| Next changeset 1:fdc21382376d (2024-03-29) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit d3d2bb547caccd2d217e5b77d62ea181f8e870c7 |
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added:
macros.xml seqkit_sort.xml test-data/fx2tab_output1.tabular test-data/fx2tab_output2.tabular test-data/fx2tab_output3.tabular test-data/fx2tab_output4.tabular test-data/input1.fasta.gz test-data/input1.fastq.gz test-data/locate_output1.tabular test-data/locate_output2.bed test-data/locate_output3.gtf test-data/motif_sequence.fasta test-data/sort_output1.fastq.gz test-data/sort_output2.fasta.gz test-data/sort_output3.fasta.gz test-data/sort_output4.fasta.gz test-data/sort_output5.fastq.gz test-data/sort_output6.fastq.gz test-data/stats_output1.tabular test-data/stats_output2.tabular |
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| diff -r 000000000000 -r 1f08834f987e macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Mar 26 21:49:37 2024 +0000 |
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| @@ -0,0 +1,21 @@ +<macros> + <token name="@TOOL_VERSION@">2.3.1</token> + <token name="@VERSION_SUFFIX@">1</token> + <token name="@PROFILE@">20.09</token> + <xml name="bio_tools"> + <xrefs> + <xref type="bio.tools">seqkit</xref> + </xrefs> + </xml> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">seqkit</requirement> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1371/journal.pone.0163962</citation> + </citations> + </xml> +</macros> + |
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| diff -r 000000000000 -r 1f08834f987e seqkit_sort.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/seqkit_sort.xml Tue Mar 26 21:49:37 2024 +0000 |
| [ |
| @@ -0,0 +1,81 @@ +<tool id="seqkit_sort" name="SeqKit sort" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description>FASTA or FASTQ files</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="bio_tools"/> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ + #set $input_fn='input.' + str($input.ext) + #set $output_fn='seqkitsort_output.' + str($output.ext) + + ln -s '$input' '$input_fn' + && + seqkit sort + '$input_fn' + $reverse + $sort_by + -o '$output_fn' + --threads \${GALAXY_SLOTS:-4} + +]]></command> + <inputs> + <param name="input" type="data" format="fasta,fasta.gz,fastqsanger,fastqsanger.gz" label="Input file"/> + <param name="sort_by" type="select" label="Sort by:"> + <option value="" selected="true">Sequence ID</option> + <option value="--by-bases">Non-gap bases</option> + <option value="--by-length">Sequence length</option> + <option value="--by-name">Full name (instead of just ID)</option> + <option value="--by-seq">Sequence</option> + </param> + <param argument="--reverse" type="boolean" truevalue="--reverse" falsevalue="" checked="false" label="Reverse the result?"/> + </inputs> + <outputs> + <data name="output" format_source="input" from_work_dir="seqkitsort_output.*" label="${input.name} sorted (${tool.name})"/> + </outputs> + <tests> + <!-- 1. fastq.gz --> + <test expect_num_outputs="1"> + <param name="input" value="input1.fastq.gz" ftype="fastqsanger.gz"/> + <output name="output" file="sort_output1.fastq.gz" ftype="fastqsanger.gz"/> + </test> + <!-- 2. fasta.gz --> + <test expect_num_outputs="1"> + <param name="input" value="input1.fasta.gz" ftype="fasta.gz"/> + <output name="output" file="sort_output2.fasta.gz" ftype="fasta.gz"/> + </test> + <!-- 3. by-bases, forward, fasta --> + <test expect_num_outputs="1"> + <param name="input" value="input1.fasta.gz" ftype="fasta.gz"/> + <param name="sort_by" value="--by-bases"/> + <output name="output" file="sort_output3.fasta.gz" ftype="fasta.gz"/> + </test> + <!