| Next changeset 1:4554fcd4ef6d (2018-09-05) |
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Commit message:
Uploaded kodoja_search.py v0.0.3 wrapper. https://github.com/abaizan/kodoja_galaxy/commit/55004d41a9c0750b2543f394594ee58cc4426609 |
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LICENSE README.rst kodoja_search.xml test-data/kaijuDB_test/kaiju_library.fmi test-data/kaijuDB_test/names.dmp test-data/kaijuDB_test/nodes.dmp test-data/kaiju_databases.loc test-data/krakenDB_test/accmap_file.tmp test-data/krakenDB_test/database.idx test-data/krakenDB_test/database.kdb test-data/krakenDB_test/log_file.txt test-data/krakenDB_test/taxonomy/names.dmp test-data/krakenDB_test/taxonomy/nodes.dmp test-data/kraken_databases.loc test-data/taxonomy/names.dmp test-data/taxonomy/nodes.dmp test-data/testData_1.fasta test-data/testData_1.fastq test-data/testData_2.fasta test-data/testData_2.fastq test-data/virus_table_PE_fasta.tabular test-data/virus_table_PE_fastq.tabular test-data/virus_table_SE_fastq.tabular tool-data/kaiju_databases.loc.sample tool-data/kraken_databases.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
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| diff -r 000000000000 -r 18fe33eb7775 LICENSE --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/LICENSE Wed Mar 14 12:46:57 2018 -0400 |
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| @@ -0,0 +1,23 @@ +MIT License + +Copyright 2018 by Amanda Baizan Edge (University of St Andrews, and The James +Hutton Institute). +Copyright 2018 by Peter Cock (The James Hutton Institute). + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. |
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| diff -r 000000000000 -r 18fe33eb7775 README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Wed Mar 14 12:46:57 2018 -0400 |
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| @@ -0,0 +1,115 @@ +.. image:: https://travis-ci.org/abaizan/kodoja_galaxy.svg?branch=master + :alt: Linux testing with TravisCI + :target: https://travis-ci.org/abaizan/kodoja_galaxy/branches + +This is a Galaxy wrapper for the tool Kodoja, which is available to install in +conda from bioconda. + +https://github.com/abaizan/kodoja + +Galaxy wrappers for Kodoja +========================== + +These wrappers are copyright 2018 by Amanda Baizan Edge (University of +St Andrews, and The James Hutton Institute) and Peter Cock (The James +Hutton Institute). They are released under the MIT licence. + +These wrappers are available from the Galaxy Tool Shed at: +http://toolshed.g2.bx.psu.edu/view/abaizan/kodoja + +In-development test releases are available from the Test Tool Shed at: +http://testtoolshed.g2.bx.psu.edu/view/abaizan/kodoja + + +Citation +======== + +Please refer to the main Kodoja citation instructions. + + +Automated Installation +====================== + +Galaxy should be able to automatically install the dependencies, namely +``kodoja`` and its dependencies like ``kraken`` and ``kaiju``, using the +conda and the bioconda recipes. + +See the configuration notes below. + + +Configuration +============= + +You must tell Galaxy about any Kraken and Kaiju databases using configuration +files ``kraken_databases.loc`` and ``kaiju_databases.loc`` which are located +in the ``tool-data/`` folder. Sample files are included which explain the +tab-based format to use. + + +History +======= + +======= ====================================================================== +Version Changes +------- ---------------------------------------------------------------------- +v0.0.0 - Initial release covering ``kodoja_search.py`` v0.0.3. +======= ====================================================================== + + +Bug Reports +=========== + +File a Galaxy wrapper issue at https://github.com/abaizan/kodoja_galaxy/issues + +For issues with Kodoja itself, use https://github.com/abaizan/kodoja/issues + + +Developers +========== + +For pushing a release to the test or main "Galaxy Tool Shed", use the +following Planemo commands (which requires you have set your Tool Shed access +details in ``~/.planemo.yml`` and that you have access rights on the Tool +Shed):: + + $ planemo shed_update -t testtoolshed --check_diff . + ... + +or:: + + $ planemo shed_update -t toolshed --check_diff . + ... + +To just build and check the tar ball, use:: + + $ planemo shed_upload -t testtoolshed --tar_only . + ... + $ tar -tzf shed_upload.tar.gz + LICENSE + README.rst + ... + +This simplifies ensuring a consistent set of files is bundled each time, +including all the relevant test files. + + +Licence (MIT) +============= + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in +all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +THE SOFTWARE. |
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| diff -r 000000000000 -r 18fe33eb7775 kodoja_search.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/kodoja_search.xml Wed Mar 14 12:46:57 2018 -0400 |
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| b'@@ -0,0 +1,180 @@\n+<tool id="kodoja_search" name="Kodoja database search" version="0.0.0">\n+ <description>identify viruses from plant RNA sequencing data</description>\n+ <requirements>\n+ <requirement type="package" version="0.0.3">kodoja</requirement>\n+ </requirements>\n+ <version_command>kodoja_search.py --version</version_command>\n+ <command detect_errors="exit_code"><![CDATA[\n+kodoja_search.py\n+\n+--kraken_db \'${kraken_db.fields.path}\'\n+--kaiju_db \'${kaiju_db.fields.path}\'\n+\n+#if $single_paired.single_paired_selector == \'yes\'\n+ #if $forward_input.is_of_type( \'fastq\' ):\n+ --data_format fastq\n+ #else:\n+ --data_format fasta\n+ #end if\n+ --read1 \'${single_paired.forward_input}\'\n+ --read2 \'${single_paired.reverse_input}\'\n+#else:\n+ #if $single_paired.input_sequences.is_of_type(\'fastq\')\n+ --data_format fastq\n+ #else:\n+ --data_format fasta\n+ #end if\n+ --read1 \'${single_paired.input_sequences}\'\n+#end if\n+\n+## TODO:\n+## -m min_trim\n+## -a trim_adapt\n+## -q kraken_quick\n+## -p kraken_preload\n+## -c kaiju_score\n+## -l kaiju_minlen\n+## -i kaiju_mismatch\n+\n+## We\'ll capture predictably named output files from here:\n+-o .\n+&&\n+mv ./virus_table.txt \'$combined_table\'\n+]]></command>\n+ <inputs>\n+ <param label="Select a Kraken database" name="kraken_db" type="select">\n+ <options from_data_table="kraken_databases">\n+ <validator message="No Kraken database is available" type="no_options" />\n+ </options>\n+ </param>\n+ <param label="Select a Kaiju database" name="kaiju_db" type="select">\n+ <options from_data_table="kaiju_databases">\n+ <validator message="No Kaiju database is available" type="no_options" />\n+ </options>\n+ </param>\n+ <conditional name="single_paired">\n+ <param name="single_paired_selector" type="select" label="Single or paired reads" help="--paired">\n+ <!-- TODO?