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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/ commit cbedf7b5968b45a08df88d4ad799951d6f50a2bd"
author iuc
date Mon, 11 Apr 2022 20:37:19 +0000
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files find_nested_alt_orfs.xml macros.xml test-data/aa_freq_from_bicodon.tabular test-data/all_fasta.loc test-data/bed_out.bed test-data/bicodon_out.tabular test-data/cds_fasta_out.fasta test-data/codon_freq_from_bicodon.tabular test-data/codon_freq_from_bicodon_log.txt test-data/codon_out.tabular test-data/find_naltorfs_log.txt test-data/gencode_canonical.hg38.chr6_GL0002508.bed test-data/hg38.chr6_GL000250v2_alt.2bit.gz test-data/naltorfs_fasta_out.fasta test-data/peptide_fasta_out.fasta test-data/twobit.loc tool-data/all_fasta.loc.sample tool-data/twobit.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test
diffstat 20 files changed, 425 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/find_nested_alt_orfs.xml	Mon Apr 11 20:37:19 2022 +0000
@@ -0,0 +1,115 @@
+<tool id="find_nested_alt_orfs" name="Find Nested Alternate ORFs (nAlt-ORFs)" version="@TOOL_VERSION@" profile="20.05">
+    <description>from BED and 2bit/FASTA</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="edam_ontology"/>
+    <expand macro="requirements">
+        <requirement type="package" version="377">ucsc-fatotwobit</requirement>
+    </expand>
+    <version_command>find_nested_alt_orfs.py --version</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+        #if $ref.ref_source == 'history':
+            #if  $ref.ref_file.is_of_type('fasta'):
+                #set $twobit_filename = "out.2bit"
+                faToTwoBit '${ref.ref_file}' '$twobit_filename' -stripVersion &&
+            #else:
+                #set $twobit_filename = $ref.ref_file
+            #end if
+        #else:
+            #set $twobit_filename = $ref.ref_loc.fields.path
+        #end if
+        find_nested_alt_orfs.py
+            --twobit '$twobit_filename'
+
+            --min_length '$min_length'
+
+            --reference '${input.metadata.dbkey}'
+
+            --bed '$input'
+
+            #if $no_canonical_cds:
+                --no_canonical_cds '$no_canonical_cds'
+            #end if
+
+            --translation_table '$translation_table'
+
+            --bed_out '$bed_out'
+
+            --peptide_fasta_out '$peptide_fasta_out'
+
+            --naltorfs_fasta_out '$naltorfs_fasta_out'
+
+            --cds_fasta_out '$cds_fasta_out'
+
+            $unique_sequences
+
+            #if $write_log:
+                --log '$log'
+            #end if
+    ]]></command>
+    <inputs>
+        <param argument="--bed" name="input" type="data" format="bed" label="Gene BED" help="A BED file with 12 columns"/>
+        <conditional name="ref">
+            <param name="ref_source" type="select" label="Source for Genomic Sequence Data">
+                <option value="cached">Locally cached genome</option>
+                <option value="history">History dataset genome</option>
+            </param>
+            <when value="cached">
+                <param argument="--twobit" name="ref_loc" type="select" label="Select reference genome">
+                    <options from_data_table="twobit"/>
+                </param>
+            </when>
+            <when value="history">
+                <param argument="--twobit" name="ref_file" type="data" format="twobit,fasta" label="Reference genome"/>
+            </when>
+        </conditional>
+        <param argument="--min_length" type="integer" value="150" min="1" label="Minimum length of peptide translation to report"/>
+        <param argument="--unique_sequences" type="boolean" truevalue="--unique_sequences" falsevalue="" checked="True" label="Only report the first unique occurrence of an alternate sequence"/>
+        <param argument="--no_canonical_cds" type="data" format="bed" optional="True" label="Do not report any alternate sequences that match a provided canonical CDS" help="A BED file with 12 columns"/>
+        <expand macro="translation_table_select_parameter"/>
+        <param name="write_log" type="boolean" truevalue="true" falsevalue="false" checked="True" label="Create log file"/>
+    </inputs>
+    <outputs>
+        <data name="bed_out" format="bed" label="Find Nested nAlt-ORFs on ${on_string}: nAlt-ORFs.proBed">
+            <actions>
+                <action name="column_names" type="metadata" default="chrom,chromStart,chromEnd,name,score,strand,thickStart,thickEnd,itemRgb,blockCount,blockSizes,blockStarts,proteinAccession,peptideSequence,uniqueness,genomeReferenceVersion,psmScore,fdr,modifications,charge,expMassToCharge,calcMassToCharge,psmRank,datasetID,uri"/>
+            </actions>
+        </data>
+        <data name="peptide_fasta_out" format="fasta" label="Find nAlt-ORFs on ${on_string}: peptide.fasta"/>
+        <data name="naltorfs_fasta_out" format="fasta" label="Find nAlt-ORFs on ${on_string}: nAlt-ORFs.fasta"/>
+        <data name="cds_fasta_out" format="fasta" label="Find nAlt-ORFs on ${on_string}: canonical CDS.fasta"/>
+        <data name="log" format="txt" label="Find nAlt-ORFs on ${on_string}: log.txt">
+            <filter>write_log</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="gencode_canonical.hg38.chr6_GL0002508.bed" dbkey="hg38" ftype="bed12"/>
+            <conditional name="ref">
+                <param name="ref_source" value="history"/>
+                <param name="ref_file" value="hg38.chr6_GL000250v2_alt.2bit.gz" dbkey="hg38" ftype="twobit"/>
+            </conditional>
+            <param name="min_length" value="150"/>
+            <param name="unique_sequences" value="true"/>
+            <param name="no_canonical_cds" value="gencode_canonical.hg38.chr6_GL0002508.bed" dbkey="hg38" ftype="bed12"/>
+            <param name="translation_table" value="1"/>
+            <param name="write_log" value="true"/>
+            <output name="bed_out" value="bed_out.bed"/>
+            <output name="peptide_fasta_out" value="peptide_fasta_out.fasta"/>
+            <output name="naltorfs_fasta_out" value="naltorfs_fasta_out.fasta"/>
+            <output name="cds_fasta_out" value="cds_fasta_out.fasta"/>
+            <output name="log" value="find_naltorfs_log.txt"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+Find Nested Alternate Open Reading Frames (nAlt-ORFs).
+
+Using a BED12 file containing the location of genes, and a matching reference genome,
+this tool searches in the alternate reading frames of the provided canonical coding sequence,
+and outputs nested alternate ORFs which match the provided thresholds.
+
+Translation table identifiers are based upon NCBI standards (https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi).