-- 4. by-length, rev, fasta --> + <test expect_num_outputs="1"> + <param name="input" value="input1.fasta.gz" ftype="fasta.gz"/> + <param name="reverse" value="true"/> + <param name="sort_by" value="--by-length"/> + <output name="output" file="sort_output4.fasta.gz" ftype="fasta.gz"/> + </test> + <!-- 5. by-name, forward, fastq --> + <test expect_num_outputs="1"> + <param name="input" value="input1.fastq.gz" ftype="fastqsanger.gz"/> + <param name="sort_by" value="--by-name"/> + <output name="output" file="sort_output5.fastq.gz" ftype="fastqsanger.gz"/> + </test> + <!-- 6. by-seq, rev, fastq --> + <test expect_num_outputs="1"> + <param name="input" value="input1.fastq.gz" ftype="fastqsanger.gz"/> + <param name="reverse" value="true"/> + <param name="sort_by" value="--by-seq"/> + <output name="output" file="sort_output6.fastq.gz" ftype="fastqsanger.gz"/> + </test> + </tests> + <help> +**What it does** + +Sort sequences (FASTA, FASTQ) by id, name, sequence, or length. + + </help> + <expand macro="citations"/> +</tool> |
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| diff -r 000000000000 -r 1f08834f987e test-data/fx2tab_output1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fx2tab_output1.tabular Tue Mar 26 21:49:37 2024 +0000 |
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| @@ -0,0 +1,5 @@ +1/2 TATACTACTGTCATGTTTGCTTTTTTCGTGCTCATTACCTTATCGTATGCTTCCATCCAAAGATCTAGTTGTTTATAATATTCTCCCGGCCTTACTTCAAC ?@<DDDADDFAAC@>GG<FDCBHIIGB:8??DEAHGAFEDF<B?F9DBFFCDHF>48BBCF)8877=@=@C7=E??EBD:AADA;>C3;BB6:A@>>@:3> +2/2 AAAAAAACTTTCTTTACAGGCGTAAAGAAAGTGAAATTGACAGTATTTATACATGAAATAGCAATGTCTTTCCCACTTCCCTACGCTGGCATTAACCAGAT <@@DA6DDF42ABGF9F?F@C<EDDDFBGI>04BGC>BFF><?*88BDFDEAFFDGCGEFEEFIFFFEF>EBDBB@@:ACCCAB8@?=;B<@BABBBBB?# +3/2 GTGCCATCATTTTCTATCCATTATTATGGATTATTGGCTCATCGTTTAATCCGGGTGATAGTTTATCTGGATCAAGTATTATTCCACAAAATGCAACGTTA =BBFFFFFHHHHHJJJJJJJJJJJJIJIJEIIGIJJJHGIGGIIGHIDIJGHIIJ?FFHGIIJJJJJJJJHGIHHHCEHFFFFFFFFEAECCDADDDDDDD +4/2 TTCAAAACACATAAAGCTAATTGCCGCATATGACAATATTGCTAAAATAATTTTTTTACCAGATATCGGTGTTAATCGAAATAATGTACTTTCGGTCATTT BBCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJJJJJIJJJJJJIJJJJJJIIJJJJJJJIJJHHHHHFFDDCDEEEDDDDDDDDEDDDFFFEDDDDDDDDE +5/2 ACTTGCCAATGCGATGCACCAATCTTTTCAGCAATAATCGGCAAAATTGGGTCGACTACTCCTATACCTGAAAAGGCAAGGAAAGTAGCCAACACTGTAAT BCCFFFFFHHHHHIJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJIHIIJIJHHHHFFFFFFEEEEEEDDDDDDDDDDDDDCDDDDDDDDDDDDDED |
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| diff -r 000000000000 -r 1f08834f987e test-data/fx2tab_output2.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fx2tab_output2.tabular Tue Mar 26 21:49:37 2024 +0000 |
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| @@ -0,0 +1,6 @@ +#id length avg.qual +1/2 101 24.98 +2/2 101 20.44 +3/2 101 37.13 +4/2 101 37.61 +5/2 101 37.28 |
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| diff -r 000000000000 -r 1f08834f987e test-data/fx2tab_output3.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fx2tab_output3.tabular Tue Mar 26 21:49:37 2024 +0000 |
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| b'@@ -0,0 +1,3 @@\n+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.\tGAGAGGACGAGGTGCCGCTGCCTGGAGAATCCTCCGCTGCCGTCGGCTCCCGGAGCCCAGCCCTTTCCTAACCCAACCCAACCTAGCCCAGTCCCAGCCGCCAGCGCCTGTCCCTGTCACGGACCCCAGCGTTACCATGCATCCTGCCGTCTTCCTATCCTTACCCGACCTCAGATGCTCCCTTCTGCTCCTGGTAACTTGGGTTTTTACTCCTGTAACAACTGAAATAACAAGTCTTGATACAGAGAATATAGATGAAATTTTAAACAATGCTGATGTTGCTTTAGTAAATTTTTATGCTGACTGGTGTCGTTTCAGTCAGATGTTGCATCCAATTTTTGAGGAAGCTTCCGATGTCATTAAGGAAGAATTTCCAAATGAAAATCAAGTAGTGTTTGCCAGAGTTGATTGTGATCAGCACTCTGACATAGCCCAGAGATACAGGATAAGCAAATACCCAACCCTCAAATTGTTTCGTAATGGGATGATGATGAAGAGAGAATACAGGGGTCAGCGATCAGTGAAAGCATTGGCAGATTACATCAGGCAACAAAAAAGTGACCCCATTCAAGAAATTCGGGACTTAGCAGAAATCACCACTCTTGATCGCAGCAAAAGAAATATCATTGGATATTTTGAGCAAAAGGACTCGGACAACTATAGAGTTTTTGAACGAGTAGCGAATATTTTGCATGATGACTGTGCCTTTCTTTCTGCATTTGGGGATGTTTCAAAACCGGAAAGATATAGTGGCGACAACATAATCTACAAACCACCAGGGCATTCTGCTCCGGATATGGTGTACTTGGGAGCTATGACAAATTTTGATGTGACTTACAATTGGATTCAAGATAAATGTGTTCCTCTTGTCCGAGAAATAACATTTGAAAATGGAGAGGAATTGACAGAAGAAGGACTGCCTTTTCTCATACTCTTTCACATGAAAGAAGATACAGAAAGTTTAGAAATATTCCAGAATGAAGTAGCTCGGCAATTAATAAGTGAAAAAGGTACAATAAACTTTTTACATGCCGATTGTGACAAATTTAGACATCCTCTTCTGCACATACAGAAAACTCCAGCAGATTGTCCTGTAATCGCTATTGACAGCTTTAGGCATATGTATGTGTTTGGAGACTTCAAAGATGTATTAATTCCTGGAAAACTCAAGCAATTCGTATTTGACTTACATTCTGGAAAACTGCACAGAGAATTCCATCATGGACCTGACCCAACTGATACAGCCCCAGGAGAGCAAGCCCAAGATGTAGCAAGCAGTCCACCTGAGAGCTCCTTCCAGAAACTAGCACCCAGTGAATATAGGTATACTCTATTGAGGGATCGAGATGAGCTTTAAAAACTTGAAAAACAGTTTGTAAGCCTTTCAACAGCAGCATCAACCTACGTGGTGGAAATAGTAAACCTATATTTTCATAATTCTATGTGTATTTTTATTTTGAATAAACAGAAAGAAATTTTGGGTTTTTAATTTTTTTCTCCCCGACTCAAAATGCATTGTCATTTAATATAGTAGCCTCTTAAAAAAAAAAAAACCTGCTAGGATTTAAAAATAAAAATCAGAGGCCTATCTCCACTTTAAATCTGTCCTGTAAAAGTTTTATAAATCAAATGAAAGGTGACATTGCCAGAAACTTACCATTAACTTGCACTACTAGGGTAGGGAGGACTTAGGATGTTTCCTGTGTCGTATGTGCTTTTCTTTCTTTCATATGATCAATTCTGTTGGTATTTTCAGTATCTCATTTCTCAAAGCTAAAGAGATATACATTCTGGATACTTGGGAGGGGAATAAATTAAAGTTTTCACACTGTGTACTGTGTTTTACTGATTGGTTGGATATTGCTTATGAAAATTCCATAGTGGTATTTTTTTGGATTCTTAATGTGTAACTTAAACATACTTTGAAGTGGAGGAGAGTCATAAGACAGAACATTTGGCAGGAATTGTCCTTATGAAACAAGAAAAAGAAAATGAAAAGTATTATTAAGCTTCTGTGTTTGTCTAAAAATGTGGCATATGGATGGCATTTAAAACTTTGAATGAATTATACCTAAATCTGGGACAGGGAGGTGACAGTGGAACAGGCTACCAATCAGAACTAGATGACTTTTAAGGCTCCTCCTATTATGAGACTTCAATTTCCAAAGAGAAGAACTAGCAGAGAAATTGTATTTCAGTAATTTTAAGCTCCTTCTGTCTTGTAGAGTCTTGTTATAGTTGTATAAATCAAAAACACAGAATAAGGAACATATTTAACTTTTTTTCATTATAAAATGGTTAGAGGACCCTACCCCCTCTAGATTCCCTGATTTCCCCAGGCCTGCAGCATACAGTAAGATGGGTCCCTGTGCCAGGCCTCAATACTGCCAGGGAATAAAACCAGAGGGAGAGGACCCTCAGTGTCATATCAGGAAGCCCAGTGCCAGAGGACAGACAGGTTCAAAACTGGCTTTTCCTCTGGGCCTGGGTTGGTGCTATAGGCCAAGGGTCATTTTATACTTGGGTATAAATCAATCCCAGTTTGGGAAAAGATTATTTTTAAGCTTAAAAGGCTGACATGTGCCATTATATGTAGTATGTAATATATGTAACATCTTCCAATTCTTTTAAAATAAAATTAATATTTATAATGGATATTTAATGATTGTTATTTTTAAAAACCAGCTTATAATTCCTCGTTATGCATGATTTATCCAAAGTTTCCATAGTTTTATTCAAAATAATAAATGTTAATAAGGTGATAAGGGGTATATTTAATGTATTGTATCAAATTGTGAATAAGAAAGTAGGATGGAGCTTTCTAGAGGTTGGGCCTTAGTTCTGTTATCCTCATTGCTTTTAACCAATAAGTTAAATGAAGTTAGAGTTATGGTCTTCAGGTTAGATTATGGACCAGATCTGTGAGGGTCAGCATGGAAATTCACATTCAACAAGGTAGCACACAGGACCAAGAGCAGCACATGCAATCAACTGGAATAATATAGTAATCCTGTAACTGGGTTTGAAAAAATAATCAACAAAAGATACAATTCAAGGGTTAGGTTGCAGAGAGCTGGCTTGAGAGTAGTTATTATGAAAAAGGCCTCAAGGAGTACGTGTTCAGTATGCTCTAAGATGATAAAGTGGCTGTTAAAAAGGGAGTTGATTTGAGGAAGTATTACTTAGCATTCATGCATATTGGGCTTAGGCTCTAGCCCTGCCACTATCATTGTCTTCTCTGGACTGTGAAGTCACTGAGGACAAGGAAACTAAATTTAATGTCTGTATCACTAGTGCCTAGAATTTCTGGACACTTAGTAGTCACCATCAGGCGTTTATTTAATGAATGAGAAGCAAAGTGACCTTGGTTACTTTTTTACCCTGAGGGGCTCAGCACTCATTAGGACTTGGTGCCTAATTTTATAAAAAGTCACTAAGCTCAAGTGCTTGGATGAAAGGACAGCGTGGATAAAAAGGTTTTTAAAACATGGATGTTAAGGCTGTTTTGCTTGGAGAAGACTTGGGACTGGGACAGTCTTTAGATATTATTTGAAATGCTGGCACTGTCTATCTGGATCCCAGGGCTTGAACTAGGATTTGAGGAAGTCACAGGGAAGCAGATTTCAGTCTGACATTTATTCAGTGCAAGTTTTTTGGTGCTGTAGTATATGATGAAAGATGTAAAGCTGAATAAAGCATTATTTCTGCCCTAGAGTTGTTCACAGCCTAGTCAGGCATATGGATATGTAAACAATGACTGTAACGTGTTATAGATGTAAAGACAAAATAAAGGTTAAAGAGGGCATAAAGGAGCACTCAATTGCAGAGATTTGAGGACATTATTTTTATTTTGAGCTTTAAAAAGATGAATAGGTGTTCTCAGGAGGTAGGGATCTGGCTGAGAG'..b'GATTATTCTGAAGTGGAAACCACCCTCCGACCCCAATGGCAACATCACCCACTACCTGGTTTTCTGGGAGAGGCAGGCGGAAGACAGTGAGCTGTTCGAGCTGGATTATTGCCTCAAAGGGCTGAAGCTGCCCTCGAGGACCTGGTCTCCACCATTCGAGTCTGAAGATTCTCAGAAGCACAACCAGAGTGAGTATGAGGATTCGGCCGGCGAATGCTGCTCCTGTCCAAAGACAGACTCTCAGATCCTGAAGGAGCTGGAGGAGTCCTCGTTTAGGAAGACGTTTGAGGATTACCTGCACAACGTGGTTTTCGTCCCCAGAAAAACCTCTTCAGGCACTGGTGCCGAGGACCCTAGGCCATCTCGGAAACGCAGGTCCCTTGGCGATGTTGGGAATGTGACGGTGGCCGTGCCCACGGTGGCAGCTTTCCCCAACACTTCCTCGACCAGCGTGCCCACGAGTCCGGAGGAGCACAGGCCTTTTGAGAAGGTGGTGAACAAGGAGTCGCTGGTCATCTCCGGCTTGCGACACTTCACGGGCTATCGCATCGAGCTGCAGGCTTGCAACCAGGACACCCCTGAGGAACGGTGCAGTGTGGCAGCCTACGTCAGTGCGAGGACCATGCCTGAAGCCAAGGCTGATGACATTGTTGGCCCTGTGACGCATGAAATCTTTGAGAACAACGTCGTCCACTTGATGTGGCAGGAGCCGAAGGAGCCCAATGGTCTGATCGTGCTGTATGAAGTGAGTTATCGGCGATATGGTGATGAGGAGCTGCATCTCTGCGTCTCCCGCAAGCACTTCGCTCTGGAACGGGGCTGCAGGCTGCGTGGGCTGTCACCGGGGAACTACAGCGTGCGAATCCGGGCCACCTCCCTTGCGGGCAACGGCTCTTGGACGGAACCCACCTATTTCTACGTGACAGACTATTTAGACGTCCCGTCAAATATTGCAAAAATTATCATCGGCCCCCTCATCTTTGTCTTTCTCTTCAGTGTTGTGATTGGAAGTATTTATCTATTCCTGAGAAAGAGGCAGCCAGATGGGCCGCTGGGACCGCTTTACGCTTCTTCAAACCCTGAGTATCTCAGTGCCAGTGATGTGTTTCCATGCTCTGTGTACGTGCCGGACGAGTGGGAGGTGTCTCGAGAGAAGATCACCCTCCTTCGAGAGCTGGGGCAGGGCTCCTTCGGCATGGTGTATGAGGGCAATGCCAGGGACATCATCAAGGGTGAGGCAGAGACCCGCGTGGCGGTGAAGACGGTCAACGAGTCAGCCAGTCTCCGAGAGCGGATTGAGTTCCTCAATGAGGCCTCGGTCATGAAGGGCTTCACCTGCCATCACGTGGTGCGCCTCCTGGGAGTGGTGTCCAAGGGCCAGCCCACGCTGGTGGTGATGGAGCTGATGGCTCACGGAGACCTGAAGAGCTACCTCCGTTCTCTGCGGCCAGAGGCTGAGAATAATCCTGGCCGCCCTCCCCCTACCCTTCAAGAGATGATTCAGATGGCGGCAGAGATTGCTGACGGGATGGCCTACCTGAACGCCAAGAAGTTTGTGCATCGGGACCTGGCAGCGAGAAACTGCATGGTCGCCCATGATTTTACTGTCAAAATTGGAGACTTTGGAATGACCAGAGACATCTATGAAACGGATTACTACCGGAAAGGGGGCAAGGGTCTGCTCCCTGTACGGTGGATGGCACCGGAGTCCCTGAAGGATGGGGTCTTCACCACTTCTTCTGACATGTGGTCCTTTGGCGTGGTCCTTTGGGAAATCACCAGCTTGGCAGAACAGCCTTACCAAGGCCTGTCTAATGAACAGGTGTTGAAATTTGTCATGGATGGAGGGTATCTGGATCAACCCGACAACTGTCCAGAGAGAGTCACTGACCTCATGCGCATGTGCTGGCAATTCAACCCCAAGATGAGGCCAACCTTCCTGGAGATTGTCAACCTGCTCAAGGACGACCTGCACCCCAGCTTTCCAGAGGTGTCGTTCTTCCACAGCGAGGAGAACAAGGCTCCCGAGAGTGAGGAGCTGGAGATGGAGTTTGAGGACATGGAGAATGTGCCCCTGGACCGTTCCTCGCACTGTCAGAGGGAGGAGGCGGGGGGCCGGGATGGAGGGTCCTCGCTGGGTTTCAAGCGGAGCTACGAGGAACACATCCCTTACACACACATGAACGGAGGCAAGAAAAACGGGCGGATTCTGACCTTGCCTCGGTCCAATCCTTCCTAACAGTGCCTACCGTGGCGGGGGCGGGCAGGGGTTCCCATTTTCGCTTTCCTCTGGTTTGAAAGCCTCTGGAAAACTCAGGATTCTCACGACTCTACCATGTCCAGTGGAGTTCAGAGATCGTTCCTATACATTTCTGTTCATCTTAAGGTGGACTCGTTTGGTTACCAATTTAACTAGTCCTGCAGAGGATTTAACTGTGAACCTGGAGGGCAAGGGGTTTCCACAGTTGCTGCTCCTTTGGGGCAACGACGGTTTCAAACCAGGATTTTGTGTTTTTTCGTTCCCCCCACCCGCCCCCAGCAGATGGAAAGAAAGCACCTGTTTTTACAAATTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTGCTGGTGTCTGAGCTTCAGTATAAAAGACAAAACTTCCTGTTTGTGGAACAAAATTTCGAAAGAAAAAACCAAA\t\n+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.\tCCAGCTGGAGCCCTGAGTGGCTGAGCTCAGGCCTTCGCAGCATTCTTGGGTGGGAGCAGCCACGGGTCAGCCACAAGGGCCACAGCCATGAATGGCACAGAAGGCCCTAACTTCTACGTGCCCTTCTCCAATGCGACGGGTGTGGTACGCAGCCCCTTCGAGTACCCACAGTACTACCTGGCTGAGCCATGGCAGTTCTCCATGCTGGCCGCCTACATGTTTCTGCTGATCGTGCTGGGCTTCCCCATCAACTTCCTCACGCTCTACGTCACCGTCCAGCACAAGAAGCTGCGCACGCCTCTCAACTACATCCTGCTCAACCTAGCCGTGGCTGACCTCTTCATGGTCCTAGGTGGCTTCACCAGCACCCTCTACACCTCTCTGCATGGATACTTCGTCTTCGGGCCCACAGGATGCAATTTGGAGGGCTTCTTTGCCACCCTGGGCGGTGAAATTGCCCTGTGGTCCTTGGTGGTCCTGGCCATCGAGCGGTACGTGGTGGTGTGTAAGCCCATGAGCAACTTCCGCTTCGGGGAGAACCATGCCATCATGGGCGTTGCCTTCACCTGGGTCATGGCGCTGGCCTGCGCCGCACCCCCACTCGCCGGCTGGTCCAGGTACATCCCCGAGGGCCTGCAGTGCTCGTGTGGAATCGACTACTACACGCTCAAGCCGGAGGTCAACAACGAGTCTTTTGTCATCTACATGTTCGTGGTCCACTTCACCATCCCCATGATTATCATCTTTTTCTGCTATGGGCAGCTCGTCTTCACCGTCAAGGAGGCCGCTGCCCAGCAGCAGGAGTCAGCCACCACACAGAAGGCAGAGAAGGAGGTCACCCGCATGGTCATCATCATGGTCATCGCTTTCCTGATCTGCTGGGTGCCCTACGCCAGCGTGGCATTCTACATCTTCACCCACCAGGGCTCCAACTTCGGTCCCATCTTCATGACCATCCCAGCGTTCTTTGCCAAGAGCGCCGCCATCTACAACCCTGTCATCTATATCATGATGAACAAGCAGTTCCGGAACTGCATGCTCACCACCATCTGCTGCGGCAAGAACCCACTGGGTGACGATGAGGCCTCTGCTACCGTGTCCAAGACGGAGACGAGCCAGGTGGCCCCGGCCTAAGACCTGCCTAGGACTCTGTGGCCGACTATAGGCGTCTCCCATCCCCTACACCTTCCCCCAGCCACAGCCATCCCACCAG\t\n' |
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| diff -r 000000000000 -r 1f08834f987e test-data/fx2tab_output4.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fx2tab_output4.tabular Tue Mar 26 21:49:37 2024 +0000 |
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| @@ -0,0 +1,4 @@ +#id length GC GC-Skew alphabet avg.qual seq.hash +ENA|AB011145|AB011145.1 4796 38.47 11.65 ACGT 0.00 c19cf05cadbdbc26e22efc2201acfcec +ENA|M10051|M10051.1 4723 55.24 0.50 ACGT 0.00 4f6bbf79e427ef90b6f31de5023ad241 +ENA|BC112106|BC112106.1 1213 58.78 -15.01 ACGT 0.00 3b099f7df389373bb7e3269efc819599 |