\n+ <option value="collection">Collection</option>\n+ -->\n+ <option value="yes">Paired</option>\n+ <option selected="True" value="no">Single</option>\n+ </param>\n+ <when value="yes">\n+ <param format="fasta,fastq" name="forward_input" type="data" label="Forward strand" help="FASTA or FASTQ dataset"/>\n+ <param format="fasta,fastq" name="reverse_input" type="data" label="Reverse strand" help="FASTA or FASTQ dataset"/>\n+ </when>\n+ <when value="no">\n+ <param format="fasta,fastq" label="Input sequences" name="input_sequences" type="data" help="FASTA or FASTQ datasets"/>\n+ </when>\n+ </conditional>\n+ </inputs>\n+ <outputs>\n+ <data name="combined_table" format="tabular" label="Kodoja species report for ${on_string}" />\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="kraken_db" value="kraken3viruses" />\n+ <param name="kaiju_db" value="kaiju3viruses" />\n+ <param name="single_paired_selector" value="no" />\n+ <param name="input_sequences" value="testData_1.fastq" ftype="fastq" />\n+ <output name="combined_table" file="virus_table_SE_fastq.tabular" ftype="tabular" />\n+ </test>\n+ <test>\n+ <param name="kraken_db" value="kraken3viruses" />\n+ <param name="kaiju_db" value="kaiju3viruses" />\n+ <param name="single_paired_selector" value="yes" />\n+ <param name="forward_input" value="testData_1.fastq" ftype="fastq" />\n+ <param name="reverse_input" value="testData_2.fastq" ftype="fastq" />\n+ <output name="combined_table" file="virus_table_PE_fastq.tabular" ftype="tabular" />\n+ </test>\n+ <test>\n+ <param name="kraken_db" value="kraken3viruses" />\n+ <param name="kaiju_db" value="kaiju3viruses" />\n+ <param name="single_paired_selecto'..b' <param name="reverse_input" value="testData_2.fasta" ftype="fasta" />\n+ <output name="combined_table" file="virus_table_PE_fasta.tabular" ftype="tabular" />\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+Kodoja is a tool intended to identify viral sequences in a\n+FASTQ/FASTA sequencing run by matching them against both\n+Kraken and Kaiju databases.\n+\n+The main output is a five column tab-separated table as follows\n+(tabular format in Galaxy):\n+\n+1. Species name\n+2. Species NCBI taxonomy identifier (TaxID)\n+3. Number of reads assigned by *either* Kraken or Kaiju to this species\n+4. Number of Reads assigned by *both* Kraken and Kaiju to this species\n+5. Genus name\n+6. Number of reads assigned by *either* Kraken or Kaiju to this genus\n+7. Number of reads assigned by *both* Kraken and Kaiju to this genus\n+\n+For example,\n+\n+================================== ============= ================= ============================= ========== =============== ===========================\n+Species Species TaxID Species sequences Species sequences (stringent) Genus Genus sequences Genus sequences (stringent)\n+---------------------------------- ------------- ----------------- ----------------------------- ---------- --------------- ---------------------------\n+Cassava brown streak virus 137758 45 45 Ipomovirus\n+Ugandan cassava brown streak virus 946046 28 28 Ipomovirus\n+Tobacco etch virus 12227 21 19 Potyvirus\n+================================== ============= ================= ============================= ========== =============== ===========================\n+\n+This is the command line tool\'s help::\n+\n+ usage: kodoja_search.py [-h] [--version] -o OUTPUT_DIR -d1 KRAKEN_DB -d2\n+ KAIJU_DB -r1 READ1 [-r2 READ2] [-f DATA_FORMAT]\n+ [-t THREADS] [-s] [-m TRIM_MINLEN] [-a TRIM_ADAPT]\n+ [-q KRAKEN_QUICK] [-p] [-c KAIJU_SCORE]\n+ [-l KAIJU_MINLEN] [-i KAIJU_MISMATCH]\n+\n+ Kodoja\n+\n+ optional arguments:\n+ -h, --help show this help message and exit\n+ --version show program\'s version number and exit\n+ -o OUTPUT_DIR, --output_dir OUTPUT_DIR\n+ Output directory path, required\n+ -d1 KRAKEN_DB, --kraken_db KRAKEN_DB\n+ Kraken database path, required\n+ -d2 KAIJU_DB, --kaiju_db KAIJU_DB\n+ Kaiju database path, required\n+ -r1 READ1, --read1 READ1\n+ Read 1 file path, required\n+ -r2 READ2, --read2 READ2\n+ Read 2 file path\n+ -f DATA_FORMAT, --data_format DATA_FORMAT\n+ Sequence data format\n+ -t THREADS, --threads THREADS\n+ Number of threads\n+ -s, --host_subset Subset host sequences before Kaiju\n+ -m TRIM_MINLEN, --trim_minlen TRIM_MINLEN\n+ Trimmomatic minimum length\n+ -a TRIM_ADAPT, --trim_adapt TRIM_ADAPT\n+ Illumina adapter sequence file\n+ -q KRAKEN_QUICK, --kraken_quick KRAKEN_QUICK\n+ Number of minium hits by Kraken\n+ -p, --kraken_preload Kraken preload database\n+ -c KAIJU_SCORE, --kaiju_score KAIJU_SCORE\n+ Kaju alignment score\n+ -l KAIJU_MINLEN, --kaiju_minlen KAIJU_MINLEN\n+ Kaju minimum length\n+ -i KAIJU_MISMATCH, --kaiju_mismatch KAIJU_MISMATCH\n+ Kaju allowed mismatches\n+\n+ ]]></help>\n+ <citations>\n+ <citation type="bibtex">\n+@misc{githubkodoja,\n+ author = {Baizan Edge, Amanda},\n+ year = {2018},\n+ title = {Kodoja},\n+ publisher = {GitHub},\n+ journal = {GitHub repository},\n+ url = {https://github.com/abaizan/kodoja},\n+}</citation>\n+ </citations>\n+</tool>\n' |
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| diff -r 000000000000 -r 18fe33eb7775 test-data/kaijuDB_test/names.dmp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kaijuDB_test/names.dmp Wed Mar 14 12:46:57 2018 -0400 |
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| @@ -0,0 +1,18 @@ +1 | all | | synonym | +1 | root | | scientific name | +10239 | Vira | | synonym | +10239 | Viridae | | synonym | +10239 | Viruses | | scientific name | +10239 | viruses | viruses<blast10239> | blast name | +12195 | Potyvirus | | scientific name | +12227 | TEV | | acronym | +12227 | Tobacco etch virus | | scientific name | +12227 | tobacco etch potyvirus | | synonym | +35278 | ssRNA positive-strand viruses, no DNA stage | | scientific name | +39729 | Potyviridae | | scientific name | +137757 | Ipomovirus | | scientific name | +137758 | Cassava brown streak virus | | scientific name | +439488 | ssRNA viruses | | scientific name | +946046 | Cassava brown streak Uganda virus | | synonym | +946046 | UCBSV | | acronym | +946046 | Ugandan cassava brown streak virus | | scientific name | |
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| @@ -0,0 +1,10 @@ +1 | 1 | no rank | | 8 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | | +10239 | 1 | superkingdom | | 9 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | | +12195 | 39729 | genus | | 9 | 1 | 1 | 1 | 0 | 1 | 0 | 0 | | +12227 | 12195 | species | TE | 9 | 1 | 1 | 1 | 0 | 1 | 1 | 0 | | +35278 | 439488 | no rank | | 9 | 1 | 1 | 1 | 0 | 1 | 0 | 0 | | +39729 | 35278 | family | | 9 | 1 | 1 | 1 | 0 | 1 | 0 | 0 | | +137757 | 39729 | genus | | 9 | 1 | 1 | 1 | 0 | 1 | 0 | 0 | | +137758 | 137757 | species | CB | 9 | 1 | 1 | 1 | 0 | 1 | 1 | 0 | | +439488 | 10239 | no rank | | 9 | 1 | 1 | 1 | 0 | 1 | 0 | 0 | | +946046 | 137757 | species | UC | 9 | 1 | 1 | 1 | 0 | 1 | 1 | 0 | | |
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| @@ -0,0 +1,14 @@ +# This is a tab-separated file listing any Kaiju databases +# available local for tool wrapper tests. +# +# - Column 1 - value, the key which Galaxy will record in DB +# - Column 2 - name, the text caption which Galaxy show users +# - Column 3 - path, the directory name (which will contain +# files named ``kaiju_library.fmi``, ``names.dmp`` and +# ``nodes.dmp`` (the later being NCBI taxonomy files). +# +# e.g. +# +# plants_dec_2017(tab)Plants (December 2017)(tab)/mnt/shared/kaiju_db/plants_2017_12/ +# +kaiju3viruses Sample databse using k18 m5 and three viruses ${__HERE__}/kaijuDB_test |
