# HG changeset patch
# User iuc
# Date 1652352345 0
# Node ID f172b1f77d6c9b74653d2a13d69dc65a8c5ec824

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c

diff -r 000000000000 -r f172b1f77d6c parse_mito_blast.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/parse_mito_blast.xml	Thu May 12 10:45:45 2022 +0000
@@ -0,0 +1,50 @@
+ <tool id="parse_mito_blast" name="Parse mitochondrial blast" version="@TOOL_VERSION@" profile="21.05">
+    <description>overlap-conscious coverage calculation between scaffold-accession number pairs from blast output</description>
+    <macros>
+        <token name="@TOOL_VERSION@">1.0.1</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">parse_mito_blast</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+parse_mito_blast.py
+    --blastout '$blastout' 
+]]>
+    </command>
+    <inputs>
+        <param argument="blastout" type="data" format="tabular" label="Tabular file generated by mito-blast"/>
+    </inputs>
+    <outputs>
+        <data name="cov_report" format="tabular" from_work_dir="cov_report.tsv" label="${tool.name} on ${on_string}" />
+        <data name="mito_scaff_names" format="txt" from_work_dir="mito_scaff_names.txt" label="contaminant scaffolds on ${on_string}" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="blastout" value="test_input.tsv" />
+            <output name="cov_report" file="test_cov_report.tsv" ftype="tabular" /> 
+            <output name="mito_scaff_names" file="test_mito_scaff_names.txt" ftype="txt" />
+        </test>
+    </tests>
+    <help><![CDATA[
+	
+	This tool is intended for use on the tabular (format 6) output generated by blastn. Depending on filtering choices, blast will output \
+	all the alignments it generates. Often there are multiple overlapping alignments for a unique query sequence-accession number pair. This tool \
+	collects all alignments between a given pair and calculates the total coverage between the query and accession number, taking into /
+	account overlapping alignments. Therefore a user can figure out how much of their query sequence actually identifies with a subject /
+	sequence (acc #). This tool was designed for use in the VGP decontamination pipeline - in particular for deciding whether a scaffold /
+	(sequence) is of mitochondrial origin. Parse_mito_blast generates a synthesized, tabular report of coverage for scaffolds with >95% /
+	identity to a mitochondrial subject sequence. To use, pass a format 6 blast output (--blastout) and the desired name of the report. 
+
+	NOTE: This tool is currently designed for use with the blast headers 'qseqid','sseqid','qlen','length','qcovhsp','eval','qstart','qend','qcovs' /
+	and will be sensitive to this order. 
