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add a test
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@shiltemann
shiltemann committed Jan 21, 2025
1 parent f1aead3 commit 7091963
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7 changes: 7 additions & 0 deletions tools/emboss/emboss_backtranseq.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -71,6 +71,13 @@ $osformat2
<param name="osformat2" value="fasta"/>
<output name="output_nucleotide_sequences" file="emboss_backtranseq_out2.fasta" ftype="fasta" />
</test>
<!-- Test with different cfile and outpute format -->
<test>
<param name="protein_sequences" value="emboss_getorf_out.fasta" />
<param name="cfile" value="Espo_h.cut"/>
<param name="osformat2" value="embl"/>
<output name="output_nucleotide_sequences" file="emboss_backtranseq_out2.embl" ftype="embl" />
</test>
</tests>
<help><![CDATA[
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248 changes: 248 additions & 0 deletions tools/emboss/test-data/emboss_backtranseq_out2.embl
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@@ -0,0 +1,248 @@
ID Sequence_1; SV 1; linear; unassigned DNA; STD; UNC; 51 BP.
XX
DE [1 - 51] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
XX
SQ Sequence 51 BP; 6 A; 11 C; 10 G; 24 T; 0 other;
GTTCGTTGTT TGAAGTACTT GTTGTTGTCT TTGCACCGTC CTCAATTCTC T 51
//
ID Sequence_2; SV 1; linear; unassigned DNA; STD; UNC; 81 BP.
XX
DE [14 - 94] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
XX
SQ Sequence 81 BP; 16 A; 27 C; 7 G; 31 T; 0 other;
AACACTTTCT TCTGTCCTTA CACTGATCAC TCTTTCCCTA ACGGTTTCAC TCCTACTCGT 60
AACTCTTGTG CTTCTACTAA C 81
//
ID Sequence_3; SV 1; linear; unassigned DNA; STD; UNC; 36 BP.
XX
DE [94 - 129] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
XX
SQ Sequence 36 BP; 4 A; 4 C; 12 G; 16 T; 0 other;
TTGAAGGCTG TTGGTTTGGA GTGTTACCGT TTCGTT 36
//
ID Sequence_4; SV 1; linear; unassigned DNA; STD; UNC; 99 BP.
XX
DE [133 - 231] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
XX
SQ Sequence 99 BP; 13 A; 17 C; 21 G; 48 T; 0 other;
TTGTCTGCTT CTTTGGCTTT GATTAAGGGT TCTTTCTCTT TGTTGTGGAA GACTTTGTGG 60
AAGAACACTA CTTCTACTTC TTTGTCTCCT TTGGTTTGT 99
//
ID Sequence_5; SV 1; linear; unassigned DNA; STD; UNC; 96 BP.
XX
DE [155 - 250] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
XX
SQ Sequence 96 BP; 14 A; 21 C; 21 G; 40 T; 0 other;
TCTAAGGTTC ACTTCTTGTA CTTCGGTCGT CGTTGTGGTC GTATTCAACA AGTTCGTGTT 60
TCTCCTCCTT GGTTCGCTGA TTACTGGATT CAATTG 96
//
ID Sequence_6; SV 1; linear; unassigned DNA; STD; UNC; 270 BP.
XX
DE [3 - 272] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
XX
SQ Sequence 270 BP; 44 A; 54 C; 59 G; 113 T; 0 other;
TCTATGCCTA AGATTCCTTC TTTCGTTCCT ACTCAAACTA CTGTTTTCTT GATGGCTTTG 60
CACCGTTTGG AGATTTTGGT TCAAGCTTTG ATTGAGTCTG GTTGGCCTCG TGTTTTGCCT 120
GTTTGTATTG CTGAGCGTGT TTCTTGTCCT GATCAACGTT TCATTTTCTC TACTTTGGAG 180
GATGTTGTTG AGGAGTACAA CAAGTACGAG TCTTTGCCTC CTGGTTTGTT GATTACTGGT 240
TACTCTTGTA ACACTTTGCG TAACACTGCT 270
//
ID Sequence_7; SV 1; linear; unassigned DNA; STD; UNC; 75 BP.
XX
DE [235 - 309] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
XX
SQ Sequence 75 BP; 12 A; 16 C; 13 G; 34 T; 0 other;
TTGTTGGATA CTGTTGTTAT TCCTTTCGCT ACTCCTCGTA ACTACTTGTA CGAGTTGTTC 60
TCTTTGTACT ACATG 75
//
ID Sequence_8; SV 1; linear; unassigned DNA; STD; UNC; 48 BP.
XX
DE [288 - 335] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
XX
SQ Sequence 48 BP; 4 A; 7 C; 8 G; 29 T; 0 other;
ATTATTTTCC CTTTGTTGTA CGTTGTTGGT TCTTCTTTGA TTTTCTTG 48
//
ID Sequence_9; SV 1; linear; unassigned DNA; STD; UNC; 39 BP.
XX
DE [339 - 377] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
XX
SQ Sequence 39 BP; 5 A; 10 C; 5 G; 19 T; 0 other;
CAAGTTTTCT ACTGTTTCCG TCCTCAATGT TCTTGTTCT 39
//
ID Sequence_10; SV 1; linear; unassigned DNA; STD; UNC; 138 BP.