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| @@ -0,0 +1,4 @@ +output_dir = test/example_db/ +kraken_kmer = 18 +kraken_minimizer = 5 +Genomes added to db = ['GCF_000861345.1', 'GCF_000884835.1', 'GCF_000888855.1'] |
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| diff -r 000000000000 -r 18fe33eb7775 test-data/krakenDB_test/taxonomy/names.dmp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/krakenDB_test/taxonomy/names.dmp Wed Mar 14 12:46:57 2018 -0400 |
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| @@ -0,0 +1,18 @@ +1 | all | | synonym | +1 | root | | scientific name | +10239 | Vira | | synonym | +10239 | Viridae | | synonym | +10239 | Viruses | | scientific name | +10239 | viruses | viruses<blast10239> | blast name | +12195 | Potyvirus | | scientific name | +12227 | TEV | | acronym | +12227 | Tobacco etch virus | | scientific name | +12227 | tobacco etch potyvirus | | synonym | +35278 | ssRNA positive-strand viruses, no DNA stage | | scientific name | +39729 | Potyviridae | | scientific name | +137757 | Ipomovirus | | scientific name | +137758 | Cassava brown streak virus | | scientific name | +439488 | ssRNA viruses | | scientific name | +946046 | Cassava brown streak Uganda virus | | synonym | +946046 | UCBSV | | acronym | +946046 | Ugandan cassava brown streak virus | | scientific name | |
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| diff -r 000000000000 -r 18fe33eb7775 test-data/krakenDB_test/taxonomy/nodes.dmp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/krakenDB_test/taxonomy/nodes.dmp Wed Mar 14 12:46:57 2018 -0400 |
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| @@ -0,0 +1,10 @@ +1 | 1 | no rank | | 8 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | | +10239 | 1 | superkingdom | | 9 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | | +12195 | 39729 | genus | | 9 | 1 | 1 | 1 | 0 | 1 | 0 | 0 | | +12227 | 12195 | species | TE | 9 | 1 | 1 | 1 | 0 | 1 | 1 | 0 | | +35278 | 439488 | no rank | | 9 | 1 | 1 | 1 | 0 | 1 | 0 | 0 | | +39729 | 35278 | family | | 9 | 1 | 1 | 1 | 0 | 1 | 0 | 0 | | +137757 | 39729 | genus | | 9 | 1 | 1 | 1 | 0 | 1 | 0 | 0 | | +137758 | 137757 | species | CB | 9 | 1 | 1 | 1 | 0 | 1 | 1 | 0 | | +439488 | 10239 | no rank | | 9 | 1 | 1 | 1 | 0 | 1 | 0 | 0 | | +946046 | 137757 | species | UC | 9 | 1 | 1 | 1 | 0 | 1 | 1 | 0 | | |
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| @@ -0,0 +1,15 @@ +# This is a tab-separated file listing any Kraken databases +# available locally for tool wrapper tests. +# +# - Column 1 - value, the key which Galaxy will record in DB +# - Column 2 - name, the text caption which Galaxy show users +# - Column 3 - path, the directory name (which will contain +# files named ``database.idx``, ``database.kdb`` and a +# sub-directory named taxonomy containing files from the +# NCBI named ``names.dmp`` and ``nodes.dmp`` +# +# e.g. +# +# plants_dec_2017(tab)Plants (December 2017)(tab)/mnt/shared/kraken_db/plants_2017_12/ +# +kraken3viruses Sample databse using k18 m5 and three viruses ${__HERE__}/krakenDB_test |
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| diff -r 000000000000 -r 18fe33eb7775 test-data/taxonomy/names.dmp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/taxonomy/names.dmp Wed Mar 14 12:46:57 2018 -0400 |
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| @@ -0,0 +1,18 @@ +1 | all | | synonym | +1 | root | | scientific name | +10239 | Vira | | synonym | +10239 | Viridae | | synonym | +10239 | Viruses | | scientific name | +10239 | viruses | viruses<blast10239> | blast name | +12195 | Potyvirus | | scientific name | +12227 | TEV | | acronym | +12227 | Tobacco etch virus | | scientific name | +12227 | tobacco etch potyvirus | | synonym | +35278 | ssRNA positive-strand viruses, no DNA stage | | scientific name | +39729 | Potyviridae | | scientific name | +137757 | Ipomovirus | | scientific name | +137758 | Cassava brown streak virus | | scientific name | +439488 | ssRNA viruses | | scientific name | +946046 | Cassava brown streak Uganda virus | | synonym | +946046 | UCBSV | | acronym | +946046 | Ugandan cassava brown streak virus | | scientific name | |
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| diff -r 000000000000 -r 18fe33eb7775 test-data/taxonomy/nodes.dmp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/taxonomy/nodes.dmp Wed Mar 14 12:46:57 2018 -0400 |
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| @@ -0,0 +1,10 @@ +1 | 1 | no rank | | 8 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | | +10239 | 1 | superkingdom | | 9 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | | +12195 | 39729 | genus | | 9 | 1 | 1 | 1 | 0 | 1 | 0 | 0 | | +12227 | 12195 | species | TE | 9 | 1 | 1 | 1 | 0 | 1 | 1 | 0 | | +35278 | 439488 | no rank | | 9 | 1 | 1 | 1 | 0 | 1 | 0 | 0 | | +39729 | 35278 | family | | 9 | 1 | 1 | 1 | 0 | 1 | 0 | 0 | | +137757 | 39729 | genus | | 9 | 1 | 1 | 1 | 0 | 1 | 0 | 0 | | +137758 | 137757 | species | CB | 9 | 1 | 1 | 1 | 0 | 1 | 1 | 0 | | +439488 | 10239 | no rank | | 9 | 1 | 1 | 1 | 0 | 1 | 0 | 0 | | +946046 | 137757 | species | UC | 9 | 1 | 1 | 1 | 0 | 1 | 1 | 0 | | |
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| diff -r 000000000000 -r 18fe33eb7775 test-data/testData_1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/testData_1.fasta Wed Mar 14 12:46:57 2018 -0400 |
| b |
| b'@@ -0,0 +1,200 @@\n+>SRR3466597.2160184/1\n+TTGAGTTTCACGGGAAACTGAGTTGTGAATTCAACTTCTCTACCTGGTGGTGTGGCTGACACTTTGAGGACTTTTCCTTCAAATTCATGTTCAAACAG\n+>SRR3466597.1867187/1\n+TCTATAATGTGGCTTCACGTTGCCTCGGCTGATTTGGTTGTTCCACCATTGCTTAAAAGTGACTCCAGGAAGGCTCGTCTTG\n+>SRR3466597.1714296/1\n+TCCCTTCAGGAGTTCCAAGTGGAACTTGAAAAGCGATTTCACAGACAAGTCTATATGTCCGCCGCAATCTACGGTGTTTTTCATGATTAAAGGCTTTCGC\n+>SRR3466597.979054/1\n+CCGACCGCGTACAATGAACATACCATGTCGATACCAATGCGCAGGTCCGTACGAGCCTTGCCTCAAAACTAGGCCACTTGAACCAAAAGTGAGCTTCGAT\n+>SRR3466597.1842453/1\n+GTGAAATTCGATGCTGAGTGTATACCAACAATGAACCCATCTCTAGTTGATACTAATGGACTGCCACACTGCCCATCCTTGGTTTGAATCCAATGCTTCC\n+>SRR3466597.1967334/1\n+CCTTTAATCATGAAAAACACCGTAGATTGCGGCGGACATATAGACTTGTCTGTGAAATCGCTTTTCAAG\n+>SRR3466597.881543/1\n+TTGACTGCATGATAAGGGCACACCGAGAGGCGAAGGTTGCTGCACAGTTGCAGAAAGAGAGCGAGTGGGACAATATCATCAATAGAACTTTCCAGTATTC\n+>SRR3466597.2337588/1\n+AGTTCCACGAATAAATGCTATGGCCACAAAACTTCAATATCCAAGGATGAGGGGAGAGGTGGTTGTAAACTTGAATCACCTTTTAGGATACAAGCCACAG\n+>SRR3466597.864405/1\n+GCTATAGCAGAAGCATCATTCACATGACATTCATCAATTATGACAAAATCGTATGTTTTTACCTCAGCTATGTTTCGTGCAAAATGGTGTAAAGCGAATC\n+>SRR3466597.1545177/1\n+ACAAAGCATGTGGTTAAAGGAAAGTGTCCCCTCTTTGAGCTCTACTTGCAGTTGAATCCAGAAAAGGAAGCATATTTTAAACCGATGATGGGAGCATATA\n+>SRR3466597.1972168/1\n+TCAACCTTAAGAACTTTCTTCGTGCCACTATTCACCAAATAAGCATGGATTGTGGTGTGGGTGCTAAGACTTTGAGGCTCTATCTCATCGTCAATTAA\n+>SRR3466597.431651/1\n+CGCACTACATAGGAGAATTAGACCGAGGTGACCTCACTTTGTCGTTCGCCTAAGTAATGAGACTAATAAGACATATTAAAACATATAAGATACCATTCAA\n+>SRR3466597.1360962/1\n+TCATTAAGAAGCATAAAGGCAACAATAGCGGGCAACCTTCAACAGTGGTGGACAACACACTCATGGTCATTATTGCAATGTTATACACATGTGAGAAGTG\n+>SRR3466597.1276425/1\n+ACTTTGAATCGCCAGAGTTGCCAATGACCAGATGTCTCTTCGTTGGATGCTTTAGATCCGAATATTGAGCCTTACCATCTTCAAGAGTAACACAACAACA\n+>SRR3466597.833605/1\n+CACGATGTGAACCGTAACATGCACACACTATTAGGGGTCCGCCAGTGATAGTTTCTGCGTGTCTTTGCTTTCCGCTTTTAAGCTTATTGTAATATATATG\n+>SRR3466597.1371609/1\n+GACTGTGTCAGGGTTAACCATTCGCTATCCCTAGCAATGGAAATTGTTACTATTAAGCTGGCCACCCAAGAGATGGACATGGCGT\n+>SRR3466597.2181878/1\n+AGAGAAGTTGAATTCACAACTCAGTTTCCCGTGAAACTCAAGATAGAA\n+>SRR3466597.899074/1\n+GCAAGAAGTTTTTCTGCTTCTTACGCTTTGGCATACTATTATGCACAAGTTGAGTGG\n+>SRR3466597.1751537/1\n+GTCATCACTGCCTGATGCCACGCGGCAAACTGCTCATGTGTGGCTC\n+>SRR3466597.2102827/1\n+ATGCTACAAAGCATACGAAAGAAAATATTGCAGTGCTTCAGCAGGCAAAAGATCAATTGCTAGAG\n+>SRR3466597.847861/1\n+CTACAAGTTTATCACAGTCTCGAGTGTCCTTTCCTTGTTGTTGACATTCTTATTTCAAATTGACTGCATGATAAGGGCACACCGAGAGGCGAAGGTTGCT\n+>SRR3466597.1902260/1\n+ACATATACTAGTATGTTGTCGCCACAACTAATCACATCGGCGTTGGCACCTGTCCCTTGTAAACTTACAAATTCCTGAA\n+>SRR3466597.966077/1\n+TACTCTTGAAGATGGTAAGGCTCAATATTCGGATCTAAAGCATCCAACGAAGAGACATCTGGTCATTGGCAACTCTGGCGATTCAAAGTACCTAGACC\n+>SRR3466597.29276/1\n+ATGCGCTCTTCCCTTTGTGGCTCTCTAAATTTCAGCTTTTGAGGAAATGGTGGGAAATCCTTAGGCATGCGAATAATTATCATGTCCCTCCCATCAATGA\n+>SRR3466597.1001991/1\n+GCGTGGGGCTAGAGGGCAATATGAGGTTGCAGCGGAGCCAGAGGCGCTAGAACATTACTTTGGAAGCGCATATAATAACAAAGGAAAGCGCAAGGGCACC\n+>ERR996011.39031/1\n+ACCTGCAGCAACACTATTCTGATACATGAGGATAGCTTGGCTAGAGAAGTTTCTCATAACCTTCCTCATAGTTGGCAATGCAAATTTGTAC\n+>ERR996011.157056/1\n+CTTTGATGACGTGATTATGATAAACCTCGCGATTAACATAACCAACAATCATTAAGTTACCATCAATTAAT\n+>ERR996011.182572/1\n+GTTCGGTTTTTCAGTGAGAATCCTCATTCAGCAGAATATCTTGAATCACAATGTGCCAGTGATTATATTGAGGAGAAGG\n+>ERR996011.250248/1\n+CTCGCGTTCCACCCAGTACGTATAGAGATTTGATGAACCTATACCTAGTTTCAAACACAAACGTTCGCGCCAAGAAAATAACTCTCCGTACTGATGTTTGATGAGCTCGCGAGACATAATTTCTTG\n+>ERR996011.278646/1\n+GACACACTCAGCTAACTTAACGATAAAGTCATCACTCATGTCCGAGCAGTACCACGGAATTTGAACTTCTTGCACATGACGTGAG\n+>ERR996011.296484/1\n+CCTGCAGCAACACTATTCTGATACATGAGGATAGCTTGGCTAGAGAAGTTTCTCATAACCTTCCTCATAGTTGGCAATGCAAATTTGTACATTGG\n+>ERR996011.304884/1\n+CTCTCTCTTCCCTTTGATGACGTGATTATGATAAACCTCGCGATTAACATAACCAACAATCATTAAGTTACCATCAATTAATTCTTCACCTTCATTCGCTTGCACCGTGATGGTATTAATCGCTTTTGTCATAGGGAAAAACGTTGATACTCTTGCCACGGAATTCCACTCA\n+>ERR996011.319320/1\n+CCAGCATTTCTAGCAGCTTTTATCACAAATGCCTTACCTGCAGCAACACTATTCTGATACATGAGGATAGCTTGGCTAGAGAAGTTTCTCATAACCTTCCTCATAGTTGGCAATGCAAA\n+>ERR996011.335413/1\n+CTCTATTCCCGGTTTGGAAATGATGCAAGAGATTGCACTCGATTTCTCTGATTGTTTTTCCTCGCGTTCCACCCAGTACGTATAGAGATTTGATGAAC'..b'TATTGATGTTTGATGAGCTCGCGAGAAATAACTTCTTGTGCTTCTAACTCTCTTTTTTTATCAATGATC\n+>ERR996013.453686/1\n+GCGAAACATCAAAGCCGTATAAAGCCATATACGACTCGTGCAGTGCGTTTGCTAACACTCGCGTAGGAACACAAATTAGCACAGAA\n+>ERR996013.484483/1\n+GGATAATTTTGCAGAATCGAAACCAATGTTGATTAAAAGTCGCTCTCGCAGCGAAAACAAATCGCCGTATTGATGTTTGATGAGCTCGCGAGAGATAAC\n+>ERR996013.489616/1\n+CCACGATATGCAAGCGAAACATCAAAGCCGTATAAAGCCATATACGACTCGTGCAGTGCGTTTGCTAACACTCGCGTAGGAACACAAATTAGC\n+>ERR996013.497754/1\n+ATTGGTTTTGATCCTGTACGCACACGACCACGATATGCAAGCGAAACATCAAAGCCGTATAAAGCCATATACGACTCGTGCAGTGCGTTTGCTAACACTCGCG\n+>ERR996013.515914/1\n+CGGGAGAGCAAATTTGTACATTGGTTCCATAGGGTATTCTGAATCATCAATATCCTCACCCTGCGCATTTAGCTCAACAGCTCTCCAC\n+>ERR996013.518430/1\n+TGCAGAATCGAAACCAATGTTGATTAAAAGTCGCTCTCGCAGCGAAAACAAATCGCCGTATTGATGTTTGATGAGCTCGCGAGAGATAACTTCTTGTGC\n+>ERR996013.656197/1\n+CTCGCAGCGAAAACAAATCGCCGTATTGATGTTTGATGAGCTCGCGAGAGATAACTTCTTGTGCTTCTAACTCTCTTTTTTTGTCAATGATCCTGTCAATGAG\n+>ERR996013.656523/1\n+GTCATAATTGTTATTGGTTTTGATCCTGTACGCACACGACCACGATATGCAAGCGAAACATCAAAGCCGTATAAAGCCATATACGACTCGTGCAGTGCGTTTGC\n+>ERR996013.692538/1\n+GATTAAAAGTCGCTCTCGCAGCGAAAACAAATCGCCGTATTGATGTTTGATGAGCTCGCGAGAGATAACTTCTTGTGCTTCTAACTCTCTTTTT\n+>ERR996013.696477/1\n+TATTGGTTTTGATCCTGTACGCACACGACCACGATATGCAAGCGAAACATCAAAGCCGTATAAAGCCATATACGACTCGTGCAGTGCGTTTGCTAACACTCGCGTAGGAACACA\n+>ERR996013.738638/1\n+GGATAATTTTGCAGAATCGAAACCAATGTTGATTAAAAGTCGCTCTCGCAGCGAAAACAAATCGCCGTATTGATGTTTGATGAGCTCGCGAGAGATAAC\n+>ERR996013.747299/1\n+GCAGAATCGAAACCAATGTTGATTAAAAGTCGCTCTCGCAGCGAAAACAAATCGCCGTATTGATGTTTGATGAGCTCGCGAGAGATAACTTCTTGTGCTTCTAACTCTCTTTTTTTGTC\n+>ERR996013.752745/1\n+TGTTATTGGTTTTGATCCTGTACGCACACGACCACGATATGCAAGCGAAACATCAAAGCCGTATAAAGCCATATACGACTCGTGCAGTGCGTTTGCTAACACTCGCGTAGGA\n+>ERR996013.756913/1\n+CTTGGCTGGAAAAATTTCTCATTATTTTCCTCATTGTTGGGAGAGCAAATTTGTACATTGGTTCCATAGGGTATTCTGAATCATCAATATCCTCACCCTGCGCATTTAGCTCAACAGCTCTCCACGATTT\n+>ERR996013.793496/1\n+CAGCGAAAACAAATCGCCGTATTGATGTTTGATGAGCTCGCGAGAGATAACTTCTTGTGCTTCTAACTCTCTTTTTTT\n+>ERR996013.804840/1\n+CTTGGCTGGAAAAATTTCTCATTATTTTCCTCATTGTTGGGAGAGCAAATTTGTACATTGGTTCCATAGGGTATTCTGAATCATCA\n+>ERR996013.860827/1\n+CAAGTATGTCAACCAATGGGCTACCTTTAAGTATCATATGATCAACATATTTGTAAAATCTAGCCTTCTTCGCATAGAGCCAAAGAGTG\n+>ERR996013.909965/1\n+ATTGATGTTTGATGAGCTCGCGAGAGATAACTTCTTGTGCTTCTAACTCTCTTTTTTTGTCAATGATCCTGTCAATGAGTTCATATTTATTTGAC\n+>ERR996013.937909/1\n+GCCGTATTGATGTTTGATGAGCTCGCGAGAGATAACTTCTTGTGCTTCTAACTCTCTTTTTTTGTCAATGATCCTGTCAATGAGTTCATATTTAT\n+>ERR996013.947899/1\n+CTCCATCTTTACAAGTATGTCAACCAATGGGCTACCTTTAAGTATCATATGATCAACATATTTGTAAAATCTAGCCTTCTTCGCATAGAGCCAAAG\n+>ERR996013.967303/1\n+CTCGCAGCGAAAACAAATCGCCGTATTGATGTTTGATGAGCTCGCGAGAGATAACTTCTTGTGCTTCTAACTCTCTTTTTTTGTCAATGATCCTGTCAATGAGTTCATATTTA\n+>ERR996013.994308/1\n+CTACCTTGATACAATGCTCCCATCGCTGCTTTCTTGTTGAGATCACTCAAAATCTCCATTGGATCCCACTCTGGTCCTGAATTCCCA\n+>ERR996013.1066941/1\n+CATCTTTACAAGTATGTCAACCAATGGGCTACCTTTAAGTATCATATGATCAACATATTTGTAAAATCTAGCCTTCTTCGCATAGAG\n+>ERR996013.1134829/1\n+TGCAGAATCGAAACCAATGTTGATTAAAAGTCGCTCTCGCAGCGAAAACAAATCGCCGTATTGATGTTTGATGAGCTCGCGAGAGATAACTTCTTGTGCTTCTAACTCTCTTTTTT\n+>ERR996013.1154101/1\n+CAAGTATGTCAACCAATGGGCTACCTTTAAGTATCATATGATCAACATATTTGTAAAATCTAGCCTTCTTCGCATAGAGCCAAAGAG\n+>ERR996013.1172801/1\n+TTGCAGAATCGAAACCAATGTTGATTAAAAGTCGCTCTCGCAGCGAAAACAAATCGCCGTATTGATGTTTGATGAGCTCGCGAGAGATAACTTCTTG\n+>ERR996013.1177982/1\n+CCCTTTCCTTCCAGAGTGAGGATAGTTTTGCAGAATCGAAACCAATGTTGATTGAAAGTCGCTCTCGCAGCGAAAACAAATCGCCGTATTGATGTTTGATGAGCTCGCGAGAAATAACTTCTTGTGCTTCTAACTCTCTTT\n+>ERR996013.1222223/1\n+CGCCGTATTGATGTTTGATGAGCTCGCGAGAAATAACTTCTTGTGCTTCTAACTCTCTTTTTTTATCAATGATCCTGTCAATGAGTT\n+>ERR996013.1249443/1\n+CATTACACATGTATTTATATTTCATTTCAATACCTTCGTGTGCCATCACTTCTCTACAGTACTCAACCACAATCATCAGAATTATG\n+>ERR996013.1295292/1\n+GCCGTATTGATGTTTGATGAGCTCGCGAGAGATAACTTCTTGTGCTTCTAACTCTCTTTTTTTGTCAATGATCCTGTCAATGAGTTCATATT\n+>ERR996013.1301772/1\n+GTCATAATTGTTATTGGTTTTGATCCTGTACGCACACGACCACGATATGCAAGCGAAACATCAAAGCCGTATAAAGCCATATACGACTCGTGCAGTGCGTTTGCTAACACTCGCG\n+>ERR996013.1308814/1\n+TATTGATGTTTGATGAGCTCGCGAGAGATAACTTCTTGTGCTTCTAACTCTCTTTTTTTGTCAATGATCCTGTCAATGAGTTCATATTTATTT\n' |
| b |
| diff -r 000000000000 -r 18fe33eb7775 test-data/testData_1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/testData_1.fastq Wed Mar 14 12:46:57 2018 -0400 |
| b |