+    ]]>
+    </help>
+    <citations>
+	    <citation type="bibtex">
+           @misc{Danecek_et_al,
+           Author={Danecek, P., Schiffels, S., Durbin, R.},
+           title={Multiallelic calling model in bcftools (-m)},
+           url = {http://samtools.github.io/bcftools/call-m.pdf},}
+        </citation>
+    </citations>
+</tool>
diff -r 000000000000 -r f172b1f77d6c test-data/test_cov_report.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_cov_report.tsv	Thu May 12 10:45:45 2022 +0000
@@ -0,0 +1,64 @@
+	Scaffold	Acc_number	Scaffold_len	Scaffold_align_cov	Perc_align_cov
+0	SCAFFOLD_266	NC_007897.1	33195	33191	99.98794999246876
+1	SCAFFOLD_266	NC_053065.1	33195	33004	99.42461214038258
+32	SCAFFOLD_266	NC_053079.1	33195	32973	99.33122458201537
+35	SCAFFOLD_266	NC_053073.1	33195	32968	99.3161620726013
+3	SCAFFOLD_266	NC_018827.1	33195	32890	99.08118692574183
+11	SCAFFOLD_266	NC_018794.1	33195	32890	99.08118692574183
+6	SCAFFOLD_266	NC_018812.1	33195	32889	99.07817442385901
+13	SCAFFOLD_266	NC_018796.1	33195	32889	99.07817442385901
+8	SCAFFOLD_266	NC_018807.1	33195	32887	99.0721494200934
+27	SCAFFOLD_266	NC_018810.1	33195	32886	99.06913691821057
+4	SCAFFOLD_266	NC_018806.1	33195	32884	99.06311191444495
+22	SCAFFOLD_266	NC_015198.1	33195	32884	99.06311191444495
+20	SCAFFOLD_266	NC_018798.1	33195	32881	99.05407440879651
+2	SCAFFOLD_266	NC_053082.1	33195	32880	99.0510619069137
+25	SCAFFOLD_266	NC_018802.1	33195	32880	99.0510619069137
+24	SCAFFOLD_266	NC_018808.1	33195	32878	99.04503690314806
+17	SCAFFOLD_266	NC_018801.1	33195	32878	99.04503690314806
+12	SCAFFOLD_266	NC_018803.1	33195	32874	99.03298689561682
+31	SCAFFOLD_266	NC_000880.1	33195	32870	99.02093688808556
+40	SCAFFOLD_266	NC_053066.1	33195	32860	98.99081186925743
+5	SCAFFOLD_266	NC_053083.1	33195	32855	98.97574935984335
+10	SCAFFOLD_266	NC_053084.1	33195	32820	98.87031179394488
+23	SCAFFOLD_266	NC_018797.1	33195	32818	98.86428679017925
+19	SCAFFOLD_266	NC_018813.1	33195	32817	98.86127428829643
+26	SCAFFOLD_266	NC_018795.1	33195	32817	98.86127428829643
+18	SCAFFOLD_266	NC_018809.1	33195	32817	98.86127428829643
+9	SCAFFOLD_266	NC_018799.1	33195	32817	98.86127428829643
+14	SCAFFOLD_266	NC_018811.1	33195	32817	98.86127428829643
+21	SCAFFOLD_266	NC_018805.1	33195	32817	98.86127428829643
+15	SCAFFOLD_266	NC_018804.1	33195	32817	98.86127428829643
+29	SCAFFOLD_266	NC_015234.1	33195	32814	98.85223678264798
+7	SCAFFOLD_266	NC_053110.1	33195	32800	98.8100617562886
+39	SCAFFOLD_266	NC_053645.1	33195	32743	98.63834914896822
+42	SCAFFOLD_266	NC_057294.1	33195	32727	98.5901491188432
+37	SCAFFOLD_266	NC_057247.1	33195	32688	98.47266154541346
+28	SCAFFOLD_266	NC_052840.1	33195	32668	98.41241150775718
