+#
+# Author:  Amelia Fong
+#
+# File Description:
+#   Script to convert NCBI taxonomy IDs or text into taxonomy IDs suitable for
+#   filtering BLAST searches.
+#
+# N.B.: Depends on EDirect (https://www.ncbi.nlm.nih.gov/books/NBK179288/)
+#
+# ===========================================================================
+
+export PATH=/bin:/usr/bin:/am/ncbiapdata/bin:$HOME/edirect:$PATH
+set -uo pipefail
+
+TOO_MANY_MATCHES=500
+OUTPUT=`mktemp`
+TMP=`mktemp`
+trap " /bin/rm -fr $OUTPUT $TMP" INT QUIT EXIT HUP KILL ALRM
+
+usage() { 
+    echo "$0 usage:"; 
+    echo -e "\t-t <taxonomy ID>\n\t\tGet taxonomy IDs at or below input taxonomy ID level"; 
+    echo -e "\t-n <Scientific Name, Common Name or Keyword>\n\t\tGet taxonomy information for organism";
+    exit 0; 
+}
+
+error_exit() {
+    msg=$1
+    exit_code=${2:-1}
+    >&2 echo $msg;
+    exit $exit_code;
+}
+
+check_deps() {
+    for app in esearch efetch esummary; do 
+        command -v $app >/dev/null 2>&1 || error_exit "Cannot find Entrez EDirect $app tool, please see installation in https://www.ncbi.nlm.nih.gov/books/NBK179288/"
+    done
+}
+
+check_deps
+
+TAXID=""
+NAME=""
+while getopts  "ht::n::o::" OPT; do
+    case $OPT in
+        h)
+            usage
+            ;;
+        t)
+            TAXID=${OPTARG}
+            ;;
+        n)
+            NAME=${OPTARG}
+            ;;
+    esac
+done
+
+if [ -z "${TAXID}" ] && [ -z "${NAME}" ]; then
+    usage
+fi
+if [ ! -z "${TAXID}" ] && [ ! -z "${NAME}" ]; then
+    echo -e "Input Error: -t is incompatible with -n\n"
+    usage
+fi
+
+if  [ ! -z "${TAXID}" ]; then
+    esearch -db taxonomy -query "txid$TAXID[orgn]" > $OUTPUT 
+    if [ $? -ne 0 ]; then
+        error_exit  "esearch error" $?
+    fi
+
+    efetch -format uid < $OUTPUT > $TMP 
+    if [ $? -ne 0 ]; then
+        error_exit "efetch error" $?
+    fi
+
+    if [ ! -s $TMP ]; then
+        error_exit "Taxonomy ID not found"
+    fi
+
+    sort -n $TMP > $OUTPUT
+fi
+
+if [ ! -z "${NAME}" ]; then
+
+    esearch -db taxonomy -query "$NAME[All Names]" > $OUTPUT 
+    if [ $? -ne 0 ]; then
+        error_exit "esearch error" $?
+    fi
+
+    NUM_RESULTS=$(grep "<Count>" $OUTPUT | sed -e 's,.*<Count>\([^<]*\)</Count>.*,\1,g')
+
+    if [ $NUM_RESULTS -eq 0 ]; then
+        CORRECT_NAME=$(espell -db taxonomy -query "$NAME" | grep "<CorrectedQuery>" | sed -e 's,.*<CorrectedQuery>\([^<]*\)</CorrectedQuery>.*,\1,g')
+
+        if [ ! -z "${CORRECT_NAME}" ]; then
+            error_exit "No matches found for \"$NAME\". Did you mean \"$CORRECT_NAME\"?"
+        fi
+
+        esearch -db taxonomy -query "$NAME[Name Tokens]" > $OUTPUT 
+        if [ $? -ne 0 ]; then
+            error_exit "esearch error"
+        fi
+        NUM_RESULTS=$(grep "<Count>" $OUTPUT | sed -e 's,.*<Count>\([^<]*\)</Count>.*,\1,g')
+        if [ $NUM_RESULTS -gt $TOO_MANY_MATCHES ]; then
+            error_exit "More than $TOO_MANY_MATCHES matches found, please refine your search."
+        fi
+        if [ $NUM_RESULTS -eq 0 ]; then
+            error_exit "No matches for \"$NAME\"."
+        fi
+    fi
+
+    esummary -mode json < $OUTPUT > $TMP
+
+    if [ $? -ne 0 ]; then
+        error_exit "esummary error" $?
+    fi
+        
+    cat $TMP | tr ',|{' '\n' | \
+    grep 'uid\|rank\|division\|scientificname\|commonname' | \
+    grep -v "uids\|genbankdivision" | tr  '"\|,'  " " | tr -s ' ' | \
+    sed 's/ uid/Taxid/g;s/name/ name/g' | awk '/Taxid/{print ""}1' > $OUTPUT
+
+    echo -e "\n$NUM_RESULTS matche(s) found.\n" >> $OUTPUT
+fi
+
+cat $OUTPUT