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Mon Apr 11 20:37:19 2022 +0000
@@ -0,0 +1,63 @@
+<macros>
+    <token name="@TOOL_VERSION@">0.1.2</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">naltorfs</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+    <xml name="translation_table_select_parameter">
+        <param argument="--translation_table" type="select" label="Translation table">
+            <option value="1" selected="true">Table 1 Standard, SGC0</option>
+            <option value="2">Table 2 Vertebrate Mitochondrial, SGC1</option>
+            <option value="3">Table 3 Yeast Mitochondrial, SGC2</option>
+            <option value="4">Table 4 Mold Mitochondrial, Protozoan Mitochondrial, Coelenterate Mitochondrial, Mycoplasma, Spiroplasma, SGC3</option>
+            <option value="5">Table 5 Invertebrate Mitochondrial, SGC4</option>
+            <option value="6">Table 6 Ciliate Nuclear, Dasycladacean Nuclear, Hexamita Nuclear, SGC5</option>
+            <option value="9">Table 9 Echinoderm Mitochondrial, Flatworm Mitochondrial, SGC8</option>
+            <option value="10">Table 10 Euplotid Nuclear, SGC9</option>
+            <option value="11">Table 11 Bacterial, Archaeal, Plant Plastid</option>
+            <option value="12">Table 12 Alternative Yeast Nuclear</option>
+            <option value="13">Table 13 Ascidian Mitochondrial</option>
+            <option value="14">Table 14 Alternative Flatworm Mitochondrial</option>
+            <option value="15">Table 15 Blepharisma Macronuclear</option>
+            <option value="16">Table 16 Chlorophycean Mitochondrial</option>
+            <option value="21">Table 21 Trematode Mitochondrial</option>
+            <option value="22">Table 22 Scenedesmus obliquus Mitochondrial</option>
+            <option value="23">Table 23 Thraustochytrium Mitochondrial</option>
+            <option value="24">Table 24 Pterobranchia Mitochondrial</option>
+            <option value="25">Table 25 Candidate Division SR1, Gracilibacteria</option>
+            <option value="26">Table 26 Pachysolen tannophilus Nuclear</option>
+            <option value="27">Table 27 Karyorelict Nuclear</option>
+            <option value="28">Table 28 Condylostoma Nuclear</option>
+            <option value="29">Table 29 Mesodinium Nuclear</option>
+            <option value="30">Table 30 Peritrich Nuclear</option>
+            <option value="31">Table 31 Blastocrithidia Nuclear</option>
+            <option value="32">Table 32 Balanophoraceae Plastid</option>
+            <option value="33">Table 33 Cephalodiscidae Mitochondrial</option>
+        </param>
+    </xml>
+    <xml name="edam_ontology">
+        <edam_topics>
+            <edam_topic>topic_0622</edam_topic>
+            <edam_topic>topic_0091</edam_topic>
+        </edam_topics>
+        <edam_operations>
+            <edam_operation>operation_0286</edam_operation>
+            <edam_operation>operation_0284</edam_operation>
+            <edam_operation>operation_0436</edam_operation>
+            <edam_operation>operation_0362</edam_operation>
+        </edam_operations>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">
+                @UNPUBLISHED{nAltORFs,
+                    author = "Kommireddy Vasu and Debjit Khan and Iyappan Ramachandiran and Daniel Blankenberg and Paul L. Fox",
+                    title = "Nested Alternate Open Reading Frames and their Encoded Proteins: The Hidden Orfeome",
+                    year = "2022"
+                }
+            </citation>
+        </citations>
+    </xml>
+</macros>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/aa_freq_from_bicodon.tabular	Mon Apr 11 20:37:19 2022 +0000
@@ -0,0 +1,5 @@
+#frame	aa_count	*	A	C	D	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
+2-counts	855	20	74	27	11	20	27	52	15	42	18	95	31	20	81	20	72	86	59	44	26	15
+2-percent	855	2.3391812865497074724885351316	8.6549707602339189804752095370	3.1578947368421053099041273526	1.2865497076023393319132992474	2.3391812865497074724885351316	3.1578947368421053099041273526	6.0818713450292394284701913421	1.7543859649122806043664013487	4.9122807017543861363151336263	2.1052631578947367252396816184	11.1111111111111107163651467999	3.6257309941520468044018343790	2.3391812865497074724885351316	9.4736842105263168178908017580	2.3391812865497074724885351316	8.4210526315789469009587264736	10.0584795321637425757899109158	6.9005847953216372658857835631	5.1461988304093573276531969896	3.0409356725146197142350956710	1.7543859649122806043664013487
+3-counts	855	42	62	55	22	41	15	71	28	12	6	69	7	6	104	42	70	91	42	27	28	15
+3-percent	855	4.9122807017543861363151336263	7.2514619883040936088036687579	6.4327485380116957713880765368	2.5730994152046786638265984948	4.7953216374269000965568920947	1.7543859649122806043664013487	8.3040935672514617493789046421	3.2748538011695909055731590342	1.4035087719298244834931210789	0.7017543859649122417465605395	8.0701754385964914462192609790	0.8187134502923977263932897586	0.7017543859649122417465605395	12.1637426900584788569403826841	4.9122807017543861363151336263	8.1871345029239765977990828105	10.6432748538011701100458594738	4.9122807017543861363151336263	3.1578947368421053099041273526	3.2748538011695909055731590342	1.7543859649122806043664013487
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/all_fasta.loc	Mon Apr 11 20:37:19 2022 +0000
@@ -0,0 +1,18 @@
+#This file lists the locations and dbkeys of all the fasta files
+#under the "genome" directory (a directory that contains a directory
+#for each build). The script extract_fasta.py will generate the file
+#all_fasta.loc. This file has the format (white space characters are
+#TAB characters):
+#
+#<unique_build_id>	<dbkey>	<display_name>	<file_path>
+#
+#So, all_fasta.loc could look something like this:
+#
+#apiMel3	apiMel3	Honeybee (Apis mellifera): apiMel3	/path/to/genome/apiMel3/apiMel3.fa
+#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/path/to/genome/hg19/hg19canon.fa
+#hg19full	hg19	Human (Homo sapiens): hg19 Full	/path/to/genome/hg19/hg19full.fa
+#
+#Your all_fasta.loc file should contain an entry for each individual
+#fasta file. So there will be multiple fasta files for each build,
+#such as with hg19 above.
+#
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bed_out.bed	Mon Apr 11 20:37:19 2022 +0000
@@ -0,0 +1,4 @@
+chr6_GL000250v2_alt	938210	938801	ENST00000432222.1	0	-	938210	938801	12,12,120	1	591	0	ENST00000432222.1_f2_40_3	MAQNQASVLKNQAPVTRTQAPITGTLCQDARSNSHPVKPSRLNVFCCPHCSLTFSKKSYLSRHQKAHLTEPPNYCFHCSKSFSSFSRLVRHQQTHWKQKSYLCPICDLSFGEKEGLMDHWRGYKGKDLCQSSHHKCRVILGQWLGFSHDVPTMAGEEWKHGGDQSPPRIHTPRRRGLREKACKGDKTKEAVSILKHK	unique	hg38	.	.	.	.	.	.	.	.	.
+chr6_GL000250v2_alt	2862985	2871389	ENST00000448800.5	0	-	2862985	2871389	12,12,120	8	14,148,145,110,132,119,184,78	0,342,616,859,2343,4930,6063,8326	ENST00000448800.5_f3_53_3	MCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDEIDISSYIEQTR	unique	hg38	.	.	.	.	.	.	.	.	.
+chr6_GL000250v2_alt	3481820	3484425	ENST00000445122.5	0	-	3481820	3484425	12,12,120	4	176,186,216,19	0,314,1145,2586	ENST00000445122.5_f3_80_1	MSSEKSGDSLRGPTSPAAARCRRPAPAGASPDCPGPWLRGAHARGDCGHAAAGGLRSARIPPAAAALHCLRAGLPGGHAICRRDPGGNRSDLHSPPAAPGPRAGPTGAEAPATRLHAHRGADHHLLLLAYWHHCHLQGRAGAHGLGPRRHGVGRDRFTRGPELLLHLPGRGHRGHGALYHPHRSHHHRRAAPRELLGSL	unique	hg38	.	.	.	.	.	.	.	.	.
+chr6_GL000250v2_alt	3503057	3504078	ENST00000430777.2	0	-	3503057	3504078	12,12,120	3	145,134,180	0,481,841	ENST00000430777.2_f3_20_373	MDAAAAALPAAALPAAHPVVLQPQCQVLLQDGLLQWLDPLPGCARHPCVCRARTQRREHEDLASNAAPHQIPVRDPSGGARGSPLPSLAALCCCLQPPELSRSAWDDGGTARPLCAHCQARATVGWLCRAGLLAGRSHLHRPEAHGGCHQCHV	unique	hg38	.	.	.	.	.	.	.	.	.