+34	SCAFFOLD_266	NC_053068.1	33195	32654	98.3702364813978
+47	SCAFFOLD_266	NC_015613.1	33195	32638	98.3220364512728
+43	SCAFFOLD_266	NC_014455.1	33195	32638	98.3220364512728
+59	SCAFFOLD_266	NC_015195.1	33195	32637	98.31902394938997
+55	SCAFFOLD_266	NC_057295.1	33195	32630	98.29793643621028
+38	SCAFFOLD_266	NC_053109.1	33195	32626	98.28588642867902
+46	SCAFFOLD_266	NC_015237.1	33195	32606	98.22563639102275
+60	SCAFFOLD_266	NC_053050.1	33195	32606	98.22563639102275
+41	SCAFFOLD_266	NC_015898.1	33195	32606	98.22563639102275
+16	SCAFFOLD_266	NC_018800.1	33195	32606	98.22563639102275
+62	SCAFFOLD_266	NC_053077.1	33195	32605	98.22262388913992
+50	SCAFFOLD_266	NC_053917.1	33195	32580	98.14731134206959
+51	SCAFFOLD_266	NC_015232.1	33195	32578	98.14128633830396
+54	SCAFFOLD_266	NC_015802.1	33195	32570	98.11718632324146
+30	SCAFFOLD_266	NC_021408.1	33195	32568	98.11116131947583
+49	SCAFFOLD_266	NC_015074.1	33195	32560	98.08706130441331
+52	SCAFFOLD_266	NC_054298.1	33195	32558	98.08103630064768
+44	SCAFFOLD_266	NC_053053.1	33195	32530	97.9966862479289
+58	SCAFFOLD_266	NC_052843.1	33195	32528	97.99066124416328
+48	SCAFFOLD_266	NC_053059.1	33195	32522	97.9725862328664
+53	SCAFFOLD_266	NC_014341.1	33195	32522	97.9725862328664
+61	SCAFFOLD_266	NC_057250.1	33195	32522	97.9725862328664
+45	SCAFFOLD_266	NC_020423.1	33195	32521	97.96957373098358
+33	SCAFFOLD_266	NC_015233.1	33195	32486	97.8641361650851
+56	SCAFFOLD_266	NC_053061.1	33195	32476	97.83401114625697
+57	SCAFFOLD_266	NC_052841.1	33195	31845	95.93312245820154
+36	SCAFFOLD_266	NC_054361.1	33195	31741	95.61982226238891
diff -r 000000000000 -r f172b1f77d6c test-data/test_input.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_input.tsv	Thu May 12 10:45:45 2022 +0000
@@ -0,0 +1,200 @@
+SCAFFOLD_266	NC_007897.1	16856	3436	20290	0.0	33195	99	51
+SCAFFOLD_266	NC_007897.1	12905	20291	33195	0.0	33195	99	39
+SCAFFOLD_266	NC_007897.1	3435	2	3435	0.0	33195	99	10
+SCAFFOLD_266	NC_053065.1	16821	3530	20290	0.0	33195	99	50
+SCAFFOLD_266	NC_053065.1	12859	20385	33195	0.0	33195	99	39
+SCAFFOLD_266	NC_053065.1	3446	1	3435	0.0	33195	99	10
+SCAFFOLD_266	NC_053082.1	16784	3590	20290	0.0	33195	99	50
+SCAFFOLD_266	NC_053082.1	12805	20445	33195	0.0	33195	99	38
+SCAFFOLD_266	NC_053082.1	3456	5	3435	0.0	33195	99	10
+SCAFFOLD_266	NC_018827.1	16751	3587	20290	0.0	33195	99	50
+SCAFFOLD_266	NC_018827.1	12786	20442	33195	0.0	33195	99	38
+SCAFFOLD_266	NC_018827.1	3447	1	3435	0.0	33195	99	10
+SCAFFOLD_266	NC_018806.1	16758	3590	20290	0.0	33195	99	50
+SCAFFOLD_266	NC_018806.1	12797	20445	33195	0.0	33195	99	38
+SCAFFOLD_266	NC_018806.1	3444	1	3435	0.0	33195	99	10
+SCAFFOLD_266	NC_053083.1	16756	3604	20290	0.0	33195	99	50