XX
DE [254 - 391] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
XX
SQ Sequence 138 BP; 18 A; 32 C; 20 G; 68 T; 0 other;
TACCCTTCTC AACACCGTGT TACTATTTAC ATGAACTACT TCCCTTTCAT TATTTGTTCT 60
CGTTTCGTTT TCAACTTGCC TTTGGCTTCT TTGTTGTTGT TCTCTACTTC TATGTTCATG 120
TTCTTGGGTT GTTTCGGT 138
//
ID Sequence_11; SV 1; linear; unassigned DNA; STD; UNC; 33 BP.
XX
DE [395 - 427] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
XX
SQ Sequence 33 BP; 2 A; 6 C; 5 G; 20 T; 0 other;
TACGCTGTTT CTTTGATTTT CGTTGTTTCT TCT 33
//
ID Sequence_12; SV 1; linear; unassigned DNA; STD; UNC; 120 BP.
XX
DE [328 - 447] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
XX
SQ Sequence 120 BP; 17 A; 21 C; 22 G; 60 T; 0 other;
TCTTCTTTCT CTAAGTCTTT CACTGTTTTC GATTTGAACG TTCACGTTTT GCGTTTGTTC 60
TGGATTATTT GTGGTCAATT CAACTTGCGT TGTTTCTTCT TGAAGTACTT GTTCATGGTT 120
//
ID Sequence_13; SV 1; linear; unassigned DNA; STD; UNC; 111 BP.
XX
DE [411 - 521] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
XX
SQ Sequence 111 BP; 18 A; 20 C; 16 G; 57 T; 0 other;
TCTTCTTTGT TCTTGTTGAA GATTTTCATT CACGGTTTGA TTTTCGGTTT GTACTTGTTC 60
CGTGGTCAAT TCATTATTTA CTCTGTTTGT ATTCAACAAT TCTTCTACTT C 111
//
ID Sequence_14; SV 1; linear; unassigned DNA; STD; UNC; 96 BP.
XX
DE [431 - 526] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
XX
SQ Sequence 96 BP; 12 A; 17 C; 20 G; 47 T; 0 other;
AACATTTACT CTTGGTTCAA CTTCTGGTTC GTTTTGGTTC AAGGTCCTGT TCACTACTTG 60
TTGTGTTTGT ACACTGCTGT TTTGTTGTTC TTGGTT 96
//
ID Sequence_15; SV 1; linear; unassigned DNA; STD; UNC; 87 BP.
XX
DE [451 - 537] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
XX
SQ Sequence 87 BP; 7 A; 16 C; 12 G; 52 T; 0 other;
TTCTTGGTTT GTACTTGTTC TGGTGCTTCT TCTTTGTTCA CTTTGTTCGT TTACTCTTCT 60
TCTTTCATTT TCTCTATGAT TTTGATT 87
//
ID Sequence_16; SV 1; linear; unassigned DNA; STD; UNC; 45 BP.
XX
DE [531 - 487] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
XX
SQ Sequence 45 BP; 18 A; 11 C; 7 G; 9 T; 0 other;
AACCACACTA AGAACAAGCG TACTGCTGTT TACAAGCAAT CTAAG 45
//
ID Sequence_17; SV 1; linear; unassigned DNA; STD; UNC; 87 BP.
XX
DE [536 - 450] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
XX
SQ Sequence 87 BP; 30 A; 13 C; 18 G; 26 T; 0 other;
ATTAAGATTA TTTTGAAGAT TAAGGAGTTG TTGTACACTA ACCGTGTTAA CAACGAGTTG 60
GCTCCTGAGC AAGTTCAAAC TAAGAAC 87
//
ID Sequence_18; SV 1; linear; unassigned DNA; STD; UNC; 45 BP.
XX
DE [487 - 443] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
XX
SQ Sequence 45 BP; 16 A; 9 C; 8 G; 12 T; 0 other;
ATTATGAACT GGCCTTTGAA CAAGTACAAG CCTAAGATTA AGCCT 45
//
ID Sequence_19; SV 1; linear; unassigned DNA; STD; UNC; 30 BP.
XX
DE [468 - 439] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
XX
SQ Sequence 30 BP; 12 A; 8 C; 4 G; 6 T; 0 other;
ACTTCTACTA ACCAAAAGTT GAACCACGAG 30
//
ID Sequence_20; SV 1; linear; unassigned DNA; STD; UNC; 30 BP.
XX
DE [439 - 410] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
XX
SQ Sequence 30 BP; 10 A; 5 C; 6 G; 9 T; 0 other;
ATTAACATTT TGCGTCGTAA CAACGAGGAT 30
//
ID Sequence_21; SV 1; linear; unassigned DNA; STD; UNC; 42 BP.
XX
DE [446 - 405] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
XX
SQ Sequence 42 BP; 17 A; 8 C; 8 G; 9 T; 0 other;
ACTATGAACA AGTACTTCAA GAAGAAGCAA CGTCGTTTGA AC 42
//
ID Sequence_22; SV 1; linear; unassigned DNA; STD; UNC; 30 BP.
