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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal commit fc5c69375318ffee0a71a69378d51c97003427b6 |
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added:
prodigal.xml test-data/input.fna test-data/output test-data/output.faa test-data/output.fnn test-data/output.gff test-data/output.start test-data/output_c_n_m test-data/output_c_n_m.faa test-data/output_c_n_m.fnn test-data/output_c_n_m.start test-data/output_train test-data/output_train.faa test-data/output_train.fnn test-data/output_train.start test-data/output_tt test-data/output_tt.faa test-data/output_tt.fnn test-data/output_tt.start test-data/train_file.trn |
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| diff -r 000000000000 -r 91791b6ecd38 prodigal.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/prodigal.xml Thu Mar 14 16:49:04 2024 +0000 |
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| @@ -0,0 +1,131 @@ +<tool id="prodigal" name="Prodigal Gene Predictor" version="@VERSION@+galaxy0" profile="22.05"> + <description>A tool for gene prediction in microbial genomes</description> + <macros> + <token name="@VERSION@">2.6.3</token> + </macros> + <xrefs> + <xref type="bio.tools">prodigal</xref> + </xrefs> + <requirements> + <requirement type="package" version="@VERSION@">prodigal</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + prodigal + -i '$input_fa' + #if $input_train + -t '$input_train' + #end if + -o '$output' + -f '$out_format' + -p '$procedure' + -g '$trans_table' + -a '$output_faa' + -d '$output_fnn' + -s '$output_start' + $closed + $force_nonsd + $masked_seq + ]]></command> + <inputs> + <param type="data" name="input_fa" format="fasta" label="Specify input file" help="-i" /> + <param type="data" name="input_train" format="fasta" label="Specify training file" optional="true" help="Read and use the specified training file (-t)" /> + <param type="select" name="out_format" label="Specify output format" help="-f" > + <option value="gbk" selected="true">GBK (default)</option> + <option value="gff">GFF</option> + <option value="sqn">SQN</option> + <option value="sco">SCO</option> + </param> + <param type="select" name="procedure" label="Specify mode" help="-p" > + <option value="single" selected="true">Single : Single genome, any number of + sequences (default)</option> + <option value="meta">Meta : Anonymous sequences, analyze + using preset training files, ideal for metagenomic data or single short sequences</option> + </param> + <param type="select" name="trans_table" label="Specify a translation table to use" help="-g" > + <option value="11">11 : Standard Bacteria/Archaea (default)</option> + <option value="4">4 : Mycoplasma/Spiroplasma</option> + <option value="#"># : Other genetic codes 1-25</option> + </param> + <param name="closed" type="boolean" label="Closed ends" truevalue="-c" falsevalue="" optional="true" help="Closed ends. Do not allow partial genes + at edges of sequence (-c)" /> + <param name="force_nonsd" type="boolean" label="Force Prodigal to scan for + motifs" truevalue="-n" falsevalue="" optional="true" help="Do not use the Shine-Dalgarno RBS finder and instead force Prodigal to scan for motifs (-n)" /> + <param name="masked_seq" type="boolean" label="Treat runs of N as masked sequence" truevalue="-m" falsevalue="" optional="true" help="Treat runs of N as masked sequence; don't build genes across them (-m)" /> + </inputs> + <outputs> + <data name="output" format="genbank" label="${tool.name} on ${on_string} : coordinates"> + <change_format> + <when input="out_format" value="gff" format="gff3" /> + <when input="out_format" value="sqn" format="asn1" /> + <when input="out_format" value="sco" format="genbank" /> + </change_format> + </data> + <data name="output_faa" format="fasta" label="${tool.name} on ${on_string} : protein translations file" /> + <data name="output_fnn" format="fasta" label="${tool.name} on ${on_string} : nucleotide sequences file" /> + <data name="output_start" format="tabular" label="${tool.name} on ${on_string} : complete starts file" /> + </outputs> + <tests> + <test> + <param name="input_fa" value="input.fna"/> + <output name="output" file="output"/> + </test> + <test> + <param name="input_fa" value="input.fna"/> + <output name="output" file="output" ftype="genbank"/> + <output name="output_faa" file="output.faa"/> + <output name="output_fnn" file="output.fnn"/> + <output name="output_start" file="output.start"/> + </test> + <test> + <param name="input_fa" value="input.fna"/> + <param name="out_format" value="gff"/> + <output name="output" file="output.gff" ftype="gff3" /> + <output name="output_faa" file="output.faa"/> + <output name="output_fnn" file="output.fnn"/> + <output name="output_start" file="output.start"/> + </test> + <test> + <param name="input_fa" value="input.fna"/> + <param name="trans_table" value="4"/> + <output name="output" file="output_tt" ftype="genbank"/> + <output name="output_faa" file="output_tt.faa"/> + <output name="output_fnn" file="output_tt.fnn"/> + <output