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| diff -r 000000000000 -r 1f08834f987e test-data/input1.fasta.gz |
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| Binary file test-data/input1.fasta.gz has changed |
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| diff -r 000000000000 -r 1f08834f987e test-data/input1.fastq.gz |
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| Binary file test-data/input1.fastq.gz has changed |
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| diff -r 000000000000 -r 1f08834f987e test-data/locate_output1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/locate_output1.tabular Tue Mar 26 21:49:37 2024 +0000 |
| b |
| @@ -0,0 +1,95 @@ +seqID patternName pattern strand start end matched +ENA|AB011145|AB011145.1 ATAGAT ATAGAT + 251 256 ATAGAT +ENA|AB011145|AB011145.1 ATAGAT ATAGAT + 435 440 AGAGAT +ENA|AB011145|AB011145.1 ATAGAT ATAGAT + 660 665 ATAGAG +ENA|AB011145|AB011145.1 ATAGAT ATAGAT + 741 746 AAAGAT +ENA|AB011145|AB011145.1 ATAGAT ATAGAT + 852 857 ATAAAT +ENA|AB011145|AB011145.1 ATAGAT ATAGAT + 1142 1147 AAAGAT +ENA|AB011145|AB011145.1 ATAGAT ATAGAT + 1320 1325 ATAGGT +ENA|AB011145|AB011145.1 ATAGAT ATAGAT + 1621 1626 ATAAAT +ENA|AB011145|AB011145.1 ATAGAT ATAGAT + 1778 1783 AGAGAT +ENA|AB011145|AB011145.1 ATAGAT ATAGAT + 1784 1789 ATACAT +ENA|AB011145|AB011145.1 ATAGAT ATAGAT + 1810 1815 ATAAAT +ENA|AB011145|AB011145.1 ATAGAT ATAGAT + 2038 2043 ATGGAT +ENA|AB011145|AB011145.1 ATAGAT ATAGAT + 2120 2125 CTAGAT +ENA|AB011145|AB011145.1 ATAGAT ATAGAT + 2235 2240 ATAGTT +ENA|AB011145|AB011145.1 ATAGAT ATAGAT + 2243 2248 ATAAAT +ENA|AB011145|AB011145.1 ATAGAT ATAGAT + 2318 2323 CTAGAT +ENA|AB011145|AB011145.1 ATAGAT ATAGAT + 2527 2532 ATAAAT +ENA|AB011145|AB011145.1 ATAGAT ATAGAT + 2549 2554 AAAGAT +ENA|AB011145|AB011145.1 ATAGAT ATAGAT + 2603 2608 ATATAT +ENA|AB011145|AB011145.1 ATAGAT ATAGAT + 2651 2656 ATGGAT +ENA|AB011145|AB011145.1 ATAGAT ATAGAT + 2726 2731 ATAGTT +ENA|AB011145|AB011145.1 ATAGAT ATAGAT + 2744 2749 ATAAAT +ENA|AB011145|AB011145.1 ATAGAT ATAGAT + 2902 2907 TTAGAT +ENA|AB011145|AB011145.1 ATAGAT ATAGAT + 3041 3046 AAAGAT +ENA|AB011145|AB011145.1 ATAGAT ATAGAT + 3488 3493 ATGGAT +ENA|AB011145|AB011145.1 ATAGAT ATAGAT + 3539 3544 TTAGAT +ENA|AB011145|AB011145.1 ATAGAT ATAGAT + 3675 3680 AAAGAT +ENA|AB011145|AB011145.1 ATAGAT ATAGAT + 3739 3744 ATGGAT +ENA|AB011145|AB011145.1 ATAGAT ATAGAT + 3770 3775 ATAGAT +ENA|AB011145|AB011145.1 ATAGAT ATAGAT + 3825 3830 AGAGAT +ENA|AB011145|AB011145.1 ATAGAT ATAGAT + 3862 3867 AAAGAT +ENA|AB011145|AB011145.1 ATAGAT ATAGAT + 3870 3875 ATAGGT +ENA|AB011145|AB011145.1 ATAGAT ATAGAT + 4052 4057 ATATAT +ENA|AB011145|AB011145.1 ATAGAT ATAGAT + 4068 4073 AGAGAT +ENA|AB011145|AB011145.1 ATAGAT ATAGAT + 4080 4085 ACAGAT +ENA|AB011145|AB011145.1 ATAGAT ATAGAT + 4388 4393 TTAGAT +ENA|AB011145|AB011145.1 ATAGAT ATAGAT + 4446 4451 ATAGAG +ENA|AB011145|AB011145.1 ATAGAT ATAGAT + 4500 4505 AAAGAT +ENA|AB011145|AB011145.1 ATAGAT ATAGAT + 4563 4568 ATAGAA +ENA|AB011145|AB011145.1 ATAGAT ATAGAT + 4607 4612 ATAGAA +ENA|AB011145|AB011145.1 ATAGAT ATAGAT + 4675 4680 ATGGAT +ENA|AB011145|AB011145.1 ATAGAT ATAGAT + 4692 4697 ATGGAT +ENA|AB011145|AB011145.1 ATAGAT ATAGAT - 4603 4608 ATAAAT +ENA|AB011145|AB011145.1 ATAGAT ATAGAT - 4459 4464 TTAGAT +ENA|AB011145|AB011145.1 ATAGAT ATAGAT - 4223 4228 GTAGAT +ENA|AB011145|AB011145.1 ATAGAT ATAGAT - 4072 4077 ATGGAT +ENA|AB011145|AB011145.1 ATAGAT ATAGAT - 4052 4057 ATATAT +ENA|AB011145|AB011145.1 ATAGAT ATAGAT - 3634 3639 ATAAAT +ENA|AB011145|AB011145.1 ATAGAT ATAGAT - 3566 3571 ATAGAC +ENA|AB011145|AB011145.1 ATAGAT ATAGAT - 2918 2923 ACAGAT +ENA|AB011145|AB011145.1 ATAGAT ATAGAT - 2778 2783 ATACAT +ENA|AB011145|AB011145.1 ATAGAT ATAGAT - 2709 2714 ATAAAT +ENA|AB011145|AB011145.1 ATAGAT ATAGAT - 2644 2649 ATAAAT +ENA|AB011145|AB011145.1 ATAGAT ATAGAT - 2603 2608 ATATAT +ENA|AB011145|AB011145.1 ATAGAT ATAGAT - 2531 2536 ATTGAT +ENA|AB011145|AB011145.1 ATAGAT ATAGAT - 1734 1739 ATTGAT +ENA|AB011145|AB011145.1 ATAGAT ATAGAT - 1601 1606 ACAGAT +ENA|AB011145|AB011145.1 ATAGAT ATAGAT - 1438 1443 ATAGAA +ENA|AB011145|AB011145.1 ATAGAT ATAGAT - 1422 1427 ATAGGT +ENA|AB011145|AB011145.1 ATAGAT ATAGAT - 1329 1334 ATAGAG +ENA|AB011145|AB011145.1 ATAGAT ATAGAT - 1146 1151 ATACAT +ENA|AB011145|AB011145.1 ATAGAT ATAGAT - 1121 1126 ATACAT +ENA|AB011145|AB011145.1 ATAGAT ATAGAT - 811 816 ATAGCT +ENA|AB011145|AB011145.1 ATAGAT ATAGAT - 764 769 GTAGAT +ENA|AB011145|AB011145.1 ATAGAT ATAGAT - 656 661 ATAGTT +ENA|M10051|M10051.1 ATAGAT ATAGAT + 250 255 ATGGAT +ENA|M10051|M10051.1 ATAGAT ATAGAT + 664 669 AAAGAT +ENA|M10051|M10051.1 ATAGAT ATAGAT + 1987 1992 ACAGAT +ENA|M10051|M10051.1 ATAGAT ATAGAT + 3540 3545 AGAGAT +ENA|M10051|M10051.1 ATAGAT ATAGAT + 3561 3566 AGAGAT +ENA|M10051|M10051.1 ATAGAT ATAGAT + 3886 3891 ATGGAT +ENA|M10051|M10051.1 ATAGAT ATAGAT + 4400 4405 AGAGAT +ENA|M10051|M10051.1 ATAGAT ATAGAT + 4413 4418 ATACAT +ENA|M10051|M10051.1 ATAGAT ATAGAT - 3688 3693 ATAGAT +ENA|M10051|M10051.1 ATAGAT ATAGAT - 3065 3070 ATAGAT +ENA|M10051|M10051.1 ATAGAT ATAGAT - 3061 3066 ATAAAT +ENA|M10051|M10051.1 ATAGAT ATAGAT - 3025 3030 AAAGAT +ENA|M10051|M10051.1 ATAGAT ATAGAT - 2956 2961 ATAGGT +ENA|M10051|M10051.1 ATAGAT ATAGAT - 2828 2833 AGAGAT +ENA|M10051|M10051.1 ATAGAT ATAGAT - 2719 2724 AAAGAT +ENA|M10051|M10051.1 ATAGAT ATAGAT - 1975 1980 ATAAAT +ENA|M10051|M10051.1 ATAGAT ATAGAT - 1951 1956 ATAGGT +ENA|M10051|M10051.1 ATAGAT ATAGAT - 1909 1914 AAAGAT +ENA|M10051|M10051.1 ATAGAT ATAGAT - 1659 1664 AAAGAT +ENA|M10051|M10051.1 ATAGAT ATAGAT - 1417 1422 ATAGAA +ENA|M10051|M10051.1 ATAGAT ATAGAT - 1319 1324 TTAGAT +ENA|M10051|M10051.1 ATAGAT ATAGAT - 802 807 ACAGAT +ENA|M10051|M10051.1 ATAGAT ATAGAT - 691 696 ACAGAT +ENA|M10051|M10051.1 ATAGAT ATAGAT - 415 420 ATAGAC +ENA|BC112106|BC112106.1 ATAGAT ATAGAT + 386 391 ATGGAT +ENA|BC112106|BC112106.1 ATAGAT ATAGAT - 1000 1005 ATAGAT +ENA|BC112106|BC112106.1 ATAGAT ATAGAT - 985 990 GTAGAT +ENA|BC112106|BC112106.1 ATAGAT ATAGAT - 742 747 AAAGAT +ENA|BC112106|BC112106.1 ATAGAT ATAGAT - 700 705 GTAGAT |
| b |
| diff -r 000000000000 -r 1f08834f987e test-data/locate_output2.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/locate_output2.bed Tue Mar 26 21:49:37 2024 +0000 |
| [ |
| b'@@ -0,0 +1,202 @@\n+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.\t136\t139\tA[TU]G\t0\t+\n+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.\t174\t177\tA[TU]G\t0\t+\n+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.\t254\t257\tA[TU]G\t0\t+\n+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.\t269\t272\tA[TU]G\t0\t+\n+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.\t275\t278\tA[TU]G\t0\t+\n+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.\t296\t299\tA[TU]G\t0\t+\n+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.\t322\t325\tA[TU]G\t0\t+\n+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.\t353\t356\tA[TU]G\t0\t+\n+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.\t377\t380\tA[TU]G\t0\t+\n+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.\t479\t482\tA[TU]G\t0\t+\n+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.\t484\t487\tA[TU]G\t0\t+\n+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.\t487\t490\tA[TU]G\t0\t+\n+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.\t490\t493\tA[TU]G\t0\t+\n+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.