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bicodon_out.tabular	Mon Apr 11 20:37:19 2022 +0000
@@ -0,0 +1,2 @@
+Division	Assembly	Taxid	Species	Organelle	Translation Table	# CDS	# Codon 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+custom	hg38	9606	Homo 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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cds_fasta_out.fasta	Mon Apr 11 20:37:19 2022 +0000
@@ -0,0 +1,8 @@
+>ENST00000432222.1
+GGCCAGGTCCCAGGAACCCATATTTAGAACTGAGGGTCCTATGGCCCAGAACCAGGCATCTGTACTTAAGAACCAAGCACCTGTGACCAGGACCCAGGCACCCATCACTGGAACCCTCTGTCAGGATGCCAGATCCAACTCTCATCCAGTGAAGCCCTCAAGACTCAATGTCTTCTGTTGCCCCCATTGTTCTTTGACTTTTAGCAAGAAATCCTATCTCTCCAGACACCAGAAGGCCCACCTCACAGAGCCGCCCAACTACTGCTTCCATTGCAGCAAGTCTTTCAGCTCATTTTCCAGGCTGGTCAGACACCAGCAGACCCACTGGAAGCAGAAGAGCTACCTTTGCCCTATCTGTGACCTCTCCTTTGGGGAGAAAGAGGGCCTTATGGATCACTGGAGGGGCTATAAAGGCAAGGACCTGTGCCAGAGCAGCCACCATAAATGCCGGGTGATCCTGGGCCAGTGGCTTGGCTTCTCTCATGATGTCCCCACTATGGCTGGGGAGGAATGGAAGCATGGAGGTGATCAATCTCCCCCCAGGATCCATACCCCCAGGAGAAGAGGCCTAAGAGAGAAGGCCTGCAAAGGAGACAAAACAAAGGAGGCAGTGAGCATCTTGAAACATAAATA
+>ENST00000448800.5
+TGGCCACACTGCAACAGCTGGAGCCAGTTACTGGGCAGGTGTCTGTACTGGTGATGTGTCACACTCGGGAGTTGGCTTTTCAGATCAGCAAGGAATATGAGCGCTTCTCTAAATACATGCCCAATGTCAAGGTTGCTGTTTTTTTTGGTGGTCTGTCTATCAAGAAGGATGAAGAGGTGCTGAAGAAGAACTGCCCGCATATCGTCGTGGGGACTCCAGGCCGTATCCTAGCCCTGGCTCGAAATAAGAGCCTCAACCTCAAACACATTAAACACTTTATTTTGGATGAATGTGATAAGATGCTTGAACAGCTCGACATGCGTCGGGATGTCCAGGAAATTTTTCGCATGACCCCCCACGAGAAGCAGGTCATGATGTTCAGTGCTACCTTGAGCAAAGAGATCCGTCCAGTCTGCCGCAAGTTCATGCAAGATCCAATGGAGATCTTCGTGGATGATGAGACGAAGTTGACGCTGCATGGGTTGCAGCAGTACTACGTGAAACTGAAGGACAACGAGAAGAACCGGAAGCTCTTTGACCTTCTGGATGTCCTTGAGTTCAACCAGGTGGTGATCTTTGTGAAGTCTGTGCAGCGGTGCATTGCCTTGGCCCAGCTACTAGTGGAGCAGAACTTCCCAGCCATTGCCATCCACCGTGGGATGCCCCAGGAGGAGAGGCTTTCTCGGTATCAGCAGTTTAAAGATTTTCAACGACGAATTCTTGTGGCTACCAACCTATTTGGCCGAGGCATGGACATCGAGCGGGTGAACATTGCTTTTAATTATGACATGCCTGAGGATTCTGACACCTACCTGCATCGGGTGGCCAGAGCAGGCCGGTTTGGCACCAAGGGCTTGGCTATCACATTTGTGTCCGATGAGAATGATGCCAAGATCCTCAATGATGTGCAGGATCGCTTTGAGGTCAATATTAGTGAGCTGCCTGATGAGATAGACATCTCCTCCTACATTGAACAGACACGGT
+>ENST00000445122.5
+ATGCCGGGCACCCAGACTCCAGCACCGGCCGAGGACCCCCACTCCGGCTGCAGGGACCCTGTCCCAGCGAGACCGCAGGCATGTCATCCGAAAAGTCAGGAGACTCGCTTCGAGGGCCCACTTcccccgccgccgcccgctgccgccgccccgcccccgccggcgccagccCAGACTGCCCAGGCCCCTGGCTTCGTGGTGCCCACGCACGCGGGGACTGTGGGCACGCTGCCGCTGGGGGGCTACGTAGCGCCCGGATACCCCCTGCAGCTGCAGCCTTGCACTGCTTACGTGCCGGTCTACCCGGTGGGCACGCCATATGCAGGCGGGACCCCGGGGGGAACAGGAGTGACCTCCACTCTCCCCCCGCCGCCCCAGGGCCCAGGGCTGGCCCTACTGGAGCCGAGGCGCCCGCCACACGACTACATGCCCATCGCGGTGCTGACCACCATCTGTTGCTTCTGGCCTACTGGCATCATTGCCATCTTCAAGGCCGTGCAGGTGCGCACGGCCTTGGCCCGCGGAGACATGGTGTCGGCCGAGATCGCTTCACGCGAGGCCCGGAACTTCTCCTTCATCTCCCTGGCCGTGGGCATCGCGGCCATGGTGCTCTGTACCATCCTCACCGTAGTCATCATCATCGCCGCGCAGCACCACGAGAACTACTGGGATCCCTAA
+>ENST00000430777.2
+ATGGATTTGTGGCCAGGGGCATGGAtgctgctgctgctgctcttcctgctgctgctcttcctgctgcCCACCCTGTGGTTCTGCAGCCCCAGTGCCAAGTACTTCTTCAAGATGGCCTTCTACAATGGCTGGATCCTCTTCCTGGCTGTGCTCGCCATCCCTGTGTGTGCCGTGCGAGGACGCAACGTCGAGAACATGAAGATCTTGCGTCTAATGCTGCTCCACATCAAATACCTGTACGGGATCCGAGTGGAGGTGCGAGGGGCTCACCACTTCCCTCCCTCGCAGCCCTATGTTGTTGTCTCCAACCACCAGAGCTCTCTCGATCTGCTTGGGATGATGGAGGTACTGCCAGGCCGCTGTGTGCCCATTGCCAAGCGCGAGCTACTGTGggctggctctgccgggctggcctgctggctggcaggAGTCATCTTCATCGACCGGAAGCGCACGGGGGATGCCATCAGTGTCATGTCTGAGGTCGCCCAGACCCTGCTCACCCAGGACGTGAGGGTCTGGGTGTTTCCTGAGGGAACGAGAAACCACAATGGCTCCATGCTGCCCTTCAAACGTGGCGCCTTCCATCTTGCAGTGCAGGCCCAGGTTCCCATTGTCCCCATAGTCATGTCCTCCTACCAAGACTTCTACTGCAAGAAGGAGCGTCGCTTCACCTCGGGACAATGTCAGGTGCGGGTGCTGCCCCCAGTGCCCACGGAAGGGCTGACACCAGATGACGTCCCAGCTCTGGCTGACAGAGTCCGGCACTCCATGCTCACTGTTTTCCGGGAAATCTCCACTGATGGCCGGGGTGGTGGTGACTATCTGAAGAAGCCTGGGGGCGGTGGGTGA
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/codon_freq_from_bicodon.tabular	Mon Apr 11 20:37:19 2022 +0000
@@ -0,0 +1,5 @@
+#frame	codon_count	aaa	aac	aag	aat	aca	acc	acg	act	aga	agc	agg	agt	ata	atc	atg	att	caa	cac	cag	cat	cca	ccc	ccg	cct	cga	cgc	cgg	cgt	cta	ctc	ctg	ctt	gaa	gac	gag	gat	gca	gcc	gcg	gct	gga	ggc	ggg	ggt	gta	gtc	gtg	gtt	taa	tac	tag	tat	tca	tcc	tcg	tct	tga	tgc	tgg	tgt	tta	ttc	ttg	ttt
+2-counts	855	4	12	14	8	13	23	8	15	28	18	25	12	8	27	31	7	3	11	17	4	23	28	16	14	4	12	2	1	10	16	35	7	4	7	16	4	16	38	6	14	15	15	18	4	4	11	25	4	1	12	3	3	18	15	7	16	16	17	26	10	8	20	19	7
