Repository 'seqkit_locate'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/seqkit_locate

Changeset 0:642d73815dd1 (2022-11-03)
Next changeset 1:6510652376b1 (2022-11-06)
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 202bb1229cb0b8e8040a87d140edb6fdf7654628
added:
macros.xml
seqkit_locate.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/stats_output1.tabular
test-data/stats_output2.tabular
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diff -r 000000000000 -r 642d73815dd1 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Thu Nov 03 19:35:37 2022 +0000
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@@ -0,0 +1,21 @@
+<macros>
+    <token name="@TOOL_VERSION@">2.3.1</token>
+    <token name="@VERSION_SUFFIX@">0</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 642d73815dd1 seqkit_locate.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/seqkit_locate.xml Thu Nov 03 19:35:37 2022 +0000
[
b'@@ -0,0 +1,177 @@\n+<tool id="seqkit_locate" name="SeqKit locate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">\n+    <description>subsequences/motifs, mismatch allowed</description>\n+    <macros>\n+        <import>macros.xml</import>\n+    </macros>\n+    <expand macro="bio_tools"/>\n+    <expand macro="requirements"/>\n+    <command detect_errors="exit_code"><![CDATA[\n+#import re\n+\n+#set input_identifier = re.sub(\'[^\\s\\w\\-]\', \'_\', str($input.element_identifier))\n+ln -s \'${input}\' \'${input_identifier}\' &&\n+\n+seqkit locate \n+--threads \\${GALAXY_SLOTS:-4}\n+#if $conditional_pattern.mode == \'expression\'\n+    --pattern \'"$conditional_pattern.pattern"\'\n+    $conditional_pattern.use_regexp\n+#else\n+    --pattern-file \'$conditional_pattern.pattern_file\'\n+#end if\n+$output_mode\n+--validate-seq-length $advanced_options.validate_seq_length\n+$advanced_options.circular\n+$advanced_options.degenerate\n+$advanced_options.hide_matched\n+$advanced_options.ignore_case\n+#if not $advanced_options.degenerate\n+    --max-mismatch $advanced_options.max_mismatch\n+    $advanced_options.use_fmi\n+#end if\n+$advanced_options.non_greedy\n+$advanced_options.only_positive_strand\n+$advanced_options.id_ncbi\n+\'${input_identifier}\'\n+> \'$output\'\n+]]></command>\n+    <inputs>\n+        <param name="input" type="data" format="fasta,fasta.gz" label="Input file"/>\n+        <conditional name="conditional_pattern">\n+            <param name="mode" type="select" label="Pattern mode" \n+                help="Specify a pattern/motif sequence or a FASTA file with the motif of interest. Motifs could be EITHER plain sequence containing \'ACTGN\' OR regular\n+                    expression like \'A[TU]G(?:.{3})+?[TU](?:AG|AA|GA)\' for ORFs">\n+                <option value="expression">Pattern/motif sequence</option>\n+                <option value="file">FASTA file with the pattern/motif of interest</option>\n+            </param>\n+            <when value="expression">\n+                <param argument="--pattern" type="text" value="" label="Pattern/motif sequence" help="Perl regular expressions are allowed">\n+                    <sanitizer invalid_char="">\n+                        <valid initial="string.letters,string.digits">\n+                        <add value="^"/>\n+                        <add value="$"/>\n+                        <add value="("/>\n+                        <add value=")"/>\n+                        <add value="|"/>\n+                        <add value="?"/>\n+                        <add value="*"/>\n+                        <add value="+"/>\n+                        <add value="{"/>\n+                        <add value="}"/>\n+                        <add value="\\"/>\n+                        <add value="["/>\n+                        <add value="]"/>\n+                        <add value="."/>\n+                        <add value=","/>\n+                        </valid>\n+                    </sanitizer>\n+                    <validator type="regex" message="Pattern must not end with backslash.">.*[^\\\\]$</validator>\n+                </param>\n+                <param argument="--use-regexp" type="boolean" truevalue="--use-regexp" falsevalue="" checked="false" label="Pattern/motifs are regular expressions"/>\n+            </when>\n+            <when value="file">\n+                <param argument="--pattern-file" type="data" format="fasta" label="Pattern/motif file"/>\n+            </when>\n+        </conditional>\n+        <param name="output_mode" type="select" label="Output mode">\n+            <option value="">Tabular (default format)</option>\n+            <option value="--gtf">GTF</option>\n+            <option value="--bed">BED6</option>\n+        </param>\n+        <section name="advanced_options" title="Advanced options">\n+            <param argument="--validate-seq-length" type="integer" min="0" value="10000" label="Lenth of the sequence to validate" help="Default: 10000" />\n+            <param argument="--circular" type="boolean" truevalue="--circular" falsevalue="" checke'..b'ed="false" label="FM-index" \n+                help="Use FM-index for much faster search of lots of sequence patterns. This option is not compatible with the --degenerate option"/>\n+            <param argument="--id-ncbi" type="boolean" truevalue="--id-ncbi" falsevalue="" checked="false" label="FASTA head is NCBI stype" help="Example: >gi|110645304|ref|NC_002516.2| Pseud..." />\n+        </section>\n+    </inputs>\n+    <outputs>\n+        <data name="output" format="tabular" label="${tool.name} on ${on_string}">\n+            <change_format>\n+                <when input="output_mode" value="--gtf" format="gtf"/>\n+                <when input="output_mode" value="--bed" format="bed"/>\n+            </change_format>\n+        </data>\n+    </outputs>\n+    <tests>\n+        <test expect_num_outputs="1">\n+            <param name="input" value="input1.fasta.gz" ftype="fasta.gz"/>\n+            <conditional name="conditional_pattern">\n+                <param name="mode" value="expression"/>\n+                <param name="pattern" value="ATAGAT"/>\n+            </conditional>\n+            <section name="advanced_options">\n+                <param name="max_mismatch" value="1"/>\n+            </section>\n+            <output name="output" file="locate_output1.tabular" ftype="tabular"/>\n+        </test>\n+        <test expect_num_outputs="1">\n+            <param name="input" value="input1.fasta.gz" ftype="fasta.gz"/>\n+            <conditional name="conditional_pattern">\n+                <param name="mode" value="expression"/>\n+                <param name="pattern" value="A[TU]G"/>\n+                <param name="use_regexp" value="true"/>\n+            </conditional>\n+            <param name="output_mode" value="--bed"/>\n+            <section name="advanced_options">\n+                <param name="circular" value="true"/>\n+                <param name="hide_matched" value="true"/>\n+                <param name="ignore_case" value="true"/>\n+                <param name="only_positive_strand" value="true"/>\n+                <param name="id_ncbi" value="true"/>\n+            </section>\n+            <output name="output" file="locate_output2.bed" ftype="bed"/>\n+        </test>\n+        <test expect_num_outputs="1">\n+            <param name="input" value="input1.fasta.gz" ftype="fasta.gz"/>\n+            <conditional name="conditional_pattern">\n+                <param name="mode" value="file"/>\n+                <param name="pattern_file" value="motif_sequence.fasta"/>\n+            </conditional>\n+            <param name="output_mode" value="--gtf"/>\n+            <section name="advanced_options">\n+                <param name="use_fmi" value="true"/>\n+            </section>\n+            <output name="output" file="locate_output3.gtf" ftype="gtf"/>\n+        </test>\n+    </tests>\n+    <help>\n+.. class:: infomark\n+\n+**Purpose**\n+\n+Locate subsequences/motifs, mismatch allowed.\n+\n+------\n+\n+.. class:: infomark\n+\n+**Attention**\n+\n+  1. Motifs could be EITHER plain sequence containing "ACTGN" OR regular\n+     expression like "A[TU]G(?:.{3})+?[TU](?:AG|AA|GA)" for ORFs.     \n+  2. Degenerate bases/residues like "RYMM.." are also supported by flag -d.\n+     But do not use degenerate bases/residues in regular expression, you need\n+     convert them to regular expression, e.g., change "N" or "X"  to ".".\n+  3. When providing search patterns (motifs) via flag \'-p\',\n+     please use double quotation marks for patterns containing comma, \n+     e.g., -p \'"A{2,}"\' or -p "\\"A{2,}\\"". Because the command line argument\n+     parser accepts comma-separated-values (CSV) for multiple values (motifs).\n+     Patterns in file do not follow this rule.     \n+  4. Mismatch is allowed using flag "-m/--max-mismatch",\n+     you can increase the value of "-j/--threads" to accelerate processing.\n+  5. When using flag --circular, end position of matched subsequence that \n+     crossing genome sequence end would be greater than sequence length.\n+    </help>\n+    <expand macro="citations"/>\n+</tool>\n+\n'
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diff -r 000000000000 -r 642d73815dd1 test-data/fx2tab_output1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fx2tab_output1.tabular Thu Nov 03 19:35:37 2022 +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 642d73815dd1 test-data/fx2tab_output2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fx2tab_output2.tabular Thu Nov 03 19:35:37 2022 +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 642d73815dd1 test-data/fx2tab_output3.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fx2tab_output3.tabular Thu Nov 03 19:35:37 2022 +0000
b
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'
b
diff -r 000000000000 -r 642d73815dd1 test-data/fx2tab_output4.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fx2tab_output4.tabular Thu Nov 03 19:35:37 2022 +0000
b
@@ -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
b
diff -r 000000000000 -r 642d73815dd1 test-data/input1.fasta.gz
b
Binary file test-data/input1.fasta.gz has changed
b
diff -r 000000000000 -r 642d73815dd1 test-data/input1.fastq.gz
b
Binary file test-data/input1.fastq.gz has changed
b
diff -r 000000000000 -r 642d73815dd1 test-data/locate_output1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/locate_output1.tabular Thu Nov 03 19:35:37 2022 +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 642d73815dd1 test-data/locate_output2.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/locate_output2.bed Thu Nov 03 19:35:37 2022 +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 642d73815dd1 test-data/locate_output3.gtf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/locate_output3.gtf Thu Nov 03 19:35:37 2022 +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 642d73815dd1 test-data/motif_sequence.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/motif_sequence.fasta Thu Nov 03 19:35:37 2022 +0000
b
@@ -0,0 +1,4 @@
+>test_motif
+ATATACTAT
+>test_motif2
+ATATTTA
b
diff -r 000000000000 -r 642d73815dd1 test-data/stats_output1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/stats_output1.tabular Thu Nov 03 19:35:37 2022 +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 642d73815dd1 test-data/stats_output2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/stats_output2.tabular Thu Nov 03 19:35:37 2022 +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