\t692\t695\tA[TU]G\t0\t+\n+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.\t695\t698\tA[TU]G\t0\t+\n+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.\t725\t728\tA[TU]G\t0\t+\n+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.\t796\t799\tA[TU]G\t0\t+\n+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.\t814\t817\tA[TU]G\t0\t+\n+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.\t827\t830\tA[TU]G\t0\t+\n+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.\t855\t858\tA[TU]G\t0\t+\n+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.\t890\t893\tA[TU]G\t0\t+\n+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.\t940\t943\tA[TU]G\t0\t+\n+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.\t977\t980\tA[TU]G\t0\t+\n+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.\t1028\t1031\tA[TU]G\t0\t+\n+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.\t1120\t1123\tA[TU]G\t0\t+\n+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.\t1124\t1127\tA[TU]G\t0\t+\n+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.\t1145\t1148\tA[TU]G\t0\t+\n+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.\t1220\t1223\tA[TU]G\t0\t+\n+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.\t1265\t1268\tA[TU]G\t0\t+\n+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.\t1346\t1349\tA[TU]G\t0\t+\n+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.\t1441\t1444\tA[TU]G\t0\t+\n+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.\t1510\t1513\tA[TU]G\t0\t+\n+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.\t1629\t1632\tA[TU]G\t0\t+\n+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.\t1693\t1696\tA[TU]G\t0\t+\n+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.\t1709\t1712\tA[TU]G\t0\t+\n+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.\t1730\t1733\tA[TU]G\t0\t+\n+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.\t1866\t1869\tA[TU]G\t0\t+\n+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.\t1902\t1905\tA[TU]G\t0\t+\n+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.\t1972\t1975\tA[TU]G\t0\t+\n+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.\t1991\t1994\tA[TU]G\t0\t+\n+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, pa'..b'051|M10051.1 Human insulin receptor mRNA, complete cds.\t3862\t3865\tA[TU]G\t0\t+\n+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.\t3885\t3888\tA[TU]G\t0\t+\n+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.\t3889\t3892\tA[TU]G\t0\t+\n+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.\t3942\t3945\tA[TU]G\t0\t+\n+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.\t3948\t3951\tA[TU]G\t0\t+\n+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.\t3972\t3975\tA[TU]G\t0\t+\n+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.\t4092\t4095\tA[TU]G\t0\t+\n+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.\t4107\t4110\tA[TU]G\t0\t+\n+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.\t4114\t4117\tA[TU]G\t0\t+\n+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.\t4168\t4171\tA[TU]G\t0\t+\n+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.\t4227\t4230\tA[TU]G\t0\t+\n+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.\t4383\t4386\tA[TU]G\t0\t+\n+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.\t4590\t4593\tA[TU]G\t0\t+\n+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.\t87\t90\tA[TU]G\t0\t+\n+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.\t91\t94\tA[TU]G\t0\t+\n+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.\t130\t133\tA[TU]G\t0\t+\n+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.\t188\t191\tA[TU]G\t0\t+\n+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.\t201\t204\tA[TU]G\t0\t+\n+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.\t216\t219\tA[TU]G\t0\t+\n+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.