+2-percent	855	0.4678362573099415500088582576	1.4035087719298244834931210789	1.6374269005847954527865795171	0.9356725146198831000177165151	1.5204678362573098571175478355	2.6900584795321638154064203263	0.9356725146198831000177165151	1.7543859649122806043664013487	3.2748538011695909055731590342	2.1052631578947367252396816184	2.9239766081871341185660639894	1.4035087719298244834931210789	0.9356725146198831000177165151	3.1578947368421053099041273526	3.6257309941520468044018343790	0.8187134502923977263932897586	0.3508771929824561208732802697	1.2865497076023393319132992474	1.9883040935672515736598597869	0.4678362573099415500088582576	2.6900584795321638154064203263	3.2748538011695909055731590342	1.8713450292397662000354330303	1.6374269005847954527865795171	0.4678362573099415500088582576	1.4035087719298244834931210789	0.2339181286549707750044291288	0.1169590643274853875022145644	1.1695906432748537362442675658	1.8713450292397662000354330303	4.0935672514619882988995414053	0.8187134502923977263932897586	0.4678362573099415500088582576	0.8187134502923977263932897586	1.8713450292397662000354330303	0.4678362573099415500088582576	1.8713450292397662000354330303	4.4444444444444446418174266000	0.7017543859649122417465605395	1.6374269005847954527865795171	1.7543859649122806043664013487	1.7543859649122806043664013487	2.1052631578947367252396816184	0.4678362573099415500088582576	0.4678362573099415500088582576	1.2865497076023393319132992474	2.9239766081871341185660639894	0.4678362573099415500088582576	0.1169590643274853875022145644	1.4035087719298244834931210789	0.3508771929824561208732802697	0.3508771929824561208732802697	2.1052631578947367252396816184	1.7543859649122806043664013487	0.8187134502923977263932897586	1.8713450292397662000354330303	1.8713450292397662000354330303	1.9883040935672515736598597869	3.0409356725146197142350956710	1.1695906432748537362442675658	0.9356725146198831000177165151	2.3391812865497074724885351316	2.2222222222222223209087133000	0.8187134502923977263932897586
+3-counts	855	3	2	3	4	12	10	10	10	17	12	16	5	2	7	7	3	23	10	19	18	37	23	19	25	7	16	10	4	8	14	19	18	27	10	14	12	23	12	8	19	31	18	11	11	3	7	8	9	11	6	4	9	22	15	17	20	27	36	28	19	1	5	9	10
+3-percent	855	0.3508771929824561208732802697	0.2339181286549707750044291288	0.3508771929824561208732802697	0.4678362573099415500088582576	1.4035087719298244834931210789	1.1695906432748537362442675658	1.1695906432748537362442675658	1.1695906432748537362442675658	1.9883040935672515736598597869	1.4035087719298244834931210789	1.8713450292397662000354330303	0.5847953216374268681221337829	0.2339181286549707750044291288	0.8187134502923977263932897586	0.8187134502923977263932897586	0.3508771929824561208732802697	2.6900584795321638154064203263	1.1695906432748537362442675658	2.2222222222222223209087133000	2.1052631578947367252396816184	4.3274853801169594902376047685	2.6900584795321638154064203263	2.2222222222222223209087133000	2.9239766081871341185660639894	0.8187134502923977263932897586	1.8713450292397662000354330303	1.1695906432748537362442675658	0.4678362573099415500088582576	0.9356725146198831000177165151	1.6374269005847954527865795171	2.2222222222222223209087133000	2.1052631578947367252396816184	3.1578947368421053099041273526	1.1695906432748537362442675658	1.6374269005847954527865795171	1.4035087719298244834931210789	2.6900584795321638154064203263	1.4035087719298244834931210789	0.9356725146198831000177165151	2.2222222222222223209087133000	3.6257309941520468044018343790	2.1052631578947367252396816184	1.2865497076023393319132992474	1.2865497076023393319132992474	0.3508771929824561208732802697	0.8187134502923977263932897586	0.9356725146198831000177165151	1.0526315789473683626198408092	1.2865497076023393319132992474	0.7017543859649122417465605395	0.4678362573099415500088582576	1.0526315789473683626198408092	2.5730994152046786638265984948	1.7543859649122806043664013487	1.9883040935672515736598597869	2.3391812865497074724885351316	3.1578947368421053099041273526	4.2105263157894734504793632368	3.2748538011695909055731590342	2.2222222222222223209087133000	0.1169590643274853875022145644	0.5847953216374268681221337829	1.0526315789473683626198408092	1.1695906432748537362442675658
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/codon_freq_from_bicodon_log.txt	Mon Apr 11 20:37:19 2022 +0000
@@ -0,0 +1,7 @@
+Using 4096 codon pairs
+Reporting 64 codons
+Found a total of 100.000000 percent for 2.
+Found a total of 100.000000 percent for 3.
+Reporting 21 amino acids
+Found a total of 100.000000 percent for 2-aa.
+Found a total of 100.000000 percent for 3-aa.
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/codon_out.tabular	Mon Apr 11 20:37:19 2022 +0000
@@ -0,0 +1,2 @@
+Division	Assembly	Taxid	Species	Organelle	Translation Table	# CDS	# Codons	aaa	aac	aag	aat	aca	acc	acg	act	aga	agc	agg	agt	ata	atc	atg	att	caa	cac	cag	cat	cca	ccc	ccg	cct	cga	cgc	cgg	cgt	cta	ctc	ctg	ctt	gaa	gac	gag	gat	gca	gcc	gcg	gct	gga	ggc	ggg	ggt	gta	gtc	gtg	gtt	taa	tac	tag	tat	tca	tcc	tcg	tct	tga	tgc	tgg	tgt	tta	ttc	ttg	ttt
+custom	hg38	9606	Homo sapiens	genomic	1	4	859	14	13	29	8	5	10	4	9	9	12	13	6	4	17	17	9	12	21	28	33	13	26	7	14	13	14	15	12	12	17	20	25	13	16	26	27	12	33	7	30	9	28	16	12	3	12	21	3	0	9	0	5	5	12	1	15	0	20	9	14	1	11	11	17
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/find_naltorfs_log.txt	Mon Apr 11 20:37:19 2022 +0000
@@ -0,0 +1,7 @@
+{'chr6_GL000250v2_alt': 4672374}
+Excluding 77 unique canonical coding sequences from 77 BED lines.