name="output_start" file="output_tt.start"/> + </test> + <test> + <param name="input_fa" value="input.fna"/> + <param name="procedure" value="single"/> + <param name="closed" value="true"/> + <param name="force_nonsd" value="true"/> + <param name="masked_seq" value="true"/> + <output name="output" file="output_c_n_m" ftype="genbank"/> + <output name="output_faa" file="output_c_n_m.faa"/> + <output name="output_fnn" file="output_c_n_m.fnn"/> + <output name="output_start" file="output_c_n_m.start"/> + </test> + <test> + <param name="input_fa" value="input.fna"/> + <param name="input_train" value="train_file.trn"/> + <output name="output" file="output_train" ftype="genbank"/> + <output name="output_faa" file="output_train.faa"/> + <output name="output_fnn" file="output_train.fnn"/> + <output name="output_start" file="output_train.start"/> + </test> + </tests> + <help><![CDATA[ + +Fast, reliable protein-coding gene prediction for prokaryotic genomes. + +Features: +* Predicts protein-coding genes: Prodigal provides fast, accurate protein-coding gene predictions in GFF3, Genbank, or Sequin table format. +* Handles draft genomes and metagenomes: Prodigal runs smoothly on finished genomes, draft genomes, and metagenomes. +* Runs quickly: Prodigal analyzes the E. coli K-12 genome in 10 seconds on a modern MacBook Pro. +* Runs unsupervised: Prodigal is an unsupervised machine learning algorithm. It does not need to be provided with any training data, and instead automatically learns the properties of the genome from the sequence itself, including RBS motif usage, start codon usage, and coding statistics. +* Handles gaps and partial genes: The user can specify if Prodigal should build genes across runs of N's as well as how to handle genes at the edges of contigs. +* Identifies translation initiation sites: Prodigal predicts the correct translation initiation site for most genes, and can output information about every potential start site in the genome, including confidence score, RBS motif, and much more. + + ]]></help> + <citations> + <citation type="doi">10.1186/1471-2105-11-119</citation> + </citations> +</tool> |
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| diff -r 000000000000 -r 91791b6ecd38 test-data/input.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input.fna Thu Mar 14 16:49:04 2024 +0000 |
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| b'@@ -0,0 +1,2500 @@\n+>NZ_CP043953.1 Acinetobacter baumannii strain K09-14 chromosome, complete genome\n+ATGCTTTGGACAGACTGCTTAACTCGCTTGCGACAAGAGCTCTCTGATAACGTCTTTGCGATGTGGATTCGCCCTTTAGT\n+AGCTGAAGAAGTAGAGGGGATACTACGTCTCTATGCTCCTAATCCTTATTGGACGCGTTATATTCAAGAGAATCATTTAG\n+AGTTAATTTCTATATTGGCTGAACAATTGTCAGAAGGGCGGGTGCGTCAGGTTGAAATCTTGGTAGATTCTCGTCCTGGT\n+AGTATTTTGTCTTCTAGTGAACAGCCTGCAACAACTACAGCAGCTTTACAAACTGCCCCTATACCTCAACCTGCTAAGGT\n+TAAAAGAGAACCGGAACCTGTTGCTAATACTGCAGTTAGTTCTAAGAGTTCAAAAAAGAAACTATTAAATCCACAATTTA\n+CTTTTTCACTATTTGTTGAAGGCCGTTCTAACCAAATGGCAGCAGAAACCTGTAGAAAAGTATTAACACAGTTAGGTGCT\n+TCTCAACATAACCCTTTGTTTTTATATGGTCCGACAGGTCTAGGTAAGACTCACTTAATGCAAGCAGTTGGTAATGCCCT\n+ACTGCAAGCGAAGCCGAATGCAAGAGTCATGTATATGACTTCAGAAAGTTTTGTACAAGATTTTGTGAGCTCATTACAAA\n+AAGGAAAGGTAGAAGAGTTTAAGAAAAATTGCCGTTCTTTAGACTTGTTATTAGTAGATGATATTCATCTTTTGGCAGGA\n+AAAGAAGCAAGTCTCGTTGAATTCTTCTATACATTTAATGCCTTACTTGATGAATCTAAACAAATTATTTTAACGTCTGA\n+TCGATATCCTAAAGAATTAACAGAACTTGATCCTCGATTGGTTTCTCGTTTTTCCTGGGGGCTATCAGTAGGTGTTGAAC\n+CACCTGATATTGAAACTCGAATCGAAATTCTGCTTAAAAAAGCTGAAAATAGTGGCGTTGATTTACCTAGAAACTGTGCG\n+TTGTTTATTGCCCAACAAGTCGTAGCGAACGTACGTGAACTTGAGGGCGCACTGAATAAAGTTGTCGCAATTTCACGTTT\n+TAAAGGTGCTCCAATTGACCTGGATGTCGTACGGGAATCTTTAAAAGATGTTTTAGCGATCCGTGCTCGTACAATTAGTG\n+TAGAAAATATCCAGCGTGTAGTGAGTGAATATTTCCGAATTCCATTAAAAGAGCTGGTAGGTCCAAAGCGTACCCGAATT\n+TATGCTCGACCACGTCAGTTGGCGATGGGGCTTGCCCGTGAATTAACGGGGGATAGTTTTCCTGAAATTGGAATGGCTTT\n+TGGTGGGCGTGATCACAGTACAGTGATGCATGCTTGTGAAAAAGTCGTCAGTTTACGGGAAGAAGACCCAATCTTTGATG\n+AAGATTATAAGAACTTATTACGTTTGCTTCAAAGTTAATGAAATAATAAGACATTGTTGCAAAGTCTACGTAAGTGCAGC\n+ATAGTACACAGCTAAAAAATGAAATGTTTGCTCCAAGTTGCTAGAGGAATGAATCGTGCGTTTGAAAATCGCTAAAGAAA\n+GTTTACTCAATGTTTTATCGCATGTGGTCGGTGCGGTAGAACGTCGTCATACCTTGAATATTCTTTCAAACGTCAAAATT\n+CAGACTAATGCTCAAGCGCTCACTATTACGGGTTCCGATTTAGAAGTTGAACTCGTAGCGAGCACCGCTTTATCAGAAGG\n+GGCGTGCCTTGAGGCAGGCGAGACAACTGTTCCTGCTCGTAAATTGATGGAAATTTGTAAATCTTTGCCTACAGCTGCAT\n+TGATTGATTTACAAATTACTGAAGATCAAAGATGTATTTTAAAATCTGGTAATAGCCGTTTTGTGCTAGGTACACTACCG\n+GCTGAAGATTATCCATTGTTAACCACTGAGAATAGCCAGGGTACGCAAGTACAGGTGACTCAACGTGAATTAAAGCGTTT\n+ATTTGAAAAAACTGCTTTTGCAATGGCTGTACAAGATGTACGTTTTTACCTCACTGGTACTTTATTAGAAATTGATGAAA\n+ATCAATTGCGTGCAGTAACAACTGATGGTCACCGTTTAGCACTTTGTGAAATTTTGGCTTCCTCTACTTCATCTCAGTTG\n+GTACAAGCGATTGTGCCTCGTAAAGCTGTGGGCGAATTGCAACGTTTACTCAGCATTGAAGATGAACAGCTCACATTGCT\n+TATTGGCCGTGAATTATTAAATGTAACGATTAATACGCCAAGCCGTGATAAAGAACAAGGTGATATTACAGTTCGTTTTA\n+CAACTAAATTGATTGATGGGAAATTCCCTGATTATCGCCGTGTTATTCCACGTGGTGGTGATAAACATGTTTTGATTGGT\n+CATGACGTATTTAAACAATCATTACAACGTGTAGCAATTTTAAGTAATGAAAAATTGCGTGGTGTTTTCCTAAATTTCAA\n+TCAGGATTCTTTACAGCTTCGTGCAAATAACCCTGAACAAGATGAAGCAATTGAAGATTTAGCGATCCAATATCAAAGTG\n+CCCCATTAGAAATGTCATTTAATGCTCAATACCTACTCGATGTATTGGGTGTATTAGATGGTGATGATGTAAATATGAGC\n+ATGACTGAGGCGAATCAGTCTGTATTGGTTCAAGATCCGGCTCATCCTGACCAGACCTATGTGGTTATGCCGATGCGTGT\n+TTAATCTGGTTTAACTATATGCATCTTACGCGCTTAAATATTGAACGTGTGCGTAATTTAAAAACGGTTGCACTCCATGG\n+GTTGCAACCGTTTAATGTCTTTTATGGCGCAAACGGTTCAGGTAAAACATCAATTTTAGAAGCGATCCATTTGCTTGCAA\n+CAGGTCGCTCATTCCGTACACATATACCCAAAAATTATATTCAATATGAAGCTGACGACGCGATTGTATTTGCTCAGTCA\n+GCAACTGAAAAAATTGGTATGCAGAAACTCGCTTCTGGTGAGCAACTCATGAAAGTGAATGGCGATACCGTTGCGACTCA\n+AGGTCAGCTCGCAAAGTTACTTCCTTTACAGCATATTGATCCACAAAGTACGGATATTATTGATCATGGTGCCAAGCCAA\n+GAAGACAACTTTTAGATTGGCTTATGTTCCACGTGGAACCTGAATTTTATTTTGCGTGGCAATATTACTCTCGTGCGCTA\n+AAGCAGCGTAATACCTTACTCAAAACACGGCGTAATCTTTCATTAGCTGATTTAGAACCGTGGAACAAAATGTTGAGTGA\n+TTATGGCGAGATTTTGCACTCACAGCGTTTAAGTATTGTCGAGCAATGGAATGTTTATTTCCAAAATGACTTAAGCCAAT\n+TACTCCCTGATTTGGAGATTGAACTGGAATATAGCCCAGGTTTTCATACAGAGCAGGGGCTTATGCAAGACTTGTTGAAT\n+CAGCATCAAAAAGACATCGAGAGACGTTATACCGAGTATGGTCCGCATCGGGCAGATTTGCGCTTAAAAACGCCATTTGG\n+ACATGCTGATGATGTTTTATCAAGAGGTCAGAAAAAACTCTTGATTATTGCCTTAAAACTGTCACAAATTGCAATGTTGC\n+ATGCGAGTAATAAGGAAACTGTGGTATTATTAGATGATCTGACAGCAGAATTAGACTTAACCGCACAACAACGTTTAATT\n+GAACGATTAAGCCAACTTGGTAGCCAGGTTTTTATGACAACTTTAGATCATGCATCGGTAAAAAAACATTTACATGATCT\n+GTCTATTTCATATCAATTATTCAGTGTTGAATCCGGTCAAGTTAGTCTTGCTGCGCCATAATTTTTTGATGTTACCCATC\n+TTTGAATAAACCTATATTTGCTAGGGAGAAACCATGAGTTCAG'..b'ATAGGTACTTCAATCATAAAGCATGAGCCTTTGCCCAACTCTGAGTAAACATGAACAGGGTA\n+ATTTAGCAAACCTGTCATACGTTGTACGATGGCAAGTCCTAGCCCTAAACCTTGTTCACCCCAAGGTGATAAATGCCCAC\n+AGCGCTCAAACTCTTGGAATAGCTTAATCCGTTGTTCTTCGGCAATACCAGGTCCAGTATCCCAAACCCCAATTCGAATA\n+TGTCCAGACTGCTGCGCAGAGCGGAGTACACCTACCACCACTCGACCTTTAGCGGTATAACGCAAAGCATTACTGACAAA\n+GTTCTGAATAATACGACGAATCCACTGCGGGTCGGTATCGATCCAGAAAGACACATCGTGGACTTTCAGTGAGATATTTC\n+GCTGAGCAGCGATCGATTTAAACTGCAACTCAAGATCACTGAGCAAATCATGCAACGGATAAGGTTGTCTCTTTGGCTGT\n+ATGGTACCGCCTTCCAAACGTGCAATATCGAGTAGGGCAGAGAGCATACTTTCTGCACCATAGAGTGCTCGGTCAAGCTG\n+TTGTAGGGTCTGGCGGTCTTCTTCGGTCGAAATACTTTGCTCAAGAACGGTACTAAACAGACGAGCAGCATGCATAGGCT\n+GTAATAGATCGTGACTTGCCGCGGCAATAAATCGACTCTTTGACATATTGGCCATATCGGCTTGTTCACGTGCAAGCTGT\n+TGCTCAGTTAAGGCATCGGCAAGCTGTTGAGTTCTATCTTTTACGCGGGCTTCAAGCACGGCTTCGTTCGCACGGAAGGC\n+CGTAATATCGGCAAATGTCGTTACAAAGCCTCCACCTGCGATTGGATTTCCTCGCATTTGAATTACACGGCCATCTTTAC\n+GAATACGTTCAAATTCGTGAGCACTTCCCACTTTCATCCAGTGAAGGCGTTTACGCACATGTTCTTCAACTGAACCGGGA\n+CCACATTCACCGCGTTCGGCGTTATAACGAATGAGGTCGGCAATTGGGCAGCCCACATAAACGAGGTCTTTTGGGTAACC\n+AAACAGTTTTAAATATTGATTGTTCCATGCGACCAAACACATATTTTTATCAACCACGCTTACCCCTTGGGTCATGTGGT\n+CAATCATGGTCATAAGAAGGTTCTGATTAAAACGTTGCCACTGCGATGCTTGGTCTAAAATATTAGCCACTTGCCCTAAA\n+GCGAGGCCGTTATTAATCATTGCTGTTGTGAGCAACGTACGTGCAGAAGCGGCACCGATAATACCGGCCAGATATTGCTC\n+GGTAAAACGCCACCACATGCCATTGGCAATACTATTTGGGTTGAGGGTGAGGTGATTTTGCTCACAAAAATTTTCGAACG\n+CTTGCGTAGTGGGTTGCTCACCCGTAATTCTTTTGGCTAGGGCAAATAAATCACCCACTTTTAAGCGGGCCGCATCATGA\n+GGAAGATAGGTTAAATCAGTAGATGTGTGCGGTGATGGTAAAGGCTTAGTTTCATAGTAGAAGAAGCTTTCTGCCTGAAT\n+TTGTTCAGCGACGCTTGGCCGATAAATTTTTGAAATCCAGATATATAAAACAATATTTAAGCCGAGTGACCAAATAACAC\n+CGTGAGTTAAAGGTGCAAATGACTCAAAACCAAATAAAGATTCCGGGCGTAGGGCATTAATGCCGAAAGGACCGAAAAGT\n+AAAATACTTTGAGCAGTTTCCTGATAGGCTTCAGGCAAGCTACGCAAAATAGTTGGAAATAGTAATGTATAACTCCACAT\n+TAAAAATCCAATAATAAGTCCTGCATAGACGCCTTGACGGCTTCCGCCACGCCAATACAAACCACCAATCAGTGCAGGTG\n+CAAACTGTGCTACAGCACTAAAGGCCAATAAGCCGAAAACTGAAAGTTGGTTAATGTCATTAAAGAAATGGAAGAATAAA\n+AAGCCAAGTAGCATCACTGCAACAATACTAATACGGCGGCTAAATTTAAGAACTTTAGGTAAGTGCTTATCGTGACGTGA\n+CAGCAACTTAAATCGCCATAGAGCAGGCATAATCAAGTCGTTACTGAGCATAATAGACAATGCTACTGATGACACCAGTA\n+ACATGCCTGTTGAGGCAGAGAACCCGCCTAAAAAGGCCAGTAATGCCAGCCACTCTTGGTTATAACTTAAAGGCAATGAC\n+AGCACAGCCACATCAGGCACGGTCAGAAACTTCGGTGCAGCATGTAAAGCCCAGCTTGCAATCGGAATAATGGCAAGAAT\n+AGTTAAAATGAGATAAACCGCGAACCATTTACGGGCACCGCGAATATGCTTCTCATCGCGTAGCTCGACCACCGCCACGT\n+GGAACTGACGTGGTAAGCAAATAATGGCTAAACCCGCCAATAATGTTTGAATCCAGAAGGTTTCGGGTACACCAAAGAGC\n+TGAACTTCCTGAAAAGTCTGGTTTACATCAGAGGTCATTTGGCTCAGGTTGGCCGGTGATTCAAAAATAAAAAATAAAGC\n+GACACAAAGTAAGGCAAATAACTTCACAAATGATTCAAATGCAACCGCAAGCATGAGGCCGCCGTGTTGCTCCGTGTTTG\n+CAATCTGCCGTGTACCAAAAATCATAGCTAAAATCGCAAGCACACTGGTGAGCAATAACACGCTGTTGGTCGTCGTATGA\n+ATATGCGAGCTTTGCTCCATAATGACCGAGGTACTTAAAGCAATCGCACGCAGCTGTAACGCGAGGTAGGGGATAATTGC\n+AATAACGGCAAGAATAGTCACCAACGATGCGAGTACACCACTTTTACCATAGCGTGCCGCGACAAAGTCAGCGATTGACG\n+AAATCGCATGATGCTGACGAACTCGACCTAGACGCCGCCAGATATCATAACCAAACCAGACAAATAACAGTGGACCTAAA\n+TAAATAGGTAAGAAGATAACGCCTTCACGTACGGCAGCCCCAGTTGCGCCATAGAATGTCCAAGAGGAACAATAGACACC\n+TAAAGTTAAGCTAAATAAAAACATACGGCCACGCGTGCTAAGACGACTGGCATGCTTCTCACCAAAAAAAGCACAGACAA\n+ATAAAAGCGCAATATAAAGAGTGAGCACCCCAATAATCAGCCAGCTGTTCATATGACCTACATAAGTGAAACCTTATGCC\n+TATCATAACCCAAGCCGAAACAAAGCTATAAATTGATTAAATTTTAACGACCAAAGTCTAAGTTACGACTGAGCTGGAAT\n+CTTGCTAACTTTAATAATGAAAAAATACATTAAAAAAAAGTGACCAAGGTTGGGCACTATGTAAGGAGTTTGGTTATGGA\n+TCAAAGCCAAGTAGAACAGATTCTACGTAATCCAAAGTTTCAAAAAATGGTCAAGAAAAAAAGTGCATTAAGCTGGACGC\n+TCACAATCATCATGTTAGTGCTTTATGTGGGCTTTATGCTACTTGTGGGCTACAACAAAGAATTTTTGATGAGTTCCTTT\n+AGTGGTGGTGTAACGACATGGGGGATCCCGCTAGGTTTAGGAATTATTGTTTTATCTTTCCTACTTTGTGGTGTGTATTC\n+CTATATCGCAAATAATACCCTTGACCAATTGAGTGAAGAAGCGTTGAAGGAAGTTGAAGCCATCACGCATGAGAAAGGAC\n+TACACTAATATGAAATGGAATTCATTCAAAGCGAAAGCCTTATTGGCAGCAGCATCGCTATATTCAACTGTTGCTATGGC\n+AAGCCCGGACTTAGGTGAAGCAGAACAGCAAGCCACCAACTGGCATGCCATTATCATGTTTATCATCTTTGTTGGCTTTA\n+CCTTGTTTATTACCAAATGGGCGGCTAAACAAACTCAATCGGCGCAAGACTTCTATACTGCTGGTGGTGGGATCAGTGGT\n+TTCCAAAACGGTTTGGCGATTGCGGGTGACTATATGTCAGCAGCGTCATTTCTTGGTATTTCTGCAATGGTGTTTAGCTC\n' |