\t342\t345\tA[TU]G\t0\t+\n+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.\t385\t388\tA[TU]G\t0\t+\n+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.\t413\t416\tA[TU]G\t0\t+\n+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.\t513\t516\tA[TU]G\t0\t+\n+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.\t541\t544\tA[TU]G\t0\t+\n+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.\t549\t552\tA[TU]G\t0\t+\n+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.\t573\t576\tA[TU]G\t0\t+\n+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.\t705\t708\tA[TU]G\t0\t+\n+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.\t732\t735\tA[TU]G\t0\t+\n+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.\t754\t757\tA[TU]G\t0\t+\n+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.\t843\t846\tA[TU]G\t0\t+\n+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.\t855\t858\tA[TU]G\t0\t+\n+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.\t948\t951\tA[TU]G\t0\t+\n+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.\t1008\t1011\tA[TU]G\t0\t+\n+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.\t1011\t1014\tA[TU]G\t0\t+\n+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.\t1035\t1038\tA[TU]G\t0\t+\n+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.\t1078\t1081\tA[TU]G\t0\t+\n' |
| b |
| diff -r 000000000000 -r 1f08834f987e test-data/locate_output3.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/locate_output3.gtf Tue Mar 26 21:49:37 2024 +0000 |
| b |
| @@ -0,0 +1,4 @@ +ENA|AB011145|AB011145.1 SeqKit location 2270 2276 0 + . gene_id "test_motif2"; +ENA|AB011145|AB011145.1 SeqKit location 2642 2648 0 + . gene_id "test_motif2"; +ENA|AB011145|AB011145.1 SeqKit location 2655 2661 0 + . gene_id "test_motif2"; +ENA|AB011145|AB011145.1 SeqKit location 2771 2777 0 + . gene_id "test_motif2"; |
| b |
| diff -r 000000000000 -r 1f08834f987e test-data/motif_sequence.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_sequence.fasta Tue Mar 26 21:49:37 2024 +0000 |
| b |
| @@ -0,0 +1,4 @@ +>test_motif +ATATACTAT +>test_motif2 +ATATTTA |
| b |
| diff -r 000000000000 -r 1f08834f987e test-data/sort_output1.fastq.gz |
| b |
| Binary file test-data/sort_output1.fastq.gz has changed |
| b |
| diff -r 000000000000 -r 1f08834f987e test-data/sort_output2.fasta.gz |
| b |
| Binary file test-data/sort_output2.fasta.gz has changed |
| b |
| diff -r 000000000000 -r 1f08834f987e test-data/sort_output3.fasta.gz |
| b |
| Binary file test-data/sort_output3.fasta.gz has changed |
| b |
| diff -r 000000000000 -r 1f08834f987e test-data/sort_output4.fasta.gz |
| b |
| Binary file test-data/sort_output4.fasta.gz has changed |
| b |
| diff -r 000000000000 -r 1f08834f987e test-data/sort_output5.fastq.gz |
| b |
| Binary file test-data/sort_output5.fastq.gz has changed |
| b |
| diff -r 000000000000 -r 1f08834f987e test-data/sort_output6.fastq.gz |
| b |
| Binary file test-data/sort_output6.fastq.gz has changed |
| b |
| diff -r 000000000000 -r 1f08834f987e test-data/stats_output1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stats_output1.tabular Tue Mar 26 21:49:37 2024 +0000 |
| b |
| @@ -0,0 +1,2 @@ +file format type num_seqs sum_len min_len avg_len max_len Q1 Q2 Q3 sum_gap N50 Q20(%) Q30(%) GC(%) +input1_fastq_gz FASTQ DNA 5 505 101 101.0 101 50.5 101.0 50.5 0 101 98.02 89.31 35.45 |
| b |
| diff -r 000000000000 -r 1f08834f987e test-data/stats_output2.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stats_output2.tabular Tue Mar 26 21:49:37 2024 +0000 |
| b |
| @@ -0,0 +1,2 @@ +file format type num_seqs sum_len min_len avg_len max_len Q1 Q2 Q3 sum_gap N50 Q20(%) Q30(%) GC(%) +input1_fasta_gz FASTA DNA 3 10732 1213 3577.3 4796 2968.0 4723.0 4759.5 0 4723 0.00 0.00 48.15 |