+cds length is not divisible by 3!!!: 634. chr6_GL000250v2_alt	938190	938841	ENST00000432222.1	0	-	938207	938841	12,12,120	1	651	0
+cds length is not divisible by 3!!!: 271. chr6_GL000250v2_alt	2057211	2060006	ENST00000420604.1	0	-	2057618	2060006	12,12,120	3	437,165,76	0,2313,2719
+cds length is not divisible by 3!!!: 986. chr6_GL000250v2_alt	2862767	2871733	ENST00000448800.5	0	-	2862982	2871733	12,12,120	9	232,148,145,110,132,119,184,93,38	0,560,834,1077,2561,5148,6281,8544,8928
+cds length is not divisible by 3!!!: 580. chr6_GL000250v2_alt	3655068	3704125	ENST00000425722.1	0	-	3655068	3703952	12,12,120	19	21,21,24,21,21,21,21,21,21,39,90,21,21,21,30,33,33,87,186	0,637,1109,8114,9561,12963,13438,14141,16499,17121,26913,32289,32814,43342,43448,45110,45965,47083,48871
+transcripts: 77	unique LNO ORFs: 4
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gencode_canonical.hg38.chr6_GL0002508.bed	Mon Apr 11 20:37:19 2022 +0000
@@ -0,0 +1,77 @@
+chr6_GL000250v2_alt	168585	189574	ENST00000437160.6	0	-	169653	189217	12,12,120	8	1664,27,33,116,23,231,96,777,	0,4234,5806,5971,8695,17011,18891,20212,
+chr6_GL000250v2_alt	260408	270885	ENST00000426120.2	0	-	260624	269578	12,12,120	7	1802,105,127,92,82,269,253,	0,3949,4702,5171,8728,9161,10224,
+chr6_GL000250v2_alt	309837	310865	ENST00000421027.1	0	-	309837	310800	12,12,120	1	1028,	0,
+chr6_GL000250v2_alt	351929	352936	ENST00000420178.3	0	-	351929	352871	12,12,120	1	1007,	0,
+chr6_GL000250v2_alt	377510	378446	ENST00000428081.1	0	+	377510	378446	12,12,120	1	936,	0,
+chr6_GL000250v2_alt	438928	440200	ENST00000440124.4	0	+	439261	440200	12,12,120	1	1272,	0,
+chr6_GL000250v2_alt	572355	573321	ENST00000420495.4	0	+	572355	573321	12,12,120	1	966,	0,
+chr6_GL000250v2_alt	691168	722731	ENST00000435232.5	0	-	692358	693306	12,12,120	5	2229,48,125,124,85,	0,3408,4796,6359,31478,
+chr6_GL000250v2_alt	704969	706618	ENST00000455234.1	0	+	705679	706618	12,12,120	1	1649,	0,
+chr6_GL000250v2_alt	722840	729989	ENST00000453467.5	0	+	727430	728381	12,12,120	4	27,116,51,2830,	0,1273,3224,4319,
+chr6_GL000250v2_alt	752426	753563	ENST00000418003.3	0	-	752426	753563	12,12,120	1	1137,	0,
+chr6_GL000250v2_alt	821306	825621	ENST00000414436.2	0	-	821574	825397	12,12,120	2	739,251,	0,4064,
+chr6_GL000250v2_alt	821306	893756	ENST00000449163.5	0	-	869267	893509	12,12,120	19	739,176,144,129,128,94,108,117,133,151,78,64,243,192,66,102,171,135,553,	0,47959,48912,49278,49987,50809,51316,51521,53020,53648,55343,56970,57662,65507,66158,66510,67711,68296,71897,
+chr6_GL000250v2_alt	853147	854731	ENST00000453513.4	0	+	853637	854576	12,12,120	1	1584,	0,
+chr6_GL000250v2_alt	922689	938078	ENST00000548017.1	0	+	922918	936889	12,12,120	7	317,348,114,21,21,21,1203,	0,2336,9166,10657,10918,13715,14186,
+chr6_GL000250v2_alt	938190	938841	ENST00000432222.1	0	-	938207	938841	12,12,120	1	651,	0,
+chr6_GL000250v2_alt	1093432	1096751	ENST00000615098.4	0	+	1093456	1095994	12,12,120	7	97,270,276,276,117,33,372,	0,226,722,1597,1995,2557,2947,
+chr6_GL000250v2_alt	1147347	1267669	ENST00000640829.1	0	+	1147490	1266858	12,12,120	11	216,16,14,240,276,276,33,84,93,35,281,	0,340,39005,53186,53667,54522,68203,118979,119506,119955,120041,
+chr6_GL000250v2_alt	1319351	1323001	ENST00000443494.6	0	+	1319622	1322789	12,12,120	4	416,101,110,237,	0,663,970,3413,
+chr6_GL000250v2_alt	1324800	1328425	ENST00000441553.5	0	+	1326768	1327398	12,12,120	3	301,109,1230,	0,1881,2395,
+chr6_GL000250v2_alt	1328357	1333979	ENST00000450015.2	0	-	1329202	1333881	12,12,120	4	1426,92,23,665,	0,2891,3190,4957,
+chr6_GL000250v2_alt	1368538	1371196	ENST00000422484.1	0	-	1368538	1370895	12,12,120	4	231,96,500,43,	0,1199,1940,2615,
+chr6_GL000250v2_alt	1394223	1406831	ENST00000433713.5	0	+	1395132	1405908	12,12,120	6	62,649,96,225,23,1011,	0,605,9866,10857,11392,11597,
+chr6_GL000250v2_alt	1410040	1419029	ENST00000449208.6	0	-	1412064	1418953	12,12,120	7	2542,33,116,23,231,96,505,	0,3782,4994,5424,6453,7204,8484,
+chr6_GL000250v2_alt	1421285	1430769	ENST00000552062.2	0	+	1421971	1430429	12,12,120	8	860,96,231,9,14,116,33,858,	0,3970,5094,6035,6633,7295,7770,8626,
+chr6_GL000250v2_alt	1442505	1471482	ENST00000425523.5	0	-	1443926	1457164	12,12,120	9	2104,33,116,23,231,96,488,104,123,	0,4719,4970,5565,12071,13984,14221,16590,28854,
+chr6_GL000250v2_alt	1656333	1673225	ENST00000458607.5	0	+	1658808	1671755	12,12,120	8	152,153,460,96,231,23,116,2018,	0,2046,2468,3938,8907,13070,13667,14874,
+chr6_GL000250v2_alt	1658801	1676354	ENST00000550581.3	0	+	1658808	1676306	12,12,120	10	460,96,231,23,116,185,101,83,126,146,	0,1470,6439,10602,11199,12406,15992,16185,17126,17407,
+chr6_GL000250v2_alt	1870880	1883062	ENST00000383450.3	0	-	1875575	1883062	12,12,120	7	4937,141,163,179,195,96,208,	0,5319,5735,5975,11091,11708,11974,
+chr6_GL000250v2_alt	1988977	2002543	ENST00000450902.6	0	-	1988977	2002347	12,12,120	12	153,99,211,116,111,192,204,255,57,163,239,403,	0,264,560,3155,3439,5329,5599,6007,10938,11318,11564,13163,
+chr6_GL000250v2_alt	2005895	2017402	ENST00000438815.2	0	-	2006775	2015525	12,12,120	3	900,211,3488,	0,2790,8019,