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| diff -r 000000000000 -r 91791b6ecd38 test-data/output --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output Thu Mar 14 16:49:04 2024 +0000 |
| b |
| b'@@ -0,0 +1,357 @@\n+DEFINITION seqnum=1;seqlen=199920;seqhdr="NZ_CP043953.1 Acinetobacter baumannii strain K09-14 chromosome, complete genome";version=Prodigal.v2.6.3;run_type=Single;model="Ab initio";gc_cont=40.29;transl_table=11;uses_sd=1\n+FEATURES Location/Qualifiers\n+ CDS <1..1398\n+ /note="ID=1_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.399;conf=99.99;score=219.18;cscore=215.97;sscore=3.22;rscore=0.00;uscore=3.22;tscore=0.00;"\n+ CDS 1496..2644\n+ /note="ID=1_2;partial=00;start_type=GTG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.393;conf=99.99;score=225.54;cscore=216.22;sscore=9.32;rscore=11.73;uscore=2.17;tscore=-4.58;"\n+ CDS 2659..3741\n+ /note="ID=1_3;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.394;conf=100.00;score=144.77;cscore=148.60;sscore=-3.83;rscore=-6.71;uscore=-1.99;tscore=3.75;"\n+ CDS 3794..6262\n+ /note="ID=1_4;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.416;conf=99.99;score=517.18;cscore=499.02;sscore=18.16;rscore=11.73;uscore=1.97;tscore=3.75;"\n+ CDS 6300..6692\n+ /note="ID=1_5;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.384;conf=100.00;score=70.66;cscore=52.89;sscore=17.76;rscore=11.73;uscore=1.41;tscore=3.75;"\n+ CDS complement(6778..7335)\n+ /note="ID=1_6;partial=00;start_type=ATG;rbs_motif=3Base/5BMM;rbs_spacer=13-15bp;gc_cont=0.360;conf=100.00;score=52.49;cscore=53.71;sscore=-1.22;rscore=-2.38;uscore=-1.95;tscore=3.75;"\n+ CDS complement(7586..9517)\n+ /note="ID=1_7;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.419;conf=99.99;score=346.92;cscore=351.91;sscore=-4.99;rscore=-6.71;uscore=-1.38;tscore=3.75;"\n+ CDS 9774..10778\n+ /note="ID=1_8;partial=00;start_type=ATG;rbs_motif=AGGA;rbs_spacer=5-10bp;gc_cont=0.405;conf=100.00;score=127.26;cscore=109.37;sscore=17.89;rscore=11.45;uscore=2.69;tscore=3.75;"\n+ CDS 11034..12041\n+ /note="ID=1_9;partial=00;start_type=ATG;rbs_motif=AGGA;rbs_spacer=5-10bp;gc_cont=0.403;conf=99.99;score=196.29;cscore=182.36;sscore=13.93;rscore=11.45;uscore=-0.61;tscore=3.75;"\n+ CDS 12384..13388\n+ /note="ID=1_10;partial=00;start_type=ATG;rbs_motif=AGGA;rbs_spacer=5-10bp;gc_cont=0.418;conf=99.99;score=179.16;cscore=162.74;sscore=16.41;rscore=11.45;uscore=1.87;tscore=3.75;"\n+ CDS 13513..13848\n+ /note="ID=1_11;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.435;conf=100.00;score=47.88;cscore=31.79;sscore=16.09;rscore=11.73;uscore=0.61;tscore=3.75;"\n+ CDS complement(13905..14750)\n+ /note="ID=1_12;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.371;conf=100.00;score=88.92;cscore=74.85;sscore=14.07;rscore=5.25;uscore=5.06;tscore=3.75;"\n+ CDS complement(14878..16005)\n+ /note="ID=1_13;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.421;conf=99.99;score=199.10;cscore=190.49;sscore=8.61;rscore=5.25;uscore=0.26;tscore=3.75;"\n+ CDS 16085..17299\n+ /note="ID=1_14;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.395;conf=99.99;score=247.97;cscore=237.49;sscore=10.48;rscore=5.25;uscore=1.48;tscore=3.75;"\n+ CDS complement(22677..23045)\n+ /note="ID=1_15;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=11-12bp;gc_cont=0.545;conf=57.05;score=1.23;cscore=0.79;sscore=0.44;rscore=0.12;uscore=-2.78;tscore=3.75;"\n+ CDS 23636..24235\n+ /note="ID=1_16;partial=00;start_type=ATG;rbs_motif=AGxAGG/'..b'.83;cscore=-2.94;sscore=3.77;rscore=2.71;uscore=-0.37;tscore=1.94;"\n+ CDS 182824..183126\n+ /note="ID=1_162;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.396;conf=100.00;score=43.35;cscore=43.66;sscore=-0.31;rscore=-6.71;uscore=2.64;tscore=3.75;"\n+ CDS 183155..184213\n+ /note="ID=1_163;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.427;conf=99.99;score=255.34;cscore=232.48;sscore=22.87;rscore=11.73;uscore=6.42;tscore=3.75;"\n+ CDS 184382..185674\n+ /note="ID=1_164;partial=00;start_type=TTG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.415;conf=99.99;score=186.70;cscore=183.93;sscore=2.77;rscore=11.73;uscore=2.04;tscore=-11.00;"\n+ CDS 185671..186378\n+ /note="ID=1_165;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.394;conf=100.00;score=113.22;cscore=104.69;sscore=8.54;rscore=-6.71;uscore=3.49;tscore=3.75;"\n+ CDS complement(186358..187338)\n+ /note="ID=1_166;partial=00;start_type=GTG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.384;conf=100.00;score=154.08;cscore=148.88;sscore=5.20;rscore=5.25;uscore=4.53;tscore=-4.58;"\n+ CDS complement(187451..188026)\n+ /note="ID=1_167;partial=00;start_type=ATG;rbs_motif=AGGA;rbs_spacer=5-10bp;gc_cont=0.387;conf=100.00;score=52.06;cscore=37.36;sscore=14.70;rscore=11.45;uscore=0.15;tscore=3.75;"\n+ CDS 188321..190270\n+ /note="ID=1_168;partial=00;start_type=ATG;rbs_motif=AGGA;rbs_spacer=5-10bp;gc_cont=0.448;conf=99.99;score=332.21;cscore=317.79;sscore=14.43;rscore=11.45;uscore=-0.77;tscore=3.75;"\n+ CDS complement(190317..190910)\n+ /note="ID=1_169;partial=00;start_type=TTG;rbs_motif=AGGA/GGAG/GAGG;rbs_spacer=11-12bp;gc_cont=0.357;conf=100.00;score=95.95;cscore=94.57;sscore=1.38;rscore=8.94;uscore=4.10;tscore=-11.00;"\n+ CDS 190965..191378\n+ /note="ID=1_170;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.362;conf=99.99;score=42.62;cscore=48.41;sscore=-5.79;rscore=-6.71;uscore=-2.84;tscore=3.75;"\n+ CDS complement(191470..192582)\n+ /note="ID=1_171;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.425;conf=99.99;score=210.20;cscore=190.78;sscore=19.42;rscore=11.73;uscore=3.14;tscore=3.75;"\n+ CDS complement(192627..193364)\n+ /note="ID=1_172;partial=00;start_type=ATG;rbs_motif=AGGA;rbs_spacer=5-10bp;gc_cont=0.424;conf=100.00;score=140.88;cscore=122.39;sscore=18.49;rscore=11.45;uscore=3.94;tscore=3.75;"\n+ CDS 193741..194391\n+ /note="ID=1_173;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.399;conf=100.00;score=111.29;cscore=113.20;sscore=-1.91;rscore=-6.71;uscore=1.05;tscore=3.75;"\n+ CDS complement(194434..195201)\n+ /note="ID=1_174;partial=00;start_type=ATG;rbs_motif=AGGA;rbs_spacer=5-10bp;gc_cont=0.409;conf=100.00;score=121.34;cscore=106.11;sscore=15.23;rscore=11.45;uscore=0.68;tscore=3.75;"\n+ CDS complement(195595..199092)\n+ /note="ID=1_175;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=3-4bp;gc_cont=0.443;conf=99.99;score=502.28;cscore=508.16;sscore=-5.88;rscore=-6.17;uscore=-2.82;tscore=3.75;"\n+ CDS 199276..199608\n+ /note="ID=1_176;partial=00;start_type=ATG;rbs_motif=AGGAG;rbs_spacer=5-10bp;gc_cont=0.390;conf=100.00;score=45.22;cscore=29.52;sscore=15.70;rscore=13.20;uscore=-1.26;tscore=3.75;"\n+ CDS 199610..>199918\n+ /note="ID=1_177;partial=01;start_type=ATG;rbs_motif=AGGA;rbs_spacer=5-10bp;gc_cont=0.447;conf=100.00;score=45.51;cscore=30.66;sscore=14.85;rscore=11.45;uscore=-1.62;tscore=3.75;"\n+//\n' |
| b |
| diff -r 000000000000 -r 91791b6ecd38 test-data/output.faa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.faa Thu Mar 14 16:49:04 2024 +0000 |
| b |
| b'@@ -0,0 +1,1232 @@\n+>NZ_CP043953.1_1 # 1 # 1398 # 1 # ID=1_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.399\n+MLWTDCLTRLRQELSDNVFAMWIRPLVAEEVEGILRLYAPNPYWTRYIQENHLELISILA\n+EQLSEGRVRQVEILVDSRPGSILSSSEQPATTTAALQTAPIPQPAKVKREPEPVANTAVS\n+SKSSKKKLLNPQFTFSLFVEGRSNQMAAETCRKVLTQLGASQHNPLFLYGPTGLGKTHLM\n+QAVGNALLQAKPNARVMYMTSESFVQDFVSSLQKGKVEEFKKNCRSLDLLLVDDIHLLAG\n+KEASLVEFFYTFNALLDESKQIILTSDRYPKELTELDPRLVSRFSWGLSVGVEPPDIETR\n+IEILLKKAENSGVDLPRNCALFIAQQVVANVRELEGALNKVVAISRFKGAPIDLDVVRES\n+LKDVLAIRARTISVENIQRVVSEYFRIPLKELVGPKRTRIYARPRQLAMGLARELTGDSF\n+PEIGMAFGGRDHSTVMHACEKVVSLREEDPIFDEDYKNLLRLLQS*\n+>NZ_CP043953.1_2 # 1496 # 2644 # 1 # ID=1_2;partial=00;start_type=GTG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.393\n+MRLKIAKESLLNVLSHVVGAVERRHTLNILSNVKIQTNAQALTITGSDLEVELVASTALS\n+EGACLEAGETTVPARKLMEICKSLPTAALIDLQITEDQRCILKSGNSRFVLGTLPAEDYP\n+LLTTENSQGTQVQVTQRELKRLFEKTAFAMAVQDVRFYLTGTLLEIDENQLRAVTTDGHR\n+LALCEILASSTSSQLVQAIVPRKAVGELQRLLSIEDEQLTLLIGRELLNVTINTPSRDKE\n+QGDITVRFTTKLIDGKFPDYRRVIPRGGDKHVLIGHDVFKQSLQRVAILSNEKLRGVFLN\n+FNQDSLQLRANNPEQDEAIEDLAIQYQSAPLEMSFNAQYLLDVLGVLDGDDVNMSMTEAN\n+QSVLVQDPAHPDQTYVVMPMRV*\n+>NZ_CP043953.1_3 # 2659 # 3741 # 1 # ID=1_3;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.394\n+MHLTRLNIERVRNLKTVALHGLQPFNVFYGANGSGKTSILEAIHLLATGRSFRTHIPKNY\n+IQYEADDAIVFAQSATEKIGMQKLASGEQLMKVNGDTVATQGQLAKLLPLQHIDPQSTDI\n+IDHGAKPRRQLLDWLMFHVEPEFYFAWQYYSRALKQRNTLLKTRRNLSLADLEPWNKMLS\n+DYGEILHSQRLSIVEQWNVYFQNDLSQLLPDLEIELEYSPGFHTEQGLMQDLLNQHQKDI\n+ERRYTEYGPHRADLRLKTPFGHADDVLSRGQKKLLIIALKLSQIAMLHASNKETVVLLDD\n+LTAELDLTAQQRLIERLSQLGSQVFMTTLDHASVKKHLHDLSISYQLFSVESGQVSLAAP\n+*\n+>NZ_CP043953.1_4 # 3794 # 6262 # 1 # ID=1_4;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.416\n+MSSESQSASQTEQTNEKAYDSSSIKVLRGLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDN\n+AIDEALAGHCDEIIVTIHEDESVSVSDNGRGIPTDIHPEEGVSAAEVILTILHAGGKFDD\n+NSYKVSGGLHGVGVSVVNALSSKLHLTIYRAGQIHEQEYHHGDPQYPLRVIGETDNTGTT\n+VRFWPSAETFSQTIFNVEILARRLRELSFLNAGVRIVLRDERINLEHVYDYEGGLSEFVK\n+YINEGKNHLNEIFHFTADADNGITVEVALQWNDSYQENVRCFTNNIPQKDGGTHLAGFRA\n+ALTRGLNQYLENENILKKEKVNVTGDDAREGLTAIISVKVPDPKFSSQTKEKLVSSEVKP\n+AVEQAMNKEFSAYLLENPQAAKSIAGKIIDAARARDAARKAREMTRRKSALDIAGLPGKL\n+ADCQEKDPALSELYLVEGDSAGGSAKQGRNRKMQAILPLKGKILNVERARFDKMISSQEV\n+GTLITALGCGIGREEYNPDKLRYHKIIIMTDADVDGSHIRTLLLTFFFRQMPELVERGHI\n+YIAQPPLYKLKKGKQEQYIKDNDALETYLISNAIDELALHISADAPAITGEALAKVIQDY\n+QVSQKSLQRLTLRYPASLLDALLEVDAFKADQNHDQAYVQQWADQVREAVEKLQPSLRPE\n+ITLETFERENAQGEKSAHYWPRVTVYVHNLPHAYLLDAGLLNSAEYARLLKNSKSWFKLI\n+EDGAYLQKGDRRIQVANFHQVWQHILQDSRRGMMIQRYKGLGEMNAEQLWETTMDPENRN\n+MLQVTIDDAIEADRMFSCLMGDDVEPRRAFIEENALNADIDA*\n+>NZ_CP043953.1_5 # 6300 # 6692 # 1 # ID=1_5;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.384\n+MMSQKILASMLISCAALVSHSAFAADLEADMKTLAKSTKAFAEAKDIDNAKQQLVIMRQA\n+ALSSKLSLPHKLEGLPPENVQVKEYQAGLDQLVAEIDRVTVFVDKGQLDQAKTEAINLVN\n+IRNENHKKFR*\n+>NZ_CP043953.1_6 # 6778 # 7335 # -1 # ID=1_6;partial=00;start_type=ATG;rbs_motif=3Base/5BMM;rbs_spacer=13-15bp;gc_cont=0.360\n+MNFIDFITNFEQFLPILIQEYGAWVYAILFLIIFSETAFVFMFFLPGDSLLLTVGALCSV\n+VELMHLGYMITLLTIAATLGYIVNYSIGRHFGNRIFEAKSRFIKKEYLNKTNRYFLQHGG\n+KTILLARFIPFARSFAPLAAGSSNMSYGKFLIYNVAGAILWICILLTAGYLFGHALIQVT\n+DFVEN*\n+>NZ_CP043953.1_7 # 7586 # 9517 # -1 # ID=1_7;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.419\n+MIQFDQVSLRRGGRVLFQKASMQLHPGWKIGLTGVNGAGKSTLFAALLGSLGADEGSLTR\n+PSVWTVAHMAQEVKALDMPAIDFVLSGDEEYWDIQNKLAQPEQLTDSDLAKLHGRFDEIH\n+GYSAPSKAAQLMAGLGFLEHQLRLNVASFSGGWRMRLNLARTLMSRSDLLLLDEPTNHLD\n+LDAILWLEDWLKAYEGTLILISHDRDFLDAITDHILHIENQELTLYTGNYSTFETTRSER\n+LAQQQQAFEKQQEARAHLQKFIDRFKAKATKARQAQSRIKQLERMQQLAPAHVDTPFTFS\n+FREPTKMSSPLLTLENASIGYGDKKIAEKIKLQITPNSRIGLLGMNGAGKSTLIKSLVGD\n+LPLLAGERKASELLNIGYFAQHQMDALDGQASPMLQLARIADKQISEATLRSFLGSFGFS\n+GERMDTPCESFSGGERARLALALIVWQRPNVLILDEPTNHLDLDMRHALSMALQDFEGAV\n+VLVSHERQLIASVCDELLLVHGGKCTEFEGDLQDYAKWLREARQQQINAQTAVAQNNSSS\n+AAPTPAKVDKEAQRKEAARRREQTRPIRKNIEKVESQIEQLQPRLAEIEEALADTSLYEA\n+NRKDDLLKLMNEQTELKAKLEQYEEQLLELMMELEEMEASFEN*\n+>NZ_CP043953.1_8 # 9774 # 10778 # 1'..b't_type=TTG;rbs_motif=AGGA/GGAG/GAGG;rbs_spacer=11-12bp;gc_cont=0.357\n+MWAENNLVLSYTNKSILMKQALLVIDVQNDYFKNGKMELVGPDQALDKIKQLEQYFNEKD\n+LSIIYVQHINPPQASFFQENTEGVLLHPELSAGGDSLIVTKHYPNSFLETNLKELLKAHQ\n+IEQLVITGMMTHICIDSGTRAAKELGYQPILIGDATATRDLSHNGKTVKAEDVQTAFLAA\n+LGMFASVQNTADFLAKS*\n+>NZ_CP043953.1_170 # 190965 # 191378 # 1 # ID=1_170;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.362\n+MNIELDPIDLKIIALLKQDSRLTNKEIGQRVHRTGQAVGARIAQLMDAGVIKNYTIAVQY\n+RHKQFIHLHLNEQRSFEEIENLVKQYEQIDECFKVMGNACYMIVSHFEPAELNAFIEVLS\n+KWCRYSVETVIREVEKA*\n+>NZ_CP043953.1_171 # 191470 # 192582 # -1 # ID=1_171;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.425\n+MTQLQQPIKFAYWVPNVSGGLVVSNIEQRTDWSYDYNVRLAQAAENNGFEYALTQIRFTA\n+GYGAENQHESVSFSHALLAKTEKLKVIAAILPGPWKPALAAKQLATIDYLTQGRIAINVV\n+SGWFRGEFDAIGEEWPEHDERYVRSEEFIRTLKGIWTTDNYSFDGKYYQFQNYTLKPKPL\n+QKPHIEVFQGGSSRAARDMASRVSDWYFTNGNTVEEIQKQVEDIRAKAKANNHQVKIGVN\n+AFIIARDTEEEAKAVLQEIIDKANTEAVNAFGDATREAGAASPEQEGNWAKSTFEDLVQY\n+NDGFKTNLIGTPQQIAERIVALKNVGVDLVLSGFLHFIEEVEYFGEKVLPLVRQLELQQE\n+KEVEIQAKSA*\n+>NZ_CP043953.1_172 # 192627 # 193364 # -1 # ID=1_172;partial=00;start_type=ATG;rbs_motif=AGGA;rbs_spacer=5-10bp;gc_cont=0.424\n+MTGITSSKPLNIVAVSGGLNTPSKTESLVQAILDELSEAIDIKVHFIKLSEIGPLLGGAF\n+YRNQLPQRVQDDLAAVEAADALIVGTPVYRASFTGLFKHFFDFVEQTALVDVPVLLAASG\n+GSDRHALVLEHQLRPLFSFFQAQTLPIGVYATDRDFTPEYTVKSEQLSDRITLAVARALP\n+ILEWAPAKGKRAEVVKPKSQQANQELGINKQIEQEEVLPSAAVPNLDAAESRLHHKSGKS\n+LTHVA*\n+>NZ_CP043953.1_173 # 193741 # 194391 # 1 # ID=1_173;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.399\n+MNILIVDDHPLFRHALIQAVRYSLPQAQIHETASVDEFYERLENGAEPDLVLLDLNLPGA\n+SGFSALVYVRAQYPSIPIIVVSAHEEASIIQRAIAHGAMGYIPKSAHPSHIGEAIRQVLD\n+GEIWLPPNLPSNINLDPRAADETALAERIQSLTPQQFRVLMMVAEGLLNKQIAYELDVSE\n+ATIKAHVTAIFRKLGVQNRTQAVLAISALNIEDKKI*\n+>NZ_CP043953.1_174 # 194434 # 195201 # -1 # ID=1_174;partial=00;start_type=ATG;rbs_motif=AGGA;rbs_spacer=5-10bp;gc_cont=0.409\n+MNISDNTPQGQLSSQQFYRQYSANALLPELDWQSIFPHSKLSEAHIKALNTIYQCAVPLA\n+LNVFHDLNFDVFAPAAYHPQGLGLFDKLAQQEENFLKVLTAESENLDHETRHQIWSMLLR\n+GGAVLVFKAWLGHVKLGENQLDMTQFDELSDLLFIKTPPHQLAERLHVDEKAKLDHIFLM\n+YGNDIFLDRFNSLETAALFVDLGVYDAAFLSLRDDRVAEYLKSKGYVTQEQIDDLQCALN\n+PLYCDSLTPKQDCLA*\n+>NZ_CP043953.1_175 # 195595 # 199092 # -1 # ID=1_175;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=3-4bp;gc_cont=0.443\n+MNSWLIIGVLTLYIALLFVCAFFGEKHASRLSTRGRMFLFSLTLGVYCSSWTFYGATGAA\n+VREGVIFLPIYLGPLLFVWFGYDIWRRLGRVRQHHAISSIADFVAARYGKSGVLASLVTI\n+LAVIAIIPYLALQLRAIALSTSVIMEQSSHIHTTTNSVLLLTSVLAILAMIFGTRQIANT\n+EQHGGLMLAVAFESFVKLFALLCVALFFIFESPANLSQMTSDVNQTFQEVQLFGVPETFW\n+IQTLLAGLAIICLPRQFHVAVVELRDEKHIRGARKWFAVYLILTILAIIPIASWALHAAP\n+KFLTVPDVAVLSLPLSYNQEWLALLAFLGGFSASTGMLLVSSVALSIMLSNDLIMPALWR\n+FKLLSRHDKHLPKVLKFSRRISIVAVMLLGFLFFHFFNDINQLSVFGLLAFSAVAQFAPA\n+LIGGLYWRGGSRQGVYAGLIIGFLMWSYTLLFPTILRSLPEAYQETAQSILLFGPFGINA\n+LRPESLFGFESFAPLTHGVIWSLGLNIVLYIWISKIYRPSVAEQIQAESFFYYETKPLPS\n+PHTSTDLTYLPHDAARLKVGDLFALAKRITGEQPTTQAFENFCEQNHLTLNPNSIANGMW\n+WRFTEQYLAGIIGAASARTLLTTAMINNGLALGQVANILDQASQWQRFNQNLLMTMIDHM\n+TQGVSVVDKNMCLVAWNNQYLKLFGYPKDLVYVGCPIADLIRYNAERGECGPGSVEEHVR\n+KRLHWMKVGSAHEFERIRKDGRVIQMRGNPIAGGGFVTTFADITAFRANEAVLEARVKDR\n+TQQLADALTEQQLAREQADMANMSKSRFIAAASHDLLQPMHAARLFSTVLEQSISTEEDR\n+QTLQQLDRALYGAESMLSALLDIARLEGGTIQPKRQPYPLHDLLSDLELQFKSIAAQRNI\n+SLKVHDVSFWIDTDPQWIRRIIQNFVSNALRYTAKGRVVVGVLRSAQQSGHIRIGVWDTG\n+PGIAEEQRIKLFQEFERCGHLSPWGEQGLGLGLAIVQRMTGLLNYPVHVYSELGKGSCFM\n+IEVPIVEPPKVATPAVQAVPLKTKAYRILCLDNDETILEGMSSLLGRWGYQVFKATEPEQ\n+ALEIIQKENIQVWLIDQHLNHNQLGVDFITQNRQEDVPVALITADSHPELPQQLKELNIV\n+LLKKPLKPASLRAWLSGLKIASTTD*\n+>NZ_CP043953.1_176 # 199276 # 199608 # 1 # ID=1_176;partial=00;start_type=ATG;rbs_motif=AGGAG;rbs_spacer=5-10bp;gc_cont=0.390\n+MDQSQVEQILRNPKFQKMVKKKSALSWTLTIIMLVLYVGFMLLVGYNKEFLMSSFSGGVT\n+TWGIPLGLGIIVLSFLLCGVYSYIANNTLDQLSEEALKEVEAITHEKGLH*\n+>NZ_CP043953.1_177 # 199610 # 199918 # 1 # ID=1_177;partial=01;start_type=ATG;rbs_motif=AGGA;rbs_spacer=5-10bp;gc_cont=0.447\n+MKWNSFKAKALLAAASLYSTVAMASPDLGEAEQQATNWHAIIMFIIFVGFTLFITKWAAK\n+QTQSAQDFYTAGGGISGFQNGLAIAGDYMSAASFLGISAMVFS\n' |