| b'@@ -0,0 +1,400 @@\n+@SRR3466597.2160184/1\n+TTGAGTTTCACGGGAAACTGAGTTGTGAATTCAACTTCTCTACCTGGTGGTGTGGCTGACACTTTGAGGACTTTTCCTTCAAATTCATGTTCAAACAG\n++\n+BCCFFDFFFHHHHIJJFIHIIGHGIHGIIIIIJIJIJJIGIJIJJGEBFHDG@GGDGIIGIIJJJEFHHFBDEFFDEEEEEEEDC>CDCDEDEECDBA\n+@SRR3466597.1867187/1\n+TCTATAATGTGGCTTCACGTTGCCTCGGCTGATTTGGTTGTTCCACCATTGCTTAAAAGTGACTCCAGGAAGGCTCGTCTTG\n++\n+B@C=DDFFHFFFHJJJIJJIJJJJIJGGIIIGGIIIIDGH@FEHGHIJFGHIIGGIJJJ@GCHGHIEHHCHFEFDC>8==@:\n+@SRR3466597.1714296/1\n+TCCCTTCAGGAGTTCCAAGTGGAACTTGAAAAGCGATTTCACAGACAAGTCTATATGTCCGCCGCAATCTACGGTGTTTTTCATGATTAAAGGCTTTCGC\n++\n+CC@DFFFFHHHHFIJJJJJGGIGJJJJJIJJJJFIHJIJJJJJIJJJJJDGIJJJJJJJJIJJJGHFFFFEDDD;;;BDDDDDDDCDFEDDDCDDDCDD@\n+@SRR3466597.979054/1\n+CCGACCGCGTACAATGAACATACCATGTCGATACCAATGCGCAGGTCCGTACGAGCCTTGCCTCAAAACTAGGCCACTTGAACCAAAAGTGAGCTTCGAT\n++\n+@@@FFFFFHFFDHIIGGIJHIJJHIBGBGGHIGHGGIEHIJDIIG=ACE=BFDCDBBCCCDCDDCDDCDCACCCC??ACC@:@BBBBDC@CCCDACDDDD\n+@SRR3466597.1842453/1\n+GTGAAATTCGATGCTGAGTGTATACCAACAATGAACCCATCTCTAGTTGATACTAATGGACTGCCACACTGCCCATCCTTGGTTTGAATCCAATGCTTCC\n++\n+B@BFFFFFHHGHHJJJJJHHHIJJJIJJJJJJJJ9HIIJJJJJJJIIIJHIJJJIJJJGIJJJJJJJJJIIJJJHHHHFFFFFFEDDEEDCDCDDDDDCC\n+@SRR3466597.1967334/1\n+CCTTTAATCATGAAAAACACCGTAGATTGCGGCGGACATATAGACTTGTCTGTGAAATCGCTTTTCAAG\n++\n+CCCFFFFFGHHFHII>GFHGIICFHGIII>AEGGG@AADFCDD?B@@C;@CCDCC@CCA8?9?@C:@C>\n+@SRR3466597.881543/1\n+TTGACTGCATGATAAGGGCACACCGAGAGGCGAAGGTTGCTGCACAGTTGCAGAAAGAGAGCGAGTGGGACAATATCATCAATAGAACTTTCCAGTATTC\n++\n+CCCFFFFFHHHHGJJJJJIJJIIIJIJJJJGIHIJJDGIIJIJJHCHDEEHFHHFFFFEEDDDDD@BBDDBDDCDCDCDDDDCDCCCCCCDDDCC@CDDD\n+@SRR3466597.2337588/1\n+AGTTCCACGAATAAATGCTATGGCCACAAAACTTCAATATCCAAGGATGAGGGGAGAGGTGGTTGTAAACTTGAATCACCTTTTAGGATACAAGCCACAG\n++\n+BCBDFFFFHHHHHJJDIJJJJJJJJJJIIJGHIJJJJJJIJJJJJJHGHHIIJJEHJIJ?CEEBFDACDEEECDDDDCDDDDDDDDACDCCDD@BDCCDD\n+@SRR3466597.864405/1\n+GCTATAGCAGAAGCATCATTCACATGACATTCATCAATTATGACAAAATCGTATGTTTTTACCTCAGCTATGTTTCGTGCAAAATGGTGTAAAGCGAATC\n++\n+CCCFFFFFHHGHHIJIJJJJJHIHJJJJIJJJJIJJJJJJIIIJJJJJIHIHHJJHIJJJJGJJJIIJJEIJHIICGAHHHFFEFDFCEDEEEDABBBD<\n+@SRR3466597.1545177/1\n+ACAAAGCATGTGGTTAAAGGAAAGTGTCCCCTCTTTGAGCTCTACTTGCAGTTGAATCCAGAAAAGGAAGCATATTTTAAACCGATGATGGGAGCATATA\n++\n+@C8:BDFFHHFHHHIIIIIIGIIIFHHIHIIIIIIIIGIIIIIIIIIIIIIIIIHIIIIIIIIIIGIIGIGIIHGEEEHHDC@DCCCCECCC?@BCCCCE\n+@SRR3466597.1972168/1\n+TCAACCTTAAGAACTTTCTTCGTGCCACTATTCACCAAATAAGCATGGATTGTGGTGTGGGTGCTAAGACTTTGAGGCTCTATCTCATCGTCAATTAA\n++\n+@@CFFFFFHFFFHHHGIGHGIICFBFCGHIJIJIJGIGHIGGCHGGIGHGHC8E=9BFFG:5@;@@G>=EHEA?:;??CAEECCDCCC:ADBABDE>C\n+@SRR3466597.431651/1\n+CGCACTACATAGGAGAATTAGACCGAGGTGACCTCACTTTGTCGTTCGCCTAAGTAATGAGACTAATAAGACATATTAAAACATATAAGATACCATTCAA\n++\n+CCCFFFFFHHGHHIIJJJIJJIJJJJJJHIJIJJIJJBIGGGIJJGIHHIJIHHFHGHHFDDDFECEDCCDDDCDDDDDDDAB@@@CDCDDDD@:>@CDD\n+@SRR3466597.1360962/1\n+TCATTAAGAAGCATAAAGGCAACAATAGCGGGCAACCTTCAACAGTGGTGGACAACACACTCATGGTCATTATTGCAATGTTATACACATGTGAGAAGTG\n++\n+CCCFFFFFHGHGHGIIIIIIIIJJJJJJIJJJJJJIJJJJIJJJIFHH=FHIIJHHHHFFFFEEEB@CDDDDEFDDDDDCDDEEEDEDDDDDDEDCDDAC\n+@SRR3466597.1276425/1\n+ACTTTGAATCGCCAGAGTTGCCAATGACCAGATGTCTCTTCGTTGGATGCTTTAGATCCGAATATTGAGCCTTACCATCTTCAAGAGTAACACAACAACA\n++\n+CCCFFFFFHHFHHJJIIGHGIJIJIIHIIIIEIJJJJJJJJIGGGIFIHIJIIIGIJGII?HGIJIIJJHEEHHFFEFFFEED@CED@CD<CABB??BDD\n+@SRR3466597.833605/1\n+CACGATGTGAACCGTAACATGCACACACTATTAGGGGTCCGCCAGTGATAGTTTCTGCGTGTCTTTGCTTTCCGCTTTTAAGCTTATTGTAATATATATG\n++\n+@CCFFFFFHGGFFGHIIIIIJJJJIGIIJIIIIJIJJ:GHIJJIJFHIIJJJJJJJJJHEH>BEFDFECEEEEDD?BDDDDDDDDDCDCACDEEEEEEEE\n+@SRR3466597.1371609/1\n+GACTGTGTCAGGGTTAACCATTCGCTATCCCTAGCAATGGAAATTGTTACTATTAAGCTGGCCACCCAAGAGATGGACATGGCGT\n++\n+@@@ABBDDFHFFFIJGFBHHHIGHIGCGGJIIIJIGGIGGDDHEHI>@DEGIFIGIHJJIJJ;CEEGHIHFEA>@@DF@@CC>>;\n+@SRR3466597.2181878/1\n+AGAGAAGTTGAATTCACAACTCAGTTTCCCGTGAAACTCAAGATAGAA\n++\n+?@@DBDADDDFDFEHGIJJIIGHIHHIGGEEDFCEGGG>EHGGGIFBE\n+@SRR3466597.899074/1\n+GCAAGAAGTTTTTCTGCTTCTTACGCTTTGGCATACTATTATGCACAAGTTGAGTGG\n++\n+BCCFFFFFFHHFHJIIIIJIJJJJGIIIJIJGCHCGIIJJJAFFHGIGIGHEHIGGH\n+@SRR3466597.1751537/1\n+GTCATCACTGCCTGATGCCACGCGGCAAACTGCTCATGTGTGGCTC\n++\n+@@@FFFFDFFDHDGHGGDHIIGDIJBHGHIGIIFIJDIGHGGGJIG\n+@SRR3466597.2102827/1\n+ATGCTACAAAGCATACGAAAGAAAATA'..b'GGGG\n+@ERR996013.793496/1\n+CAGCGAAAACAAATCGCCGTATTGATGTTTGATGAGCTCGCGAGAGATAACTTCTTGTGCTTCTAACTCTCTTTTTTT\n++\n+CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\n+@ERR996013.804840/1\n+CTTGGCTGGAAAAATTTCTCATTATTTTCCTCATTGTTGGGAGAGCAAATTTGTACATTGGTTCCATAGGGTATTCTGAATCATCA\n++\n+CCCCCGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\n+@ERR996013.860827/1\n+CAAGTATGTCAACCAATGGGCTACCTTTAAGTATCATATGATCAACATATTTGTAAAATCTAGCCTTCTTCGCATAGAGCCAAAGAGTG\n++\n+CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\n+@ERR996013.909965/1\n+ATTGATGTTTGATGAGCTCGCGAGAGATAACTTCTTGTGCTTCTAACTCTCTTTTTTTGTCAATGATCCTGTCAATGAGTTCATATTTATTTGAC\n++\n+CCCCCFEAFFGGGFGFFGGGEDGGEG<FEGGGGGGG<FFGGGGGE@FGGGGGGGGGGGGGGGEGGGFGGGGGF9EFGGGGGGGGGGGGGGGGGGG\n+@ERR996013.937909/1\n+GCCGTATTGATGTTTGATGAGCTCGCGAGAGATAACTTCTTGTGCTTCTAACTCTCTTTTTTTGTCAATGATCCTGTCAATGAGTTCATATTTAT\n++\n+CCCCBCF<EFGGFFCGGFFCFGGGCFGGGGG@F@FEE9EFFEGGGGAFFFCCDEGGGGGGGGE:FFDDGGGFGGDGGGFGGGFGGGGGGGGGGFG\n+@ERR996013.947899/1\n+CTCCATCTTTACAAGTATGTCAACCAATGGGCTACCTTTAAGTATCATATGATCAACATATTTGTAAAATCTAGCCTTCTTCGCATAGAGCCAAAG\n++\n+CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\n+@ERR996013.967303/1\n+CTCGCAGCGAAAACAAATCGCCGTATTGATGTTTGATGAGCTCGCGAGAGATAACTTCTTGTGCTTCTAACTCTCTTTTTTTGTCAATGATCCTGTCAATGAGTTCATATTTA\n++\n+CCCCCGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGG\n+@ERR996013.994308/1\n+CTACCTTGATACAATGCTCCCATCGCTGCTTTCTTGTTGAGATCACTCAAAATCTCCATTGGATCCCACTCTGGTCCTGAATTCCCA\n++\n+CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\n+@ERR996013.1066941/1\n+CATCTTTACAAGTATGTCAACCAATGGGCTACCTTTAAGTATCATATGATCAACATATTTGTAAAATCTAGCCTTCTTCGCATAGAG\n++\n+CCCCCGGGGGGGGGGGGGGGGGEGGGEFGGFGGGGGFGGGGGGGGFGGGGGGGGGGGGFGGGGFGGGGGGGGGGGGGGGGGGGGGGG\n+@ERR996013.1134829/1\n+TGCAGAATCGAAACCAATGTTGATTAAAAGTCGCTCTCGCAGCGAAAACAAATCGCCGTATTGATGTTTGATGAGCTCGCGAGAGATAACTTCTTGTGCTTCTAACTCTCTTTTTT\n++\n+CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\n+@ERR996013.1154101/1\n+CAAGTATGTCAACCAATGGGCTACCTTTAAGTATCATATGATCAACATATTTGTAAAATCTAGCCTTCTTCGCATAGAGCCAAAGAG\n++\n+CCCCCGGGGGGGGGGGGFFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\n+@ERR996013.1172801/1\n+TTGCAGAATCGAAACCAATGTTGATTAAAAGTCGCTCTCGCAGCGAAAACAAATCGCCGTATTGATGTTTGATGAGCTCGCGAGAGATAACTTCTTG\n++\n+CCCCCGGGGGGGGGGGFGGGGGGFGGFGGGGGGGGGGGGGGGGGDGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGEGGGGGGGGGGGGGGG\n+@ERR996013.1177982/1\n+CCCTTTCCTTCCAGAGTGAGGATAGTTTTGCAGAATCGAAACCAATGTTGATTGAAAGTCGCTCTCGCAGCGAAAACAAATCGCCGTATTGATGTTTGATGAGCTCGCGAGAAATAACTTCTTGTGCTTCTAACTCTCTTT\n++\n+CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\n+@ERR996013.1222223/1\n+CGCCGTATTGATGTTTGATGAGCTCGCGAGAAATAACTTCTTGTGCTTCTAACTCTCTTTTTTTATCAATGATCCTGTCAATGAGTT\n++\n+CCCCCGGGGFFFGGGGGGGGGGGGGGGGECEGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGFGGFGGG\n+@ERR996013.1249443/1\n+CATTACACATGTATTTATATTTCATTTCAATACCTTCGTGTGCCATCACTTCTCTACAGTACTCAACCACAATCATCAGAATTATG\n++\n+CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\n+@ERR996013.1295292/1\n+GCCGTATTGATGTTTGATGAGCTCGCGAGAGATAACTTCTTGTGCTTCTAACTCTCTTTTTTTGTCAATGATCCTGTCAATGAGTTCATATT\n++\n+CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGDGFGGGGFGG\n+@ERR996013.1301772/1\n+GTCATAATTGTTATTGGTTTTGATCCTGTACGCACACGACCACGATATGCAAGCGAAACATCAAAGCCGTATAAAGCCATATACGACTCGTGCAGTGCGTTTGCTAACACTCGCG\n++\n+CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGDGGGGGGGGGGGG\n+@ERR996013.1308814/1\n+TATTGATGTTTGATGAGCTCGCGAGAGATAACTTCTTGTGCTTCTAACTCTCTTTTTTTGTCAATGATCCTGTCAATGAGTTCATATTTATTT\n++\n+CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\n' |