+chr6_GL000250v2_alt	2017553	2020927	ENST00000427944.5	0	-	2018167	2020481	12,12,120	5	896,177,197,440,45,	0,1229,2000,2795,3329,
+chr6_GL000250v2_alt	2029311	2047393	ENST00000427406.6	0	-	2029969	2044679	12,12,120	15	826,111,126,183,120,2478,71,792,93,60,1481,70,381,139,645,	0,2746,2945,3297,3611,3814,7576,7758,11604,11859,12066,13840,13995,15232,17437,
+chr6_GL000250v2_alt	2049703	2054929	ENST00000421473.6	0	+	2050009	2053900	12,12,120	4	363,109,111,2087,	0,2336,2717,3139,
+chr6_GL000250v2_alt	2057211	2060006	ENST00000420604.1	0	-	2057618	2060006	12,12,120	3	437,165,76,	0,2313,2719,
+chr6_GL000250v2_alt	2217891	2218933	ENST00000434428.5	0	+	2218232	2218933	12,12,120	3	426,103,229,	0,519,813,
+chr6_GL000250v2_alt	2313217	2319398	ENST00000430305.2	0	+	2313458	2317689	12,12,120	3	302,1445,1904,	0,2514,4277,
+chr6_GL000250v2_alt	2827448	2843673	ENST00000619506.1	0	+	2838192	2842459	12,12,120	6	115,255,288,279,132,1342,	0,10718,11244,12123,12501,14883,
+chr6_GL000250v2_alt	2861265	2862781	ENST00000424816.2	0	+	2861563	2862484	12,12,120	2	469,486,	0,1030,
+chr6_GL000250v2_alt	2862767	2871733	ENST00000448800.5	0	-	2862982	2871733	12,12,120	9	232,148,145,110,132,119,184,93,38,	0,560,834,1077,2561,5148,6281,8544,8928,
+chr6_GL000250v2_alt	2909112	2910915	ENST00000445232.2	0	+	2909112	2910116	12,12,120	3	46,48,1221,	0,233,582,
+chr6_GL000250v2_alt	2913133	2915004	ENST00000457552.2	0	-	2913287	2914996	12,12,120	4	609,72,46,170,	0,1004,1259,1701,
+chr6_GL000250v2_alt	2918702	2921488	ENST00000433676.6	0	+	2919878	2921255	12,12,120	4	192,119,23,392,	0,1076,1820,2394,
+chr6_GL000250v2_alt	2921473	2925564	ENST00000432392.6	0	-	2921772	2925300	12,12,120	4	337,108,345,307,	0,631,887,3784,
+chr6_GL000250v2_alt	3089203	3095288	ENST00000430216.5	0	+	3090740	3095143	12,12,120	14	325,872,73,110,81,88,190,127,150,75,144,138,74,257,	0,830,1956,2174,2505,2833,3194,3498,4098,4596,4880,5226,5520,5828,
+chr6_GL000250v2_alt	3095410	3097463	ENST00000436320.5	0	+	3095666	3097143	12,12,120	4	370,141,96,413,	0,616,1265,1640,
+chr6_GL000250v2_alt	3098201	3109905	ENST00000452329.2	0	-	3098205	3109390	12,12,120	17	181,175,140,302,93,153,133,186,117,113,170,196,111,97,279,249,186,	0,293,655,873,1568,1772,2032,3427,4084,4410,7363,7651,8925,9742,10373,10955,11518,
+chr6_GL000250v2_alt	3130006	3139596	ENST00000432122.2	0	-	3130367	3139369	12,12,120	5	487,60,31,68,230,	0,594,1081,8680,9360,
+chr6_GL000250v2_alt	3142240	3147687	ENST00000426095.2	0	-	3142668	3144594	12,12,120	2	2367,177,	0,5270,
+chr6_GL000250v2_alt	3148164	3150568	ENST00000422919.1	0	+	3148378	3150304	12,12,120	2	289,1620,	0,784,
+chr6_GL000250v2_alt	3160359	3162874	ENST00000450744.1	0	+	3160575	3162501	12,12,120	1	2515,	0,
+chr6_GL000250v2_alt	3167532	3172376	ENST00000430690.5	0	+	3169944	3172278	12,12,120	5	283,41,219,200,219,	0,492,1382,2319,4625,
+chr6_GL000250v2_alt	3191667	3195522	ENST00000423382.2	0	-	3192334	3195392	12,12,120	6	894,223,183,263,193,289,	0,990,1387,2136,2947,3566,
+chr6_GL000250v2_alt	3195810	3211661	ENST00000550401.2	0	-	3196242	3211595	12,12,120	20	554,85,95,71,74,104,95,254,103,93,100,236,84,88,61,100,79,74,49,106,	0,1457,1621,1815,2120,2303,2495,2678,5960,6350,7406,7615,8117,8277,11264,11733,12656,12860,13838,15745,
+chr6_GL000250v2_alt	3212373	3230306	ENST00000421926.6	0	-	3212698	3230299	12,12,120	28	506,176,79,87,116,78,145,168,155,105,102,123,107,83,183,236,144,149,102,115,135,156,41,85,254,219,67,49,	0,914,1255,2940,3135,3603,4047,4633,4886,5153,6822,7016,7236,7818,8020,8282,8604,8840,9210,9469,9709,12652,12939,13071,16511,16854,17171,17884,
+chr6_GL000250v2_alt	3406267	3418718	ENST00000433037.1	0	-	3406267	3418718	12,12,120	6	306,333,306,291,297,369,	0,5366,7700,8368,10745,12082,
+chr6_GL000250v2_alt	3480956	3485682	ENST00000445122.5	0	-	3481819	3484701	12,12,120	6	1040,186,216,91,81,112,	0,1178,2009,3450,3737,4614,
+chr6_GL000250v2_alt	3497183	3500883	ENST00000414111.6	0	+	3498767	3500558	12,12,120	9	75,129,123,110,96,171,80,154,372,	0,1556,1916,2119,2328,2505,2768,2921,3328,
+chr6_GL000250v2_alt	3500813	3510698	ENST00000430777.2	0	-	3501877	3504098	12,12,120	7	1237,73,96,176,134,209,96,	0,1754,1953,2213,2725,3085,9789,
+chr6_GL000250v2_alt	3510955	3513395	ENST00000449794.2	0	+	3511113	3512928	12,12,120	6	298,19,113,55,118,565,	0,1187,1297,1523,1655,1875,
+chr6_GL000250v2_alt	3513569	3516924	ENST00000549839.5	0	-	3513744	3516824	12,12,120	5	272,83,123,107,152,	0,383,2660,2913,3203,
+chr6_GL000250v2_alt	3517334	3522785	ENST00000453487.2	0	-	3518980	3522514	12,12,120	9	1739,87,89,154,136,191,248,74,492,	0,1868,2077,2506,2911,3230,3521,3987,4959,
+chr6_GL000250v2_alt	3523364	3528122	ENST00000457070.1	0	-	3523964	3525112	12,12,120	8	738,200,103,59,84,81,93,98,	0,943,1382,1706,2275,3544,3971,4660,
+chr6_GL000250v2_alt	3527441	3536999	ENST00000425600.1	0	-	3528035	3536999	12,12,120	12	1308,98,148,296,139,82,220,176,384,524,113,253,	0,1481,2082,2456,3579,3807,4084,6000,6286,7245,8938,9305,
+chr6_GL000250v2_alt	3655068	3704125	ENST00000425722.1	0	-	3655068	3703952	12,12,120	19	21,21,24,21,21,21,21,21,21,39,90,21,21,21,30,33,33,87,186,	0,637,1109,8114,9561,12963,13438,14141,16499,17121,26913,32289,32814,43342,43448,45110,45965,47083,48871,