+SCAFFOLD_266	NC_053083.1	12785	20459	33195	0.0	33195	99	38
+SCAFFOLD_266	NC_053083.1	3452	2	3435	0.0	33195	99	10
+SCAFFOLD_266	NC_018812.1	16762	3587	20290	0.0	33195	99	50
+SCAFFOLD_266	NC_018812.1	12797	20442	33195	0.0	33195	99	38
+SCAFFOLD_266	NC_018812.1	3447	2	3435	0.0	33195	99	10
+SCAFFOLD_266	NC_053110.1	16723	3626	20286	0.0	33195	99	50
+SCAFFOLD_266	NC_053110.1	12761	20481	33195	0.0	33195	99	38
+SCAFFOLD_266	NC_053110.1	3442	5	3431	0.0	33195	99	10
+SCAFFOLD_266	NC_018807.1	16763	3588	20290	0.0	33195	99	50
+SCAFFOLD_266	NC_018807.1	12800	20443	33195	0.0	33195	99	38
+SCAFFOLD_266	NC_018807.1	3441	2	3435	0.0	33195	99	10
+SCAFFOLD_266	NC_018799.1	16730	3623	20290	0.0	33195	99	50
+SCAFFOLD_266	NC_018799.1	12768	20478	33195	0.0	33195	99	38
+SCAFFOLD_266	NC_018799.1	3443	2	3435	0.0	33195	99	10
+SCAFFOLD_266	NC_053084.1	16742	3622	20290	0.0	33195	99	50
+SCAFFOLD_266	NC_053084.1	12771	20477	33195	0.0	33195	99	38
+SCAFFOLD_266	NC_053084.1	3454	1	3435	0.0	33195	99	10
+SCAFFOLD_266	NC_018794.1	16769	3587	20290	0.0	33195	99	50
+SCAFFOLD_266	NC_018794.1	12801	20442	33195	0.0	33195	99	38
+SCAFFOLD_266	NC_018794.1	3450	1	3435	0.0	33195	99	10
+SCAFFOLD_266	NC_018803.1	16765	3590	20285	0.0	33195	99	50
+SCAFFOLD_266	NC_018803.1	12797	20445	33195	0.0	33195	99	38
+SCAFFOLD_266	NC_018803.1	3440	1	3430	0.0	33195	99	10
+SCAFFOLD_266	NC_018796.1	16766	3587	20290	0.0	33195	99	50
+SCAFFOLD_266	NC_018796.1	12804	20442	33195	0.0	33195	99	38
+SCAFFOLD_266	NC_018796.1	3443	2	3435	0.0	33195	99	10
+SCAFFOLD_266	NC_018811.1	16728	3623	20290	0.0	33195	99	50
+SCAFFOLD_266	NC_018811.1	12766	20478	33195	0.0	33195	99	38
+SCAFFOLD_266	NC_018811.1	3442	2	3435	0.0	33195	99	10
+SCAFFOLD_266	NC_018804.1	16727	3623	20290	0.0	33195	99	50
+SCAFFOLD_266	NC_018804.1	12765	20478	33195	0.0	33195	99	38
+SCAFFOLD_266	NC_018804.1	3443	2	3435	0.0	33195	99	10
+SCAFFOLD_266	NC_018800.1	16608	3729	20290	0.0	33195	98	50
+SCAFFOLD_266	NC_018800.1	12647	20584	33195	0.0	33195	98	38
+SCAFFOLD_266	NC_018800.1	3443	1	3435	0.0	33195	98	10
+SCAFFOLD_266	NC_018801.1	16761	3587	20286	0.0	33195	99	50
+SCAFFOLD_266	NC_018801.1	12801	20442	33195	0.0	33195	99	38
+SCAFFOLD_266	NC_018801.1	3439	5	3431	0.0	33195	99	10
+SCAFFOLD_266	NC_018809.1	16724	3623	20290	0.0	33195	99	50
+SCAFFOLD_266	NC_018809.1	12762	20478	33195	0.0	33195	99	38
+SCAFFOLD_266	NC_018809.1	3442	2	3435	0.0	33195	99	10
+SCAFFOLD_266	NC_018813.1	16733	3623	20290	0.0	33195	99	50
+SCAFFOLD_266	NC_018813.1	12769	20478	33195	0.0	33195	99	38
+SCAFFOLD_266	NC_018813.1	3445	2	3435	0.0	33195	99	10
+SCAFFOLD_266	NC_018798.1	16764	3591	20290	0.0	33195	99	50
+SCAFFOLD_266	NC_018798.1	12800	20446	33195	0.0	33195	99	38
+SCAFFOLD_266	NC_018798.1	3445	2	3435	0.0	33195	99	10