| b |
| diff -r 000000000000 -r 18fe33eb7775 test-data/testData_2.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/testData_2.fasta Wed Mar 14 12:46:57 2018 -0400 |
| b |
| b'@@ -0,0 +1,200 @@\n+>SRR3466597.2160184/2\n+TACAGTCATGACTAGTGGATTCGCTTTACACCATTTTGCACGAAACATAGCTGAGGTAAAAACATACGATTTTGTCATAATTGATGAATGTCATGTGAAT\n+>SRR3466597.1867187/2\n+GATTACGTTACAACCTTTGATGACAATATGACAATCAACCTCGAGTTGAATATGGATGAACTCCACAAGACGAGCCTTCCTGGAGT\n+>SRR3466597.1714296/2\n+AGCTCTTGAAATTTGGGCGAAAGCCTTTAATCATGAAAAACACCGTAGATTGCGGCGGACATATAGACTT\n+>SRR3466597.979054/2\n+CCAAACTTGGAGCATAGTGCGCAAACGCCATATGCAGGTGGAGATCATTAGCAAGAAGAGCGTCCGAGCGAGGGTCAAGAGATTTGAGGGCTCGGTGCA\n+>SRR3466597.1842453/2\n+TGTGACAACCAACTTCCAAACTAAGAGCATGTCTAGCATGGTGTCAGACACTAGTTGCACATTCCCTTCATCTGATGGCATATTCTGGAAGCATTGGATT\n+>SRR3466597.1967334/2\n+GCTACTCTTACCTTTCTTGCACCACCATTTACGGCTCTTGAGATGGTTCCCTTCAGGAGTTCCAAGTGGAACTTGAAAAGCGATTTC\n+>SRR3466597.881543/2\n+GTCAAAAGCCATTAATACAAGTGTGATGAAAGCTATAATCTTTTCAAAGTATGCTATCTCCGGTTGTTTTGCCTGTTCAACGAGG\n+>SRR3466597.2337588/2\n+CTTCATTCACTCCATAGGCTGTCATCACTGCCTGATGCCACGCGGCAAACTGCTCATGTGTGGCTCG\n+>SRR3466597.864405/2\n+CTTCCCAACTTTGAGGATGAGAGGGAAGTCAACTTTTGGGTCAT\n+>SRR3466597.1545177/2\n+TTTCACTAGCATATTTTAGAATGTCCTTGAGGAACGCCTCTCTATTAAGTCGACTTGGCTTATATGCTCCCATCATCGGTTTAAAATATGCTTCCTTTTC\n+>SRR3466597.1972168/2\n+TTCATAAACATGTATGGGTTTGATCCAACTGATTTTTCATACATTAGGTTTGTGGATCCATTGACAGGTCACACTATTGATGAGTCCACAAA\n+>SRR3466597.431651/2\n+CACACACTATTAGGGGTCCGCCAGTGATAGTTTCTGCGTGTCTTTGCTTTCCGCTTTTAAGCTTATTGTAATATATATGAATAGCTATTCACAGTGGGAC\n+>SRR3466597.1360962/2\n+GAATGGCAATCAATAGGTCATCGCCATTGACGTAATACACAATCTCTTCCTTGTTGATTCCACACTTCTCACATGTGTATAACATTGCAATAATGACCAT\n+>SRR3466597.1276425/2\n+CTTCCAGACGCTCAGGCAACAAATTCAAGGCGAAACTATTGAGCGTAAAGAAATTGGGAATCACTGCATTTCAATGCGGAATGGTAATTACGTG\n+>SRR3466597.833605/2\n+CGCACTACATAGGAGAATTAGACCGAGGTGACCTCACTTTGTCGTTCGCCTAAGTAATGAGACTAATAAGACATATTAAAACATATAAGATACCATTCAA\n+>SRR3466597.1371609/2\n+AAGTTAATTCGTCCCATGCATCCTTCAAAGCCTTTACATAGTTTTTTTCCAACATTTCATGCACCTTTTCAGAGGTCACAGCATAGCCACCTTCCCTCAA\n+>SRR3466597.2181878/2\n+ATTAGTTGCGACTATGAAATGCTTTTTCACTGAAGTACCTTCAGTGATTATTTCAGTTCCTCCACTCTTCATTGTTCTTCCATCAATCTTCGACACTTTG\n+>SRR3466597.899074/2\n+CTGTGAATAACAAGAGGAACAGGAGAAGGAAAGTGGCCAAAACGTACGTGGGGCGTGATTCCATTGTTGAGAAGATTGTA\n+>SRR3466597.1751537/2\n+TTCAGGAACATTCTCAGTTCCACGAATAAATGCTATGGCCACAAAACTTCAATATCCAAG\n+>SRR3466597.2102827/2\n+CACAGACAAAGCTATTATGATGTCCCTAGTGATTTGGCTTTTATTCCAGTGACTTTTAAGCTTCAGATGCTTAGCCACTTCGCTATCTGATTGGAGATAG\n+>SRR3466597.847861/2\n+ATAGGATTTTCAAGCTTAGAATACTGGAAAGTTCTATTGATGATATTGTCCCACTCGCTCTCTTTCTGCAACTGTGCAGCAACCTTCGCCTCTCGGTGTG\n+>SRR3466597.1902260/2\n+TACTGTTTGAACATGAATTTGAAGGAAAAGTCCTCAAAGTGTCAGCCACACCACCAGG\n+>SRR3466597.966077/2\n+AAACTTGGTGAAGTCCTTTGCATCCTCTTCCTTGACATTCACTAG\n+>SRR3466597.29276/2\n+TCATTACAAACAAGCACTTGTTTAGAAGAAATAATGGAACACTGTTGGTCCAATCACTACATGGTGTATTCAAGGTCAAGAACACCACGACTTTGCAACA\n+>SRR3466597.1001991/2\n+TTCTAACCTTTCCAAACTCATGCTGCACTAAATCAATAGGTGCGTTTGTGGACTCATCAATAGTGTGACCTGTCAATGGATCCACAAACCTAATGTATGA\n+>ERR996011.39031/2\n+GTACAAATTTGCATTGCCAACTATGAGGAAGGTTATGAGAAACTTCTCTAGCCAAGCTATCCTCATGTATCAGAATAGTGTTGCTGCAGGT\n+>ERR996011.157056/2\n+ATTAATTGATGGTAACTTAATGATTGTTGGTTATGTTAATCGCGAGGTTTATCATAATCACGTCATCAAAG\n+>ERR996011.182572/2\n+CCTTCTCCTCAATATAATCACTGGCACATTGTGATTCAAGATATTCTGCTGAATGAGGATTCTCACTGAAAAACCGAAC\n+>ERR996011.250248/2\n+CAAGAAATTATGTCTCGCGAGCTCATCAAACATCAGTACGGAGAGTTATTTTCTTGGCGCGAACGTTTGTGTTTGAAACTAGGTATAGGTTCATCAAATCTCTATACGTACTGGGTGGAACGCGAG\n+>ERR996011.278646/2\n+CTCACGTCATGTGCAAGAAGTTCAAATTCCGTGGTACTGCTCGGACATGAGTGATGACTTTATCGTTAAGTTAGCTGAGTGTGTC\n+>ERR996011.296484/2\n+CCAATGTACAAATTTGCATTGCCAACTATGAGGAAGGTTATGAGAAACTTCTCTAGCCAAGCTATCCTCATGTATCAGAATAGTGTTGCTGCAGG\n+>ERR996011.304884/2\n+TGAGTGGAATTCCGTGGCAAGAGTATCAACGTTTTTCCCTATGACAAAAGCGATTAATACCATCACGGTGCAAGCGAATGAAGGTGAAGAATTAATTGATGGTAACTTAATGATTGTTGGTTATGTTAATCGCGAGGTTTATCATAATCACGTCATCAAAGGGAAGAGAGAG\n+>ERR996011.319320/2\n+TTTGCATTGCCAACTATGAGGAAGGTTATGAGAAACTTCTCTAGCCAAGCTATCCTCATGTATCAGAATAGTGTTGCTGCAGGTAAGGCATTTGTGATAAAAGCTGCTAGAAATGCTGG\n+>ERR996011.335413/2\n+CAAGAAATTATGTCTCGCGAGCTCATCAAACATCAGTACGGAGAGTTATTTTCTTGGCGCGAACGTTTGTGTTTGAAACTAGGTATAGGTTCATCAAATCTCTATACGTACTGGGTGGAACGCGAGGAAAAACAATCAGAGAAATCGAGTGCAATC'..b'AAAGAGAGTTAGAAGCACAAGAAGTTATTTCTCGCGAGCTCATCAAACATCAATACGGCGATTTGTTTTCGCTGCGAGAGCGACTTTCAATCAACATTGGTTTCGATTCTGCAAAACTATCCTCACTCTGGA\n+>ERR996013.453686/2\n+TTCTGTGCTAATTTGTGTTCCTACGCGAGTGTTAGCAAACGCACTGCACGAGTCGTATATGGCTTTATACGGCTTTGATGTTTCGC\n+>ERR996013.484483/2\n+GTTATCTCTCGCGAGCTCATCAAACATCAATACGGCGATTTGTTTTCGCTGCGAGAGCGACTTTTAATCAACATTGGTTTCGATTCTGCAAAATTATCC\n+>ERR996013.489616/2\n+GCTAATTTGTGTTCCTACGCGAGTGTTAGCAAACGCACTGCACGAGTCGTATATGGCTTTATACGGCTTTGATGTTTCGCTTGCATATCGTGG\n+>ERR996013.497754/2\n+CGCGAGTGTTAGCAAACGCACTGCACGAGTCGTATATGGCTTTATACGGCTTTGATGTTTCGCTTGCATATCGTGGTCGTGTGCGTACAGGA\n+>ERR996013.515914/2\n+GTGGAGAGCTGTTGAGCTAAATGCGCAGGGTGAGGATATTGATGATTCAGAATACCCTATGGAACCAATGTACAAATTTGCTCTCCCG\n+>ERR996013.518430/2\n+GCACAAGAAGTTATCTCTCGCGAGCTCATCAAACATCAATACGGCGATTTGTTTTCGCTGCGAGAGCGACTTTTAATCAACATTGGTTTCGATTCTGCA\n+>ERR996013.656197/2\n+CTCATTGACAGGATCATTGACAAAAAAAGAGAGTTAGAAGCACAAGAAGTTATCTCTCGCGAGCTCATCAAACATCAATACGGCGATTTGTTTTCGCTGCGAG\n+>ERR996013.656523/2\n+GTGTTAGCAAACGCACTGCACGAGTCGTATATGGCTTTATACGGCTTTGATGTTTCGCTTGCATA\n+>ERR996013.692538/2\n+AAAAAGAGAGTTAGAAGCACAAGAAGTTATCTCTCGCGAGCTCATCAAACATCAATACGGCGATTTGTTTTCGCTGCGAGAGCGACTTTTAATC\n+>ERR996013.696477/2\n+TGTGTTCCTACGCGAGTGTTAGCAAACGCACTGCACGAGTCGTATATGGCTTTATACGGCTTTGATGTTTCGCTTGCATATCGTGGTCGTGTGCGTACAGG\n+>ERR996013.738638/2\n+GTTATCTCTCGCGAGCTCATCAAACATCAATACGGCGATTTGTTTTCGCTGCGAGAGCGACTTTTAATCAACATTGGTTTCGATTCTGCAAAATTATCC\n+>ERR996013.747299/2\n+GACAAAAAAAGAGAGTTAGAAGCACAAGAAGTTATCTCTCGCGAGCTCATCAAACATCAATACGGCGATTTGTTTTCGCTGCGAGAGCGACTTTTAATCAACATTGGTTTCGATTCTGC\n+>ERR996013.752745/2\n+TCCTACGCGAGTGTTAGCAAACGCACTGCACGAGTCGTATATGGCTTTATACGGCTTTGATGTTTCGCTTGCATATCGTGGTCGTGTGCGTACAGGATCAAAACCAATAACA\n+>ERR996013.756913/2\n+AAATCGTGGAGAGCTGTTGAGCTAAATGCGCAGGGTGAGGATATTGATGATTCAGAATACCCTATGGAACCAATGTACAAATTTGCTCTCCCAACAATGAGGAAAATAATGAGAAATTTTTCCAGCCAAG\n+>ERR996013.793496/2\n+AAAAAAAGAGAGTTAGAAGCACAAGAAGTTATCTCTCGCGAGCTCATCAAACATCAATACGGCGATTTGTTTTCGCTG\n+>ERR996013.804840/2\n+TGATGATTCAGAATACCCTATGGAACCAATGTACAAATTTGCTCTCCCAACAATGAGGAAAATAATGAGAAATTTTTCCAGCCAAG\n+>ERR996013.860827/2\n+CACTCTTTGGCTCTATGCGAAGAAGGCTAGATTTTACAAATATGTTGATCATATGATACTTAAAGGTAGCCCATTGGTTGACATACTTG\n+>ERR996013.909965/2\n+GTCAAATAAATATGAACTCATTGACAGGATCATTGACAAAAAAAGAGAGTTAGAAGCACAAGAAGTTATCTCTCGCGAGCTCATCAAACATCAAT\n+>ERR996013.937909/2\n+ATAAATATGAACTCATTGACAGGATCATTGACAAAAAAAGAGAGTTAGAAGCACAAGAAGTTATCTCTCGCGAGCTCATCAAACATCAATACGGC\n+>ERR996013.947899/2\n+CTTTGGCTCTATGCGAAGAAGGCTAGATTTTACAAATATGTTGATCATATGATACTTAAAGGTAGCCCATTGGTTGACATACTTGTAAAGATGGAG\n+>ERR996013.967303/2\n+TAAATATGAACTCATTGACAGGATCATTGACAAAAAAAGAGAGTTAGAAGCACAAGAAGTTATCTCTCGCGAGCTCATCAAACATCAATACGGCGATTTGTTTTCGCTGCGAG\n+>ERR996013.994308/2\n+TGGGAATTCAGGACCAGAGTGGGATCCAATGGAGATTTTGAGTGATCTCAACAAGAAAGCAGCGATGGGAGCATTGTATCAAGGTAG\n+>ERR996013.1066941/2\n+CTCTATGCGAAGAAGGCTAGATTTTACAAATATGTTGATCATATGATACTTAAAGGTAGCCCATTGGTTGACATACTTGTAAAGATG\n+>ERR996013.1134829/2\n+AAAAAAGAGAGTTAGAAGCACAAGAAGTTATCTCTCGCGAGCTCATCAAACATCAATACGGCGATTTGTTTTCGCTGCGAGAGCGACTTTTAATCAACATTGGTTTCGATTCTGCA\n+>ERR996013.1154101/2\n+CTCTTTGGCTCTATGCGAAGAAGGCTAGATTTTACAAATATGTTGATCATATGATACTTAAAGGTAGCCCATTGGTTGACATACTTG\n+>ERR996013.1172801/2\n+CAAGAAGTTATCTCTCGCGAGCTCATCAAACATCAATACGGCGATTTGTTTTCGCTGCGAGAGCGACTTTTAATCAACATTGGTTTCGATTCTGCAA\n+>ERR996013.1177982/2\n+AAAGAGAGTTAGAAGCACAAGAAGTTATTTCTCGCGAGCTCATCAAACATCAATACGGCGATTTGTTTTCGCTGCGAGAGCGACTTTCAATCAACATTGGTTTCGATTCTGCAAAACTATCCTCACTCTGGAAGGAAAGGG\n+>ERR996013.1222223/2\n+AACTCATTGACAGGATCATTGATAAAAAAAGAGAGTTAGAAGCACAAGAAGTTATTTCTCGCGAGCTCATCAAACATCAATACGGCG\n+>ERR996013.1249443/2\n+CATAATTCTGATGATTGTGGTTGAGTACTGTAGAGAAGTGATGGCACACGAAGGTATTGAAATGAAATATAAATACATGTGTAATG\n+>ERR996013.1295292/2\n+AATATGAACTCATTGACAGGATCATTGACAAAAAAAGAGAGTTAGAAGCACAAGAAGTTATCTCTCGCGAGCTCATCAAACATCAATACGGC\n+>ERR996013.1301772/2\n+CGCGAGTGTTAGCAAACGCACTGCACGAGTCGTATATGGCTTTATACGGCTTTGATGTTTCGCTTGCATATCGTGGTCGTGTGCGTACAGGATCAAAACCAATAACAATTATGAC\n+>ERR996013.1308814/2\n+AAATAAATATGAACTCATTGACAGGATCATTGACAAAAAAAGAGAGTTAGAAGCACAAGAAGTTATCTCTCGCGAGCTCATCAAACATCAATA\n' |
| b |
| diff -r 000000000000 -r 18fe33eb7775 test-data/testData_2.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/testData_2.fastq Wed Mar 14 12:46:57 2018 -0400 |
| b |
| b'@@ -0,0 +1,400 @@\n+@SRR3466597.2160184/2\n+TACAGTCATGACTAGTGGATTCGCTTTACACCATTTTGCACGAAACATAGCTGAGGTAAAAACATACGATTTTGTCATAATTGATGAATGTCATGTGAAT\n++\n+@@@FFDEFHHHHHGJHGID@HHBGAFGHGIGJCBFHIIIGIAHIIIJJJJFHIEIGIIJJIJIIGIIE??EFFFFECCEE@EEEEADCCCCEDCCACEEE\n+@SRR3466597.1867187/2\n+GATTACGTTACAACCTTTGATGACAATATGACAATCAACCTCGAGTTGAATATGGATGAACTCCACAAGACGAGCCTTCCTGGAGT\n++\n+CCCFFFFFFHHHHIIJIIGIJEHHIIIIIIJJIIIIIGGIIJJJDFHHJJFIIIIHGGIIIJJGHEGCCCHEHF<BECCCDDABD;\n+@SRR3466597.1714296/2\n+AGCTCTTGAAATTTGGGCGAAAGCCTTTAATCATGAAAAACACCGTAGATTGCGGCGGACATATAGACTT\n++\n+CCCFFFFFHHHHHJJIJJJJJJJGIJJJIEIIJIJIJIJJJJJJJFHIJJIJJJIHDD8<BCC@CAC@CA\n+@SRR3466597.979054/2\n+CCAAACTTGGAGCATAGTGCGCAAACGCCATATGCAGGTGGAGATCATTAGCAAGAAGAGCGTCCGAGCGAGGGTCAAGAGATTTGAGGGCTCGGTGCA\n++\n+@??DFFFFHHFHGJJIIECGEIGG@GEHGHEGGIGIIJ8BFDHDHICHGHFHIEHHGIJEEFB?<AAB@@BBDD<C?@CDDDCDCCC<ABDBBB@8?B:\n+@SRR3466597.1842453/2\n+TGTGACAACCAACTTCCAAACTAAGAGCATGTCTAGCATGGTGTCAGACACTAGTTGCACATTCCCTTCATCTGATGGCATATTCTGGAAGCATTGGATT\n++\n+CC@FFFFFHHHHHIJJJJJJJJJJJJJIJIIGIJIIIJJJJGHIIJIIJJHIIJJJJJGJIIJJJJJJJJIJJJFGHHHFHFFEFFFFEDEDEDDDDCDD\n+@SRR3466597.1967334/2\n+GCTACTCTTACCTTTCTTGCACCACCATTTACGGCTCTTGAGATGGTTCCCTTCAGGAGTTCCAAGTGGAACTTGAAAAGCGATTTC\n++\n+@@@FDFDDBDFHDGGHEHI<FHIIJIIJEFHIGGIFIGG9<F?D<FDGCEFD?==BB>C8@@DGGE==DGEHEHHDDDFDC?ACB@D\n+@SRR3466597.881543/2\n+GTCAAAAGCCATTAATACAAGTGTGATGAAAGCTATAATCTTTTCAAAGTATGCTATCTCCGGTTGTTTTGCCTGTTCAACGAGG\n++\n+BBBFFFFFHHHHHIJJJJJGIFHHIJJJJJJIIIJJJJIJJJJJJIIIFFBFIIJIJJJJJIJHGIIIJGIIJHHHHHG@DE?><\n+@SRR3466597.2337588/2\n+CTTCATTCACTCCATAGGCTGTCATCACTGCCTGATGCCACGCGGCAAACTGCTCATGTGTGGCTCG\n++\n+BCCFFFFFHHHHHJJJGGIIJJJIJJEIIIIGCHFHHIIJIGGGGIBHIJJIIGHHHHHCEEDBDE8\n+@SRR3466597.864405/2\n+CTTCCCAACTTTGAGGATGAGAGGGAAGTCAACTTTTGGGTCAT\n++\n+@@BDDDDFADDHF<@F?G<<GB@7DE@FBBFGHCHEEH@FGEHD\n+@SRR3466597.1545177/2\n+TTTCACTAGCATATTTTAGAATGTCCTTGAGGAACGCCTCTCTATTAAGTCGACTTGGCTTATATGCTCCCATCATCGGTTTAAAATATGCTTCCTTTTC\n++\n+BCCFF>D?FHFHHJJJJJJJIIJBHJJJIIJJIIJJFIJIJJIIJJIIJIIGIIIJJJJJJJJJJJJIIJHHHHHFFFFDDDCDDCCCDEDEEDDDDDDC\n+@SRR3466597.1972168/2\n+TTCATAAACATGTATGGGTTTGATCCAACTGATTTTTCATACATTAGGTTTGTGGATCCATTGACAGGTCACACTATTGATGAGTCCACAAA\n++\n+B@CFFFF;FHHFFHHJIJFGEHEHEHCEHGI@HHJIIICGGIJJDH>FDHB@GIHHIGIGIJIIGGHIAC@E;D>>?EA?EH>CDCCDAAAB\n+@SRR3466597.431651/2\n+CACACACTATTAGGGGTCCGCCAGTGATAGTTTCTGCGTGTCTTTGCTTTCCGCTTTTAAGCTTATTGTAATATATATGAATAGCTATTCACAGTGGGAC\n++\n+C@CFFFFFHHHHHJIIAGHIJJJJFGGIIFGGIJGHIJGBGGIGIGHIJJHIIIJJBHA?EHHHFFFDFFFEEDDDEDCDDDDCCDEDDDFCDDCDD@AB\n+@SRR3466597.1360962/2\n+GAATGGCAATCAATAGGTCATCGCCATTGACGTAATACACAATCTCTTCCTTGTTGATTCCACACTTCTCACATGTGTATAACATTGCAATAATGACCAT\n++\n+CCCFFFFFHHHCDCGGHFHGIJJJJHIJJJJJHHJJJJJJJJIJJJJJJJHHJJJJGJJJIJJJJJJJJJJJGHHHHHHFFFFFFFEEEECCCECDDDCD\n+@SRR3466597.1276425/2\n+CTTCCAGACGCTCAGGCAACAAATTCAAGGCGAAACTATTGAGCGTAAAGAAATTGGGAATCACTGCATTTCAATGCGGAATGGTAATTACGTG\n++\n+@CCFDBADDFHHHGHDAGHEGIIIIIIJJGEGIJJJIHEIHCBFGAGIGIGGEEEEFDDCBDCC@CCDDEAD@C;>C??@??CD>ACDCD@?8<\n+@SRR3466597.833605/2\n+CGCACTACATAGGAGAATTAGACCGAGGTGACCTCACTTTGTCGTTCGCCTAAGTAATGAGACTAATAAGACATATTAAAACATATAAGATACCATTCAA\n++\n+@@CFFFFFHHHHHGIJIGIGEHHFFHIJFDHGGHEFHHIIGHIIFGIIIIIJHHAHHFFD@DFFEEEEDEEDDDDDEEDDCCDDDCDECCCCC:ACCDEC\n+@SRR3466597.1371609/2\n+AAGTTAATTCGTCCCATGCATCCTTCAAAGCCTTTACATAGTTTTTTTCCAACATTTCATGCACCTTTTCAGAGGTCACAGCATAGCCACCTTCCCTCAA\n++\n+B@@DDAFFFFFDHIIJJJIJIIJJFGCCHGHIIIIJJGGIHGGIIJ>GHI=CB@FHIIGIGGEADEEHEHHFDFF@CE@AAB?@CCDCD9<?ACCDDDDC\n+@SRR3466597.2181878/2\n+ATTAGTTGCGACTATGAAATGCTTTTTCACTGAAGTACCTTCAGTGATTATTTCAGTTCCTCCACTCTTCATTGTTCTTCCATCAATCTTCGACACTTTG\n++\n+<@@?DABBDHFDHBGIEGHH@>FEG<E?@D><DH@??H@FBGGI@<DEIIFHIEIIAFGGHGBGGCGIGHICCHHDEEHH;CABDE;BD66;;=8>;ACC\n+@SRR3466597.899074/2\n+CTGTGAATAACAAGAGGAACAGGAGAAGGAAAGTGGCCAAAACGTACGTGGGGCGTGATTCCATTGTTGAGAAGATTGTA\n++\n+@@@DDAFFHDHHHJIIJJGIJJDHJJJEIJIIDCGHIJJIJGIJHIBEFHGGIIC<@@CCDDCCDDDCDDDBD?C>AC:@\n+@SRR3466597.1751537/2\n+TTCAGGAACATTCTCAGTTCCACGAATAAATGCTATGGCCACAAAACTTCAATATCCAAG\n++\n+@C?D?DFFHGHGFGEHIJJJJJICGEEFGIEE@FHGGGIIBGD;DEEBCB?E9D<<BBFE\n+@SRR3466597.2102827/2\n+CACAGACAAAGCTATTATGATGTCCCTAGTGATTTGGCTTTTATTCCAGTGACTTTTAAGCTTCA'..b'GGGG\n+@ERR996013.793496/2\n+AAAAAAAGAGAGTTAGAAGCACAAGAAGTTATCTCTCGCGAGCTCATCAAACATCAATACGGCGATTTGTTTTCGCTG\n++\n+CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\n+@ERR996013.804840/2\n+TGATGATTCAGAATACCCTATGGAACCAATGTACAAATTTGCTCTCCCAACAATGAGGAAAATAATGAGAAATTTTTCCAGCCAAG\n++\n+CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGEFFGGGGGG\n+@ERR996013.860827/2\n+CACTCTTTGGCTCTATGCGAAGAAGGCTAGATTTTACAAATATGTTGATCATATGATACTTAAAGGTAGCCCATTGGTTGACATACTTG\n++\n+CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDGGGGGGGGGGGGGGGGGGGG\n+@ERR996013.909965/2\n+GTCAAATAAATATGAACTCATTGACAGGATCATTGACAAAAAAAGAGAGTTAGAAGCACAAGAAGTTATCTCTCGCGAGCTCATCAAACATCAAT\n++\n+CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\n+@ERR996013.937909/2\n+ATAAATATGAACTCATTGACAGGATCATTGACAAAAAAAGAGAGTTAGAAGCACAAGAAGTTATCTCTCGCGAGCTCATCAAACATCAATACGGC\n++\n+CCCCCGGGGGGGEFGGGFGGGGGGGGGGGGGGGGGGGDGGFGGGGDGCGGGGGGGGGGGGGGGGGEGFGGGGGGGEFGC<FFFFGG@FEFGGDGG\n+@ERR996013.947899/2\n+CTTTGGCTCTATGCGAAGAAGGCTAGATTTTACAAATATGTTGATCATATGATACTTAAAGGTAGCCCATTGGTTGACATACTTGTAAAGATGGAG\n++\n+CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\n+@ERR996013.967303/2\n+TAAATATGAACTCATTGACAGGATCATTGACAAAAAAAGAGAGTTAGAAGCACAAGAAGTTATCTCTCGCGAGCTCATCAAACATCAATACGGCGATTTGTTTTCGCTGCGAG\n++\n+CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGFGGGGGGGGGGFGGGGGGGGGGGGG\n+@ERR996013.994308/2\n+TGGGAATTCAGGACCAGAGTGGGATCCAATGGAGATTTTGAGTGATCTCAACAAGAAAGCAGCGATGGGAGCATTGTATCAAGGTAG\n++\n+CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\n+@ERR996013.1066941/2\n+CTCTATGCGAAGAAGGCTAGATTTTACAAATATGTTGATCATATGATACTTAAAGGTAGCCCATTGGTTGACATACTTGTAAAGATG\n++\n+CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\n+@ERR996013.1134829/2\n+AAAAAAGAGAGTTAGAAGCACAAGAAGTTATCTCTCGCGAGCTCATCAAACATCAATACGGCGATTTGTTTTCGCTGCGAGAGCGACTTTTAATCAACATTGGTTTCGATTCTGCA\n++\n+CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGEGGGGFGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGG\n+@ERR996013.1154101/2\n+CTCTTTGGCTCTATGCGAAGAAGGCTAGATTTTACAAATATGTTGATCATATGATACTTAAAGGTAGCCCATTGGTTGACATACTTG\n++\n+<CCCCGGFGFGGGGGGGEGEEGGGGGGGGGGGGGEFGGGGGGGGGGGFFGGGFGGGGGGGGGGFGAEGGGGGGGGGGGGGGGEFGGC\n+@ERR996013.1172801/2\n+CAAGAAGTTATCTCTCGCGAGCTCATCAAACATCAATACGGCGATTTGTTTTCGCTGCGAGAGCGACTTTTAATCAACATTGGTTTCGATTCTGCAA\n++\n+CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGEGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGF\n+@ERR996013.1177982/2\n+AAAGAGAGTTAGAAGCACAAGAAGTTATTTCTCGCGAGCTCATCAAACATCAATACGGCGATTTGTTTTCGCTGCGAGAGCGACTTTCAATCAACATTGGTTTCGATTCTGCAAAACTATCCTCACTCTGGAAGGAAAGGG\n++\n+CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFDGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFCGCGFGGGG\n+@ERR996013.1222223/2\n+AACTCATTGACAGGATCATTGATAAAAAAAGAGAGTTAGAAGCACAAGAAGTTATTTCTCGCGAGCTCATCAAACATCAATACGGCG\n++\n+CCCCCGGGGGGGGGGGGGGGGFGGGGGGEFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDGGGGFGGCGGGGGGGGGGGGGGGGC\n+@ERR996013.1249443/2\n+CATAATTCTGATGATTGTGGTTGAGTACTGTAGAGAAGTGATGGCACACGAAGGTATTGAAATGAAATATAAATACATGTGTAATG\n++\n+CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGG\n+@ERR996013.1295292/2\n+AATATGAACTCATTGACAGGATCATTGACAAAAAAAGAGAGTTAGAAGCACAAGAAGTTATCTCTCGCGAGCTCATCAAACATCAATACGGC\n++\n+CCCCCGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\n+@ERR996013.1301772/2\n+CGCGAGTGTTAGCAAACGCACTGCACGAGTCGTATATGGCTTTATACGGCTTTGATGTTTCGCTTGCATATCGTGGTCGTGTGCGTACAGGATCAAAACCAATAACAATTATGAC\n++\n+CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDGGGGGGGGGGGGGGGGGGFGGG\n+@ERR996013.1308814/2\n+AAATAAATATGAACTCATTGACAGGATCATTGACAAAAAAAGAGAGTTAGAAGCACAAGAAGTTATCTCTCGCGAGCTCATCAAACATCAATA\n++\n+CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\n' |
| b |
| diff -r 000000000000 -r 18fe33eb7775 test-data/virus_table_PE_fasta.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/virus_table_PE_fasta.tabular Wed Mar 14 12:46:57 2018 -0400 |
| b |
| @@ -0,0 +1,4 @@ +Species Species TaxID Species sequences Species sequences (stringent) Genus Genus sequences Genus sequences (stringent) +Cassava brown streak virus 137758 45 45 Ipomovirus +Ugandan cassava brown streak virus 946046 30 29 Ipomovirus +Tobacco etch virus 12227 25 23 Potyvirus |
| b |
| diff -r 000000000000 -r 18fe33eb7775 test-data/virus_table_PE_fastq.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/virus_table_PE_fastq.tabular Wed Mar 14 12:46:57 2018 -0400 |
| b |
| @@ -0,0 +1,4 @@ +Species Species TaxID Species sequences Species sequences (stringent) Genus Genus sequences Genus sequences (stringent) +Cassava brown streak virus 137758 45 45 Ipomovirus +Ugandan cassava brown streak virus 946046 28 28 Ipomovirus +Tobacco etch virus 12227 21 19 Potyvirus |
| b |
| diff -r 000000000000 -r 18fe33eb7775 test-data/virus_table_SE_fastq.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/virus_table_SE_fastq.tabular Wed Mar 14 12:46:57 2018 -0400 |
| b |
| @@ -0,0 +1,4 @@ +Species Species TaxID Species sequences Species sequences (stringent) Genus Genus sequences Genus sequences (stringent) +Cassava brown streak virus 137758 45 45 Ipomovirus +Ugandan cassava brown streak virus 946046 29 29 Ipomovirus +Tobacco etch virus 12227 23 20 Potyvirus |
| b |
| diff -r 000000000000 -r 18fe33eb7775 tool-data/kaiju_databases.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/kaiju_databases.loc.sample Wed Mar 14 12:46:57 2018 -0400 |
| b |
| @@ -0,0 +1,13 @@ +# This is a tab-separated file listing any Kaiju databases +# installed locally to offer via Galaxy. +# +# - Column 1 - value, the key which Galaxy will record in DB +# - Column 2 - name, the text caption which Galaxy show users +# - Column 3 - path, the directory name (which will contain +# files named ``kaiju_library.fmi``, ``names.dmp`` and +# ``nodes.dmp`` (the later being NCBI taxonomy files). +# +# e.g. +# +# plants_dec_2017(tab)Plants (December 2017)(tab)/mnt/shared/kaiju_db/plants_2017_12/ +# |
| b |
| diff -r 000000000000 -r 18fe33eb7775 tool-data/kraken_databases.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/kraken_databases.loc.sample Wed Mar 14 12:46:57 2018 -0400 |
| b |
| @@ -0,0 +1,14 @@ +# This is a tab-separated file listing any Kraken databases +# installed locally to offer via Galaxy. +# +# - Column 1 - value, the key which Galaxy will record in DB +# - Column 2 - name, the text caption which Galaxy show users +# - Column 3 - path, the directory name (which will contain +# files named ``database.idx``, ``database.kdb`` and a +# sub-directory named taxonomy containing files from the +# NCBI named ``names.dmp`` and ``nodes.dmp`` +# +# e.g. +# +# plants_dec_2017(tab)Plants (December 2017)(tab)/mnt/shared/kraken_db/plants_2017_12/ +# |
| b |
| diff -r 000000000000 -r 18fe33eb7775 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Wed Mar 14 12:46:57 2018 -0400 |
| b |
| @@ -0,0 +1,15 @@ +<?xml version="1.0"?> +<tables> + <!-- Locations of Kraken databases --> + <!-- This is intended to match the devteam/kraken suite --> + <table name="kraken_databases" comment_char="#"> + <columns>value, name, path</columns> + <file path="tool-data/kraken_databases.loc" /> + </table> + <!-- Locations of Kaiju databses --> + <!-- This is intended to match any kaiju-only wrapper --> + <table name="kaiju_databases" comment_char="#"> + <columns>value, name, path</columns> + <file path="tool-data/kaiju_databases.loc" /> + </table> +</tables> |
| b |
| diff -r 000000000000 -r 18fe33eb7775 tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Wed Mar 14 12:46:57 2018 -0400 |
| b |
| @@ -0,0 +1,15 @@ +<?xml version="1.0"?> +<tables> + <!-- Locations of Kraken databases --> + <!-- This is intended to match the devteam/kraken suite --> + <table name="kraken_databases" comment_char="#"> + <columns>value, name, path</columns> + <file path="${__HERE__}/test-data/kraken_databases.loc" /> + </table> + <!-- Locations of Kaiju databses --> + <!-- This is intended to match any kaiju-only wrapper --> + <table name="kaiju_databases" comment_char="#"> + <columns>value, name, path</columns> + <file path="${__HERE__}/test-data/kaiju_databases.loc" /> + </table> +</tables> |