+chr6_GL000250v2_alt	3726193	3739359	ENST00000445928.5	0	-	3726199	3739352	12,12,120	7	95,282,348,21,282,348,86,	0,781,2076,7820,8970,10974,13080,
+chr6_GL000250v2_alt	3823888	3837634	ENST00000426847.2	0	-	3824827	3837535	12,12,120	6	953,24,111,282,270,199,	0,1752,2249,3043,5625,13547,
+chr6_GL000250v2_alt	4047519	4053351	ENST00000449560.5	0	+	4047581	4052533	12,12,120	4	144,249,282,973,	0,3778,4410,4859,
+chr6_GL000250v2_alt	4062236	4069674	ENST00000419685.6	0	-	4062591	4069610	12,12,120	6	369,24,111,282,267,161,	0,1184,1676,2753,5563,7277,
+chr6_GL000250v2_alt	4117786	4122072	ENST00000426644.6	0	-	4118239	4121975	12,12,120	6	489,32,111,282,270,188,	0,677,960,1557,2281,4098,
+chr6_GL000250v2_alt	4126846	4143590	ENST00000439425.6	0	-	4127302	4143099	12,12,120	12	486,137,160,174,189,129,198,206,131,115,497,75,	0,7419,7949,8286,8637,10352,10646,13173,13662,15556,15760,16669,
+chr6_GL000250v2_alt	4145581	4149568	ENST00000436627.2	0	-	4145823	4149278	12,12,120	6	331,205,130,112,148,425,	0,814,1417,1955,2225,3562,
+chr6_GL000250v2_alt	4150073	4158843	ENST00000418205.2	0	-	4150443	4158681	12,12,120	11	577,137,163,174,189,129,198,206,131,115,940,	0,1859,2304,2710,3443,3781,5109,5733,6900,7179,7830,
+chr6_GL000250v2_alt	4159070	4184429	ENST00000425855.2	0	+	4159094	4184317	12,12,120	6	84,68,130,142,93,156,	0,1932,3799,4158,22841,25203,
+chr6_GL000250v2_alt	4239473	4245915	ENST00000395312.7	0	-	4239815	4245652	12,12,120	6	359,36,117,285,282,318,	0,713,907,2543,4055,6124,
+chr6_GL000250v2_alt	4369248	4385378	ENST00000443117.5	0	-	4373329	4378232	12,12,120	6	779,167,282,246,199,31,	0,4069,4450,5072,8884,16099,
+chr6_GL000250v2_alt	4380587	4391853	ENST00000411749.6	0	+	4380703	4390890	12,12,120	6	216,264,282,111,24,663,	0,4752,9014,9843,10283,10603,
Binary file test-data/hg38.chr6_GL000250v2_alt.2bit.gz has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/naltorfs_fasta_out.fasta	Mon Apr 11 20:37:19 2022 +0000
@@ -0,0 +1,8 @@
+>ENST00000432222.1|chromosome:hg38:chr6_GL000250v2_alt:938210:938801:-
+ATGGCCCAGAACCAGGCATCTGTACTTAAGAACCAAGCACCTGTGACCAGGACCCAGGCACCCATCACTGGAACCCTCTGTCAGGATGCCAGATCCAACTCTCATCCAGTGAAGCCCTCAAGACTCAATGTCTTCTGTTGCCCCCATTGTTCTTTGACTTTTAGCAAGAAATCCTATCTCTCCAGACACCAGAAGGCCCACCTCACAGAGCCGCCCAACTACTGCTTCCATTGCAGCAAGTCTTTCAGCTCATTTTCCAGGCTGGTCAGACACCAGCAGACCCACTGGAAGCAGAAGAGCTACCTTTGCCCTATCTGTGACCTCTCCTTTGGGGAGAAAGAGGGCCTTATGGATCACTGGAGGGGCTATAAAGGCAAGGACCTGTGCCAGAGCAGCCACCATAAATGCCGGGTGATCCTGGGCCAGTGGCTTGGCTTCTCTCATGATGTCCCCACTATGGCTGGGGAGGAATGGAAGCATGGAGGTGATCAATCTCCCCCCAGGATCCATACCCCCAGGAGAAGAGGCCTAAGAGAGAAGGCCTGCAAAGGAGACAAAACAAAGGAGGCAGTGAGCATCTTGAAACATAAA
+>ENST00000448800.5|chromosome:hg38:chr6_GL000250v2_alt:2862985:2871389:-
+ATGTGTCACACTCGGGAGTTGGCTTTTCAGATCAGCAAGGAATATGAGCGCTTCTCTAAATACATGCCCAATGTCAAGGTTGCTGTTTTTTTTGGTGGTCTGTCTATCAAGAAGGATGAAGAGGTGCTGAAGAAGAACTGCCCGCATATCGTCGTGGGGACTCCAGGCCGTATCCTAGCCCTGGCTCGAAATAAGAGCCTCAACCTCAAACACATTAAACACTTTATTTTGGATGAATGTGATAAGATGCTTGAACAGCTCGACATGCGTCGGGATGTCCAGGAAATTTTTCGCATGACCCCCCACGAGAAGCAGGTCATGATGTTCAGTGCTACCTTGAGCAAAGAGATCCGTCCAGTCTGCCGCAAGTTCATGCAAGATCCAATGGAGATCTTCGTGGATGATGAGACGAAGTTGACGCTGCATGGGTTGCAGCAGTACTACGTGAAACTGAAGGACAACGAGAAGAACCGGAAGCTCTTTGACCTTCTGGATGTCCTTGAGTTCAACCAGGTGGTGATCTTTGTGAAGTCTGTGCAGCGGTGCATTGCCTTGGCCCAGCTACTAGTGGAGCAGAACTTCCCAGCCATTGCCATCCACCGTGGGATGCCCCAGGAGGAGAGGCTTTCTCGGTATCAGCAGTTTAAAGATTTTCAACGACGAATTCTTGTGGCTACCAACCTATTTGGCCGAGGCATGGACATCGAGCGGGTGAACATTGCTTTTAATTATGACATGCCTGAGGATTCTGACACCTACCTGCATCGGGTGGCCAGAGCAGGCCGGTTTGGCACCAAGGGCTTGGCTATCACATTTGTGTCCGATGAGAATGATGCCAAGATCCTCAATGATGTGCAGGATCGCTTTGAGGTCAATATTAGTGAGCTGCCTGATGAGATAGACATCTCCTCCTACATTGAACAGACACGG
+>ENST00000445122.5|chromosome:hg38:chr6_GL000250v2_alt:3481820:3484425:-
+ATGTCATCCGAAAAGTCAGGAGACTCGCTTCGAGGGCCCACTTcccccgccgccgcccgctgccgccgccccgcccccgccggcgccagccCAGACTGCCCAGGCCCCTGGCTTCGTGGTGCCCACGCACGCGGGGACTGTGGGCACGCTGCCGCTGGGGGGCTACGTAGCGCCCGGATACCCCCTGCAGCTGCAGCCTTGCACTGCTTACGTGCCGGTCTACCCGGTGGGCACGCCATATGCAGGCGGGACCCCGGGGGGAACAGGAGTGACCTCCACTCTCCCCCCGCCGCCCCAGGGCCCAGGGCTGGCCCTACTGGAGCCGAGGCGCCCGCCACACGACTACATGCCCATCGCGGTGCTGACCACCATCTGTTGCTTCTGGCCTACTGGCATCATTGCCATCTTCAAGGCCGTGCAGGTGCGCACGGCCTTGGCCCGCGGAGACATGGTGTCGGCCGAGATCGCTTCACGCGAGGCCCGGAACTTCTCCTTCATCTCCCTGGCCGTGGGCATCGCGGCCATGGTGCTCTGTACCATCCTCACCGTAGTCATCATCATCGCCGCGCAGCACCACGAGAACTACTGGGATCCCTA
+>ENST00000430777.2|chromosome:hg38:chr6_GL000250v2_alt:3503057:3504078:-
+ATGGAtgctgctgctgctgctcttcctgctgctgctcttcctgctgcCCACCCTGTGGTTCTGCAGCCCCAGTGCCAAGTACTTCTTCAAGATGGCCTTCTACAATGGCTGGATCCTCTTCCTGGCTGTGCTCGCCATCCCTGTGTGTGCCGTGCGAGGACGCAACGTCGAGAACATGAAGATCTTGCGTCTAATGCTGCTCCACATCAAATACCTGTACGGGATCCGAGTGGAGGTGCGAGGGGCTCACCACTTCCCTCCCTCGCAGCCCTATGTTGTTGTCTCCAACCACCAGAGCTCTCTCGATCTGCTTGGGATGATGGAGGTACTGCCAGGCCGCTGTGTGCCCATTGCCAAGCGCGAGCTACTGTGggctggctctgccgggctggcctgctggctggcaggAGTCATCTTCATCGACCGGAAGCGCACGGGGGATGCCATCAGTGTCATGTC
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/peptide_fasta_out.fasta	Mon Apr 11 20:37:19 2022 +0000
@@ -0,0 +1,8 @@