+SCAFFOLD_266	NC_018805.1	16725	3623	20290	0.0	33195	99	50
+SCAFFOLD_266	NC_018805.1	12765	20478	33195	0.0	33195	99	38
+SCAFFOLD_266	NC_018805.1	3442	2	3435	0.0	33195	99	10
+SCAFFOLD_266	NC_015198.1	16781	3586	20286	0.0	33195	99	50
+SCAFFOLD_266	NC_015198.1	12809	20441	33195	0.0	33195	99	38
+SCAFFOLD_266	NC_015198.1	3445	1	3431	0.0	33195	99	10
+SCAFFOLD_266	NC_018797.1	16726	3623	20290	0.0	33195	99	50
+SCAFFOLD_266	NC_018797.1	12766	20478	33195	0.0	33195	99	38
+SCAFFOLD_266	NC_018797.1	3443	1	3435	0.0	33195	99	10
+SCAFFOLD_266	NC_018808.1	16759	3591	20290	0.0	33195	99	50
+SCAFFOLD_266	NC_018808.1	12798	20446	33195	0.0	33195	99	38
+SCAFFOLD_266	NC_018808.1	3438	5	3435	0.0	33195	99	10
+SCAFFOLD_266	NC_018802.1	16753	3592	20290	0.0	33195	99	50
+SCAFFOLD_266	NC_018802.1	12794	20447	33195	0.0	33195	99	38
+SCAFFOLD_266	NC_018802.1	3441	1	3435	0.0	33195	99	10
+SCAFFOLD_266	NC_018795.1	16732	3623	20290	0.0	33195	99	50
+SCAFFOLD_266	NC_018795.1	12768	20478	33195	0.0	33195	99	38
+SCAFFOLD_266	NC_018795.1	3444	2	3435	0.0	33195	99	10
+SCAFFOLD_266	NC_018810.1	16763	3589	20290	0.0	33195	99	50
+SCAFFOLD_266	NC_018810.1	12798	20444	33195	0.0	33195	99	38
+SCAFFOLD_266	NC_018810.1	3448	1	3435	0.0	33195	99	10
+SCAFFOLD_266	NC_052840.1	16657	3692	20286	0.0	33195	98	50
+SCAFFOLD_266	NC_052840.1	12694	20547	33195	0.0	33195	98	38
+SCAFFOLD_266	NC_052840.1	3440	5	3431	0.0	33195	98	10
+SCAFFOLD_266	NC_015234.1	16744	3620	20285	0.0	33195	99	50
+SCAFFOLD_266	NC_015234.1	12775	20475	33195	0.0	33195	99	38
+SCAFFOLD_266	NC_015234.1	3445	1	3430	0.0	33195	99	10
+SCAFFOLD_266	NC_021408.1	16607	3741	20285	0.0	33195	98	50
+SCAFFOLD_266	NC_021408.1	12648	20596	33195	0.0	33195	98	38
+SCAFFOLD_266	NC_021408.1	3438	5	3430	0.0	33195	98	10
+SCAFFOLD_266	NC_000880.1	15656	4711	20305	0.0	33195	99	47
+SCAFFOLD_266	NC_000880.1	11678	21566	33195	0.0	33195	99	35
+SCAFFOLD_266	NC_000880.1	3462	1	3450	0.0	33195	99	10
+SCAFFOLD_266	NC_000880.1	1117	20442	21541	0.0	33195	99	3
+SCAFFOLD_266	NC_000880.1	1117	3587	4686	0.0	33195	99	3
+SCAFFOLD_266	NC_053079.1	16831	3545	20290	0.0	33195	99	50
+SCAFFOLD_266	NC_053079.1	12861	20400	33195	0.0	33195	99	39
+SCAFFOLD_266	NC_053079.1	3451	2	3435	0.0	33195	99	10
+SCAFFOLD_266	NC_015233.1	16566	3784	20285	0.0	33195	98	50
+SCAFFOLD_266	NC_015233.1	12596	20639	33195	0.0	33195	98	38
+SCAFFOLD_266	NC_015233.1	3450	1	3430	0.0	33195	98	10
+SCAFFOLD_266	NC_053068.1	16669	3701	20286	0.0	33195	98	50
+SCAFFOLD_266	NC_053068.1	12702	20556	33195	0.0	33195	98	38
+SCAFFOLD_266	NC_053068.1	3449	1	3431	0.0	33195	98	10
+SCAFFOLD_266	NC_053073.1	16833	3544	20286	0.0	33195	99	50
+SCAFFOLD_266	NC_053073.1	12864	20399	33195	0.0	33195	99	39
+SCAFFOLD_266	NC_053073.1	3452	1	3431	0.0	33195	99	10