XX
DE [401 - 372] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
XX
SQ Sequence 30 BP; 10 A; 9 C; 2 G; 9 T; 0 other;
CCTCACATTA TTCAAAACAA CTTGCGTACT 30
//
ID Sequence_23; SV 1; linear; unassigned DNA; STD; UNC; 42 BP.
XX
DE [368 - 327] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
XX
SQ Sequence 42 BP; 11 A; 4 C; 12 G; 15 T; 0 other;
ACTTTGCGTT CTAAGACTGT TAAGGATTTG TTGAAGGAGG AT 42
//
ID Sequence_24; SV 1; linear; unassigned DNA; STD; UNC; 135 BP.
XX
DE [426 - 292] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
XX
SQ Sequence 135 BP; 44 A; 22 C; 32 G; 37 T; 0 other;
GAGGAGACTA CTAAGATTAA GTTGACTGCT TACTACCCTA AGCAACCTAA GAACATGAAC 60
ATTGAGGTTG AGAACTCTAA GCGTTTGGCT AAGGGTCGTT TGAAGACTAA CTTGTTGCAC 120
ATTATTAAGG GTAAG 135
//
ID Sequence_25; SV 1; linear; unassigned DNA; STD; UNC; 42 BP.
XX
DE [279 - 238] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
XX
SQ Sequence 42 BP; 10 A; 6 C; 9 G; 17 T; 0 other;
ATTGTTACTC GTTGTTGTGA GGGTTACTAC AACTGTATTC AA 42
//
ID Sequence_26; SV 1; linear; unassigned DNA; STD; UNC; 60 BP.
XX
DE [234 - 175] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
XX
SQ Sequence 60 BP; 12 A; 13 C; 14 G; 21 T; 0 other;
TCTGCTAACC AAGGTGGTGA GACTCGTACT TGTTGTATTT TGCCTCAACG TTTGCCTAAG 60
//
ID Sequence_27; SV 1; linear; unassigned DNA; STD; UNC; 177 BP.
XX
DE [334 - 158] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
XX
SQ Sequence 177 BP; 41 A; 32 C; 36 G; 68 T; 0 other;
CGTAAGATTA AGGATGAGCC TACTACTTAC AACAAGGGTA AGATTATTCA CATTGATTCT 60
TACGCTGTTT TGCGTCGTGT TTTGCAATTG TACCCTGTTA TTTCTAAGCC TGGTGGTCGT 120
GATTCTTACT TGTTGTACTC TTCTACTACT TCTTCTAAGG TTGAGAAGAT GAACTTG 177
//
ID Sequence_28; SV 1; linear; unassigned DNA; STD; UNC; 156 BP.
XX
DE [275 - 120] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
XX
SQ Sequence 156 BP; 28 A; 33 C; 35 G; 60 T; 0 other;
TTGCGTGGTG TTGCTAAGGG TATTACTACT GTTTCTTCTA ACCAACAAAC TCGTGGTGAG 60
CGTTTGGTTT TGGTTGTTTT CTTCCACAAC GTTTTCCAAT CTCGTGAGAA CGAGCCTTTG 120
ATTCGTGCTC GTGATGCTTT GTCTTACACT AACCGT 156
//
ID Sequence_29; SV 1; linear; unassigned DNA; STD; UNC; 51 BP.
XX
DE [162 - 112] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
XX
SQ Sequence 51 BP; 12 A; 11 C; 11 G; 17 T; 0 other;
ACTTTCGATC AAGGTAAGCG TCGTGCTCAA TTGTACAAGC CTGTTACTTT G 51
//
ID Sequence_30; SV 1; linear; unassigned DNA; STD; UNC; 75 BP.
XX
DE [108 - 34] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
XX
SQ Sequence 75 BP; 11 A; 11 C; 22 G; 31 T; 0 other;
GCTAACCGTT TCCAATTGGT TTTGGCTCAA GAGTTCTTGG TTGGTGTTAA GCCTTTGGGT 60
AAGTTGTGGT CTGTT 75
//
ID Sequence_31; SV 1; linear; unassigned DNA; STD; UNC; 48 BP.
XX
DE [50 - 3] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
XX
SQ Sequence 48 BP; 8 A; 10 C; 14 G; 16 T; 0 other;
GAGAACTGTG GTTTGTGTCG TGATAAGCGT CGTTACTTCC GTCACCGT 48
//
ID Sequence_32; SV 1; linear; unassigned DNA; STD; UNC; 153 BP.
XX
DE [154 - 2] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
XX
SQ Sequence 153 BP; 29 A; 25 C; 37 G; 62 T; 0 other;
TCTGGTCAAG AGACTCGTTC TGCTATTCAA ACTGGTAACA CTTTGGGTCA ACCTTTGTCT 60
ATTTCTGCTT GTACTCGTAT TTCTTCTCGT TGTAAGGCTA TTCGTAAGAC TGTTGTTTGT 120
GTTGGTACTA AGGAGGGTAT TTTGGGTATT GAG 153
//

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