+>ENST00000432222.1|chromosome:hg38:chr6_GL000250v2_alt:938210:938801:-
+MAQNQASVLKNQAPVTRTQAPITGTLCQDARSNSHPVKPSRLNVFCCPHCSLTFSKKSYLSRHQKAHLTEPPNYCFHCSKSFSSFSRLVRHQQTHWKQKSYLCPICDLSFGEKEGLMDHWRGYKGKDLCQSSHHKCRVILGQWLGFSHDVPTMAGEEWKHGGDQSPPRIHTPRRRGLREKACKGDKTKEAVSILKHK
+>ENST00000448800.5|chromosome:hg38:chr6_GL000250v2_alt:2862985:2871389:-
+MCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDEIDISSYIEQTR
+>ENST00000445122.5|chromosome:hg38:chr6_GL000250v2_alt:3481820:3484425:-
+MSSEKSGDSLRGPTSPAAARCRRPAPAGASPDCPGPWLRGAHARGDCGHAAAGGLRSARIPPAAAALHCLRAGLPGGHAICRRDPGGNRSDLHSPPAAPGPRAGPTGAEAPATRLHAHRGADHHLLLLAYWHHCHLQGRAGAHGLGPRRHGVGRDRFTRGPELLLHLPGRGHRGHGALYHPHRSHHHRRAAPRELLGSL
+>ENST00000430777.2|chromosome:hg38:chr6_GL000250v2_alt:3503057:3504078:-
+MDAAAAALPAAALPAAHPVVLQPQCQVLLQDGLLQWLDPLPGCARHPCVCRARTQRREHEDLASNAAPHQIPVRDPSGGARGSPLPSLAALCCCLQPPELSRSAWDDGGTARPLCAHCQARATVGWLCRAGLLAGRSHLHRPEAHGGCHQCHV
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/twobit.loc	Mon Apr 11 20:37:19 2022 +0000
@@ -0,0 +1,26 @@
+#This is a sample file distributed with Galaxy that is used by some
+#tools.  The twobit.loc file has this format (white space characters 
+#are TAB characters):
+#
+#<Build>    <FullPathToFile>
+#
+#So, for example, if you had droPer1 twobit files stored in 
+#/depot/data2/galaxy/droPer1/, then the twobit.loc entry 
+#would look like this:
+#
+#droPer1    /depot/data2/galaxy/droPer1/droPer1.2bit
+#
+#and your /depot/data2/galaxy/droPer1/ directory would 
+#contain all of your twobit files (e.g.):
+#
+#-rw-rw-r--   1 nate   galaxy 48972650 2007-05-04 11:27 droPer1.2bit
+#...etc...
+#
+#Your twobit.loc file should include an entry per line for each twobit 
+#file you have stored.  For example:
+#
+#droPer1    /depot/data2/galaxy/droPer1/droPer1.2bit
+#apiMel2    /depot/data2/galaxy/apiMel2/apiMel2.2bit
+#droAna1    /depot/data2/galaxy/droAna1/droAna1.2bit
+#droAna2    /depot/data2/galaxy/droAna2/droAna2.2bit
+#...etc...
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/all_fasta.loc.sample	Mon Apr 11 20:37:19 2022 +0000
@@ -0,0 +1,18 @@
+#This file lists the locations and dbkeys of all the fasta files
+#under the "genome" directory (a directory that contains a directory
+#for each build). The script extract_fasta.py will generate the file
+#all_fasta.loc. This file has the format (white space characters are
+#TAB characters):
+#
+#<unique_build_id>	<dbkey>	<display_name>	<file_path>
+#
+#So, all_fasta.loc could look something like this:
+#
+#apiMel3	apiMel3	Honeybee (Apis mellifera): apiMel3	/path/to/genome/apiMel3/apiMel3.fa
+#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/path/to/genome/hg19/hg19canon.fa
+#hg19full	hg19	Human (Homo sapiens): hg19 Full	/path/to/genome/hg19/hg19full.fa
+#
+#Your all_fasta.loc file should contain an entry for each individual
+#fasta file. So there will be multiple fasta files for each build,
+#such as with hg19 above.
+#
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/twobit.loc.sample	Mon Apr 11 20:37:19 2022 +0000
@@ -0,0 +1,26 @@
+#This is a sample file distributed with Galaxy that is used by some
+#tools.  The twobit.loc file has this format (white space characters 
+#are TAB characters):
+#
+#<Build>    <FullPathToFile>
+#
+#So, for example, if you had droPer1 twobit files stored in 
+#/depot/data2/galaxy/droPer1/, then the twobit.loc entry 
+#would look like this:
+#
+#droPer1    /depot/data2/galaxy/droPer1/droPer1.2bit
+#
+#and your /depot/data2/galaxy/droPer1/ directory would 
+#contain all of your twobit files (e.g.):
+#
+#-rw-rw-r--   1 nate   galaxy 48972650 2007-05-04 11:27 droPer1.2bit
+#...etc...
+#
+#Your twobit.loc file should include an entry per line for each twobit 
+#file you have stored.  For example:
+#
+#droPer1    /depot/data2/galaxy/droPer1/droPer1.2bit
+#apiMel2    /depot/data2/galaxy/apiMel2/apiMel2.2bit
+#droAna1    /depot/data2/galaxy/droAna1/droAna1.2bit
+#droAna2    /depot/data2/galaxy/droAna2/droAna2.2bit
+#...etc...
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Mon Apr 11 20:37:19 2022 +0000
@@ -0,0 +1,13 @@
+<?xml version="1.0"?>
+<tables>
+    <!-- Locations of reference fasta files -->
+    <table name="all_fasta" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/all_fasta.loc" />
+    </table>
+    <!-- Locations of indexes in the 2bit format -->
+    <table name="twobit" comment_char="#" allow_duplicate_entries="False">
+        <columns>value, path</columns>
+        <file path="tool-data/twobit.loc" />
+    </table>
+</tables>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test	Mon Apr 11 20:37:19 2022 +0000
@@ -0,0 +1,13 @@
+<?xml version="1.0"?>
+<tables>
+    <!-- Locations of reference fasta files -->
+    <table name="all_fasta" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="${__HERE__}/test-data/all_fasta.loc" />
+    </table>
+    <!-- Locations of indexes in the 2bit format -->
+    <table name="twobit" comment_char="#" allow_duplicate_entries="False">
+        <columns>value, path</columns>
+        <file path="${__HERE__}/test-data/twobit.loc" />
+    </table>
+</tables>