+SCAFFOLD_266	NC_054361.1	16212	4161	20290	0.0	33195	96	49
+SCAFFOLD_266	NC_054361.1	12233	21016	33195	0.0	33195	96	37
+SCAFFOLD_266	NC_054361.1	3455	2	3435	0.0	33195	96	10
+SCAFFOLD_266	NC_054361.1	521	4783	5302	3.92e-124	33195	96	2
+SCAFFOLD_266	NC_054361.1	521	21638	22157	3.92e-124	33195	96	2
+SCAFFOLD_266	NC_057247.1	15631	4712	20290	0.0	33195	98	47
+SCAFFOLD_266	NC_057247.1	11658	21567	33195	0.0	33195	98	35
+SCAFFOLD_266	NC_057247.1	3457	1	3435	0.0	33195	98	10
+SCAFFOLD_266	NC_057247.1	1045	20478	21502	0.0	33195	98	3
+SCAFFOLD_266	NC_057247.1	1045	3623	4647	0.0	33195	98	3
+SCAFFOLD_266	NC_053109.1	16669	3715	20286	0.0	33195	98	50
+SCAFFOLD_266	NC_053109.1	12693	20570	33195	0.0	33195	98	38
+SCAFFOLD_266	NC_053109.1	3458	1	3431	0.0	33195	98	10
+SCAFFOLD_266	NC_053645.1	16694	3656	20286	0.0	33195	99	50
+SCAFFOLD_266	NC_053645.1	12731	20511	33195	0.0	33195	99	38
+SCAFFOLD_266	NC_053645.1	3445	2	3431	0.0	33195	99	10
+SCAFFOLD_266	NC_053066.1	16785	3602	20290	0.0	33195	99	50
+SCAFFOLD_266	NC_053066.1	12810	20457	33195	0.0	33195	99	38
+SCAFFOLD_266	NC_053066.1	3457	1	3435	0.0	33195	99	10
+SCAFFOLD_266	NC_015898.1	16653	3729	20290	0.0	33195	98	50
+SCAFFOLD_266	NC_015898.1	12683	20584	33195	0.0	33195	98	38
+SCAFFOLD_266	NC_015898.1	3452	1	3435	0.0	33195	98	10
+SCAFFOLD_266	NC_057294.1	16729	3668	20290	0.0	33195	99	50
+SCAFFOLD_266	NC_057294.1	12746	20523	33195	0.0	33195	99	38
+SCAFFOLD_266	NC_057294.1	3458	2	3435	0.0	33195	99	10
+SCAFFOLD_266	NC_014455.1	16662	3713	20290	0.0	33195	98	50
+SCAFFOLD_266	NC_014455.1	12688	20568	33195	0.0	33195	98	38
+SCAFFOLD_266	NC_014455.1	3450	1	3435	0.0	33195	98	10
+SCAFFOLD_266	NC_053053.1	16620	3767	20290	0.0	33195	98	50
+SCAFFOLD_266	NC_053053.1	12648	20622	33195	0.0	33195	98	38
+SCAFFOLD_266	NC_053053.1	3455	1	3435	0.0	33195	98	10
+SCAFFOLD_266	NC_020423.1	16627	3771	20290	0.0	33195	98	50
+SCAFFOLD_266	NC_020423.1	12654	20626	33195	0.0	33195	98	38
+SCAFFOLD_266	NC_020423.1	3451	2	3435	0.0	33195	98	10
+SCAFFOLD_266	NC_015237.1	16650	3729	20290	0.0	33195	98	50
+SCAFFOLD_266	NC_015237.1	12676	20584	33195	0.0	33195	98	38
+SCAFFOLD_266	NC_015237.1	3452	1	3435	0.0	33195	98	10
+SCAFFOLD_266	NC_015613.1	16660	3713	20290	0.0	33195	98	50
+SCAFFOLD_266	NC_015613.1	12688	20568	33195	0.0	33195	98	38
+SCAFFOLD_266	NC_015613.1	3451	1	3435	0.0	33195	98	10
+SCAFFOLD_266	NC_053059.1	16632	3771	20290	0.0	33195	98	50
+SCAFFOLD_266	NC_053059.1	12659	20626	33195	0.0	33195	98	38
+SCAFFOLD_266	NC_053059.1	3451	1	3435	0.0	33195	98	10
+SCAFFOLD_266	NC_015074.1	16657	3747	20285	0.0	33195	98	50
+SCAFFOLD_266	NC_015074.1	12668	20602	33195	0.0	33195	98	38
+SCAFFOLD_266	NC_015074.1	3457	1	3430	0.0	33195	98	10
+SCAFFOLD_266	NC_053917.1	16650	3742	20290	0.0	33195	98	50
+SCAFFOLD_266	NC_053917.1	12667	20597	33195	0.0	33195	98	38
+SCAFFOLD_266	NC_053917.1	3464	1	3435	0.0	33195	98	10
+SCAFFOLD_266	NC_015232.1	16628	3743	20290	0.0	33195	98	50
+SCAFFOLD_266	NC_015232.1	12653	20598	33195	0.0	33195	98	38
+SCAFFOLD_266	NC_015232.1	3458	1	3435	0.0	33195	98	10
+SCAFFOLD_266	NC_054298.1	16640	3753	20290	0.0	33195	98	50
+SCAFFOLD_266	NC_054298.1	12666	20608	33195	0.0	33195	98	38
+SCAFFOLD_266	NC_054298.1	3460	1	3435	0.0	33195	98	10
+SCAFFOLD_266	NC_014341.1	16628	3766	20285	0.0	33195	98	50
+SCAFFOLD_266	NC_014341.1	12646	20621	33195	0.0	33195	98	38
+SCAFFOLD_266	NC_014341.1	3457	1	3430	0.0	33195	98	10
+SCAFFOLD_266	NC_015802.1	16648	3747	20290	0.0	33195	98	50
+SCAFFOLD_266	NC_015802.1	12671	20602	33195	0.0	33195	98	38
+SCAFFOLD_266	NC_015802.1	3461	1	3435	0.0	33195	98	10
+SCAFFOLD_266	NC_057295.1	16684	3715	20290	0.0	33195	98	50
+SCAFFOLD_266	NC_057295.1	12704	20570	33195	0.0	33195	98	38
+SCAFFOLD_266	NC_057295.1	3453	5	3435	0.0	33195	98	10
+SCAFFOLD_266	NC_053061.1	16597	3794	20290	0.0	33195	98	50
+SCAFFOLD_266	NC_053061.1	12616	20649	33195	0.0	33195	98	38
+SCAFFOLD_266	NC_053061.1	3460	1	3435	0.0	33195	98	10
+SCAFFOLD_266	NC_052841.1	15643	4711	20290	0.0	33195	96	47
+SCAFFOLD_266	NC_052841.1	11665	21566	33195	0.0	33195	96	35
+SCAFFOLD_266	NC_052841.1	3452	8	3435	0.0	33195	96	10
+SCAFFOLD_266	NC_052841.1	624	20626	21231	4.08e-94	33195	96	2
+SCAFFOLD_266	NC_052841.1	624	3771	4376	4.08e-94	33195	96	2
+SCAFFOLD_266	NC_052843.1	16624	3766	20290	0.0	33195	98	50
+SCAFFOLD_266	NC_052843.1	12653	20621	33195	0.0	33195	98	38
+SCAFFOLD_266	NC_052843.1	3449	5	3435	0.0	33195	98	10
+SCAFFOLD_266	NC_015195.1	16656	3713	20290	0.0	33195	98	50
+SCAFFOLD_266	NC_015195.1	12686	20568	33195	0.0	33195	98	38
+SCAFFOLD_266	NC_015195.1	3448	2	3435	0.0	33195	98	10
+SCAFFOLD_266	NC_053050.1	16671	3729	20290	0.0	33195	98	50
+SCAFFOLD_266	NC_053050.1	12699	20584	33195	0.0	33195	98	38
+SCAFFOLD_266	NC_053050.1	3452	1	3435	0.0	33195	98	10
+SCAFFOLD_266	NC_057250.1	16607	3771	20290	0.0	33195	98	50
+SCAFFOLD_266	NC_057250.1	12640	20626	33195	0.0	33195	98	38
+SCAFFOLD_266	NC_057250.1	3448	1	3435	0.0	33195	98	10
+SCAFFOLD_266	NC_053077.1	16654	3729	20290	0.0	33195	98	50
+SCAFFOLD_266	NC_053077.1	12680	20584	33195	0.0	33195	98	38
+SCAFFOLD_266	NC_053077.1	3456	2	3435	0.0	33195	98	10
+SCAFFOLD_266	NC_058320.1	15651	4711	20291	0.0	33195	96	47
+SCAFFOLD_266	NC_058320.1	11675	21566	33195	0.0	33195	96	35
+SCAFFOLD_266	NC_058320.1	3459	1	3436	0.0	33195	96	10
diff -r 000000000000 -r f172b1f77d6c test-data/test_mito_scaff_names.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_mito_scaff_names.txt	Thu May 12 10:45:45 2022 +0000
@@ -0,0 +1,1 @@
+SCAFFOLD_266
\ No newline at end of file