| b |
| diff -r 000000000000 -r 91791b6ecd38 test-data/output.fnn --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.fnn Thu Mar 14 16:49:04 2024 +0000 |
| b |
| b'@@ -0,0 +1,2740 @@\n+>NZ_CP043953.1_1 # 1 # 1398 # 1 # ID=1_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.399\n+ATGCTTTGGACAGACTGCTTAACTCGCTTGCGACAAGAGCTCTCTGATAACGTCTTTGCGATGTGGATTC\n+GCCCTTTAGTAGCTGAAGAAGTAGAGGGGATACTACGTCTCTATGCTCCTAATCCTTATTGGACGCGTTA\n+TATTCAAGAGAATCATTTAGAGTTAATTTCTATATTGGCTGAACAATTGTCAGAAGGGCGGGTGCGTCAG\n+GTTGAAATCTTGGTAGATTCTCGTCCTGGTAGTATTTTGTCTTCTAGTGAACAGCCTGCAACAACTACAG\n+CAGCTTTACAAACTGCCCCTATACCTCAACCTGCTAAGGTTAAAAGAGAACCGGAACCTGTTGCTAATAC\n+TGCAGTTAGTTCTAAGAGTTCAAAAAAGAAACTATTAAATCCACAATTTACTTTTTCACTATTTGTTGAA\n+GGCCGTTCTAACCAAATGGCAGCAGAAACCTGTAGAAAAGTATTAACACAGTTAGGTGCTTCTCAACATA\n+ACCCTTTGTTTTTATATGGTCCGACAGGTCTAGGTAAGACTCACTTAATGCAAGCAGTTGGTAATGCCCT\n+ACTGCAAGCGAAGCCGAATGCAAGAGTCATGTATATGACTTCAGAAAGTTTTGTACAAGATTTTGTGAGC\n+TCATTACAAAAAGGAAAGGTAGAAGAGTTTAAGAAAAATTGCCGTTCTTTAGACTTGTTATTAGTAGATG\n+ATATTCATCTTTTGGCAGGAAAAGAAGCAAGTCTCGTTGAATTCTTCTATACATTTAATGCCTTACTTGA\n+TGAATCTAAACAAATTATTTTAACGTCTGATCGATATCCTAAAGAATTAACAGAACTTGATCCTCGATTG\n+GTTTCTCGTTTTTCCTGGGGGCTATCAGTAGGTGTTGAACCACCTGATATTGAAACTCGAATCGAAATTC\n+TGCTTAAAAAAGCTGAAAATAGTGGCGTTGATTTACCTAGAAACTGTGCGTTGTTTATTGCCCAACAAGT\n+CGTAGCGAACGTACGTGAACTTGAGGGCGCACTGAATAAAGTTGTCGCAATTTCACGTTTTAAAGGTGCT\n+CCAATTGACCTGGATGTCGTACGGGAATCTTTAAAAGATGTTTTAGCGATCCGTGCTCGTACAATTAGTG\n+TAGAAAATATCCAGCGTGTAGTGAGTGAATATTTCCGAATTCCATTAAAAGAGCTGGTAGGTCCAAAGCG\n+TACCCGAATTTATGCTCGACCACGTCAGTTGGCGATGGGGCTTGCCCGTGAATTAACGGGGGATAGTTTT\n+CCTGAAATTGGAATGGCTTTTGGTGGGCGTGATCACAGTACAGTGATGCATGCTTGTGAAAAAGTCGTCA\n+GTTTACGGGAAGAAGACCCAATCTTTGATGAAGATTATAAGAACTTATTACGTTTGCTTCAAAGTTAA\n+>NZ_CP043953.1_2 # 1496 # 2644 # 1 # ID=1_2;partial=00;start_type=GTG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.393\n+GTGCGTTTGAAAATCGCTAAAGAAAGTTTACTCAATGTTTTATCGCATGTGGTCGGTGCGGTAGAACGTC\n+GTCATACCTTGAATATTCTTTCAAACGTCAAAATTCAGACTAATGCTCAAGCGCTCACTATTACGGGTTC\n+CGATTTAGAAGTTGAACTCGTAGCGAGCACCGCTTTATCAGAAGGGGCGTGCCTTGAGGCAGGCGAGACA\n+ACTGTTCCTGCTCGTAAATTGATGGAAATTTGTAAATCTTTGCCTACAGCTGCATTGATTGATTTACAAA\n+TTACTGAAGATCAAAGATGTATTTTAAAATCTGGTAATAGCCGTTTTGTGCTAGGTACACTACCGGCTGA\n+AGATTATCCATTGTTAACCACTGAGAATAGCCAGGGTACGCAAGTACAGGTGACTCAACGTGAATTAAAG\n+CGTTTATTTGAAAAAACTGCTTTTGCAATGGCTGTACAAGATGTACGTTTTTACCTCACTGGTACTTTAT\n+TAGAAATTGATGAAAATCAATTGCGTGCAGTAACAACTGATGGTCACCGTTTAGCACTTTGTGAAATTTT\n+GGCTTCCTCTACTTCATCTCAGTTGGTACAAGCGATTGTGCCTCGTAAAGCTGTGGGCGAATTGCAACGT\n+TTACTCAGCATTGAAGATGAACAGCTCACATTGCTTATTGGCCGTGAATTATTAAATGTAACGATTAATA\n+CGCCAAGCCGTGATAAAGAACAAGGTGATATTACAGTTCGTTTTACAACTAAATTGATTGATGGGAAATT\n+CCCTGATTATCGCCGTGTTATTCCACGTGGTGGTGATAAACATGTTTTGATTGGTCATGACGTATTTAAA\n+CAATCATTACAACGTGTAGCAATTTTAAGTAATGAAAAATTGCGTGGTGTTTTCCTAAATTTCAATCAGG\n+ATTCTTTACAGCTTCGTGCAAATAACCCTGAACAAGATGAAGCAATTGAAGATTTAGCGATCCAATATCA\n+AAGTGCCCCATTAGAAATGTCATTTAATGCTCAATACCTACTCGATGTATTGGGTGTATTAGATGGTGAT\n+GATGTAAATATGAGCATGACTGAGGCGAATCAGTCTGTATTGGTTCAAGATCCGGCTCATCCTGACCAGA\n+CCTATGTGGTTATGCCGATGCGTGTTTAA\n+>NZ_CP043953.1_3 # 2659 # 3741 # 1 # ID=1_3;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.394\n+ATGCATCTTACGCGCTTAAATATTGAACGTGTGCGTAATTTAAAAACGGTTGCACTCCATGGGTTGCAAC\n+CGTTTAATGTCTTTTATGGCGCAAACGGTTCAGGTAAAACATCAATTTTAGAAGCGATCCATTTGCTTGC\n+AACAGGTCGCTCATTCCGTACACATATACCCAAAAATTATATTCAATATGAAGCTGACGACGCGATTGTA\n+TTTGCTCAGTCAGCAACTGAAAAAATTGGTATGCAGAAACTCGCTTCTGGTGAGCAACTCATGAAAGTGA\n+ATGGCGATACCGTTGCGACTCAAGGTCAGCTCGCAAAGTTACTTCCTTTACAGCATATTGATCCACAAAG\n+TACGGATATTATTGATCATGGTGCCAAGCCAAGAAGACAACTTTTAGATTGGCTTATGTTCCACGTGGAA\n+CCTGAATTTTATTTTGCGTGGCAATATTACTCTCGTGCGCTAAAGCAGCGTAATACCTTACTCAAAACAC\n+GGCGTAATCTTTCATTAGCTGATTTAGAACCGTGGAACAAAATGTTGAGTGATTATGGCGAGATTTTGCA\n+CTCACAGCGTTTAAGTATTGTCGAGCAATGGAATGTTTATTTCCAAAATGACTTAAGCCAATTACTCCCT\n+GATTTGGAGATTGAACTGGAATATAGCCCAGGTTTTCATACAGAGCAGGGGCTTATGCAAGACTTGTTGA\n+ATCAGCATCAAAAAGACATCGAGAGACGTTATACCGAGTATGGTCCGCATCGGGCAGATTTGCGCTTAAA\n+AACGCCATTTGGACATGCTGATGATGTTTTATCAAGAGGTCAGAAAAAACTCTTGATTATTGCCTTAAAA\n+CTGTCACAAATTGCAATGTTGCATGCGAGTAATAAGGAAACTGTGGTATTATTAGATGATCTGACAGCAG\n+AATTAGACTTAACCGCACAACAACGTTTAATTGAACGATTAAGCCAACTTGGTAGCCAGGTTTTTATGA'..b'TTTTAGCTATGATTTTTGGTACACGGCAGATTGCAAACACGGAGCAACACGGCGGCCTCAT\n+GCTTGCGGTTGCATTTGAATCATTTGTGAAGTTATTTGCCTTACTTTGTGTCGCTTTATTTTTTATTTTT\n+GAATCACCGGCCAACCTGAGCCAAATGACCTCTGATGTAAACCAGACTTTTCAGGAAGTTCAGCTCTTTG\n+GTGTACCCGAAACCTTCTGGATTCAAACATTATTGGCGGGTTTAGCCATTATTTGCTTACCACGTCAGTT\n+CCACGTGGCGGTGGTCGAGCTACGCGATGAGAAGCATATTCGCGGTGCCCGTAAATGGTTCGCGGTTTAT\n+CTCATTTTAACTATTCTTGCCATTATTCCGATTGCAAGCTGGGCTTTACATGCTGCACCGAAGTTTCTGA\n+CCGTGCCTGATGTGGCTGTGCTGTCATTGCCTTTAAGTTATAACCAAGAGTGGCTGGCATTACTGGCCTT\n+TTTAGGCGGGTTCTCTGCCTCAACAGGCATGTTACTGGTGTCATCAGTAGCATTGTCTATTATGCTCAGT\n+AACGACTTGATTATGCCTGCTCTATGGCGATTTAAGTTGCTGTCACGTCACGATAAGCACTTACCTAAAG\n+TTCTTAAATTTAGCCGCCGTATTAGTATTGTTGCAGTGATGCTACTTGGCTTTTTATTCTTCCATTTCTT\n+TAATGACATTAACCAACTTTCAGTTTTCGGCTTATTGGCCTTTAGTGCTGTAGCACAGTTTGCACCTGCA\n+CTGATTGGTGGTTTGTATTGGCGTGGCGGAAGCCGTCAAGGCGTCTATGCAGGACTTATTATTGGATTTT\n+TAATGTGGAGTTATACATTACTATTTCCAACTATTTTGCGTAGCTTGCCTGAAGCCTATCAGGAAACTGC\n+TCAAAGTATTTTACTTTTCGGTCCTTTCGGCATTAATGCCCTACGCCCGGAATCTTTATTTGGTTTTGAG\n+TCATTTGCACCTTTAACTCACGGTGTTATTTGGTCACTCGGCTTAAATATTGTTTTATATATCTGGATTT\n+CAAAAATTTATCGGCCAAGCGTCGCTGAACAAATTCAGGCAGAAAGCTTCTTCTACTATGAAACTAAGCC\n+TTTACCATCACCGCACACATCTACTGATTTAACCTATCTTCCTCATGATGCGGCCCGCTTAAAAGTGGGT\n+GATTTATTTGCCCTAGCCAAAAGAATTACGGGTGAGCAACCCACTACGCAAGCGTTCGAAAATTTTTGTG\n+AGCAAAATCACCTCACCCTCAACCCAAATAGTATTGCCAATGGCATGTGGTGGCGTTTTACCGAGCAATA\n+TCTGGCCGGTATTATCGGTGCCGCTTCTGCACGTACGTTGCTCACAACAGCAATGATTAATAACGGCCTC\n+GCTTTAGGGCAAGTGGCTAATATTTTAGACCAAGCATCGCAGTGGCAACGTTTTAATCAGAACCTTCTTA\n+TGACCATGATTGACCACATGACCCAAGGGGTAAGCGTGGTTGATAAAAATATGTGTTTGGTCGCATGGAA\n+CAATCAATATTTAAAACTGTTTGGTTACCCAAAAGACCTCGTTTATGTGGGCTGCCCAATTGCCGACCTC\n+ATTCGTTATAACGCCGAACGCGGTGAATGTGGTCCCGGTTCAGTTGAAGAACATGTGCGTAAACGCCTTC\n+ACTGGATGAAAGTGGGAAGTGCTCACGAATTTGAACGTATTCGTAAAGATGGCCGTGTAATTCAAATGCG\n+AGGAAATCCAATCGCAGGTGGAGGCTTTGTAACGACATTTGCCGATATTACGGCCTTCCGTGCGAACGAA\n+GCCGTGCTTGAAGCCCGCGTAAAAGATAGAACTCAACAGCTTGCCGATGCCTTAACTGAGCAACAGCTTG\n+CACGTGAACAAGCCGATATGGCCAATATGTCAAAGAGTCGATTTATTGCCGCGGCAAGTCACGATCTATT\n+ACAGCCTATGCATGCTGCTCGTCTGTTTAGTACCGTTCTTGAGCAAAGTATTTCGACCGAAGAAGACCGC\n+CAGACCCTACAACAGCTTGACCGAGCACTCTATGGTGCAGAAAGTATGCTCTCTGCCCTACTCGATATTG\n+CACGTTTGGAAGGCGGTACCATACAGCCAAAGAGACAACCTTATCCGTTGCATGATTTGCTCAGTGATCT\n+TGAGTTGCAGTTTAAATCGATCGCTGCTCAGCGAAATATCTCACTGAAAGTCCACGATGTGTCTTTCTGG\n+ATCGATACCGACCCGCAGTGGATTCGTCGTATTATTCAGAACTTTGTCAGTAATGCTTTGCGTTATACCG\n+CTAAAGGTCGAGTGGTGGTAGGTGTACTCCGCTCTGCGCAGCAGTCTGGACATATTCGAATTGGGGTTTG\n+GGATACTGGACCTGGTATTGCCGAAGAACAACGGATTAAGCTATTCCAAGAGTTTGAGCGCTGTGGGCAT\n+TTATCACCTTGGGGTGAACAAGGTTTAGGGCTAGGACTTGCCATCGTACAACGTATGACAGGTTTGCTAA\n+ATTACCCTGTTCATGTTTACTCAGAGTTGGGCAAAGGCTCATGCTTTATGATTGAAGTACCTATTGTCGA\n+GCCACCAAAAGTTGCAACACCAGCTGTACAAGCCGTACCTTTAAAAACTAAAGCCTACCGTATTTTGTGC\n+CTAGACAATGATGAAACTATTCTTGAAGGAATGAGTAGTTTATTAGGACGATGGGGTTATCAAGTTTTCA\n+AAGCGACTGAACCTGAACAGGCGCTAGAAATTATTCAAAAAGAGAATATTCAGGTTTGGCTCATTGACCA\n+GCACTTAAACCACAATCAACTTGGCGTTGATTTTATTACTCAAAATCGTCAAGAAGATGTTCCTGTTGCC\n+TTAATTACAGCGGACTCGCACCCTGAATTACCGCAGCAATTAAAAGAACTGAATATTGTTTTACTCAAAA\n+AACCGTTAAAACCTGCTTCATTAAGAGCATGGTTATCTGGGCTTAAAATTGCCAGCACGACAGACTAA\n+>NZ_CP043953.1_176 # 199276 # 199608 # 1 # ID=1_176;partial=00;start_type=ATG;rbs_motif=AGGAG;rbs_spacer=5-10bp;gc_cont=0.390\n+ATGGATCAAAGCCAAGTAGAACAGATTCTACGTAATCCAAAGTTTCAAAAAATGGTCAAGAAAAAAAGTG\n+CATTAAGCTGGACGCTCACAATCATCATGTTAGTGCTTTATGTGGGCTTTATGCTACTTGTGGGCTACAA\n+CAAAGAATTTTTGATGAGTTCCTTTAGTGGTGGTGTAACGACATGGGGGATCCCGCTAGGTTTAGGAATT\n+ATTGTTTTATCTTTCCTACTTTGTGGTGTGTATTCCTATATCGCAAATAATACCCTTGACCAATTGAGTG\n+AAGAAGCGTTGAAGGAAGTTGAAGCCATCACGCATGAGAAAGGACTACACTAA\n+>NZ_CP043953.1_177 # 199610 # 199918 # 1 # ID=1_177;partial=01;start_type=ATG;rbs_motif=AGGA;rbs_spacer=5-10bp;gc_cont=0.447\n+ATGAAATGGAATTCATTCAAAGCGAAAGCCTTATTGGCAGCAGCATCGCTATATTCAACTGTTGCTATGG\n+CAAGCCCGGACTTAGGTGAAGCAGAACAGCAAGCCACCAACTGGCATGCCATTATCATGTTTATCATCTT\n+TGTTGGCTTTACCTTGTTTATTACCAAATGGGCGGCTAAACAAACTCAATCGGCGCAAGACTTCTATACT\n+GCTGGTGGTGGGATCAGTGGTTTCCAAAACGGTTTGGCGATTGCGGGTGACTATATGTCAGCAGCGTCAT\n+TTCTTGGTATTTCTGCAATGGTGTTTAGC\n' |
| b |
| diff -r 000000000000 -r 91791b6ecd38 test-data/output.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.gff Thu Mar 14 16:49:04 2024 +0000 |
| b |
| b'@@ -0,0 +1,180 @@\n+##gff-version 3\n+# Sequence Data: seqnum=1;seqlen=199920;seqhdr="NZ_CP043953.1 Acinetobacter baumannii strain K09-14 chromosome, complete genome"\n+# Model Data: version=Prodigal.v2.6.3;run_type=Single;model="Ab initio";gc_cont=40.29;transl_table=11;uses_sd=1\n+NZ_CP043953.1\tProdigal_v2.6.3\tCDS\t1\t1398\t219.2\t+\t0\tID=1_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.399;conf=99.99;score=219.18;cscore=215.97;sscore=3.22;rscore=0.00;uscore=3.22;tscore=0.00;\n+NZ_CP043953.1\tProdigal_v2.6.3\tCDS\t1496\t2644\t225.5\t+\t0\tID=1_2;partial=00;start_type=GTG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.393;conf=99.99;score=225.54;cscore=216.22;sscore=9.32;rscore=11.73;uscore=2.17;tscore=-4.58;\n+NZ_CP043953.1\tProdigal_v2.6.3\tCDS\t2659\t3741\t144.8\t+\t0\tID=1_3;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.394;conf=100.00;score=144.77;cscore=148.60;sscore=-3.83;rscore=-6.71;uscore=-1.99;tscore=3.75;\n+NZ_CP043953.1\tProdigal_v2.6.3\tCDS\t3794\t6262\t517.2\t+\t0\tID=1_4;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.416;conf=99.99;score=517.18;cscore=499.02;sscore=18.16;rscore=11.73;uscore=1.97;tscore=3.75;\n+NZ_CP043953.1\tProdigal_v2.6.3\tCDS\t6300\t6692\t70.7\t+\t0\tID=1_5;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.384;conf=100.00;score=70.66;cscore=52.89;sscore=17.76;rscore=11.73;uscore=1.41;tscore=3.75;\n+NZ_CP043953.1\tProdigal_v2.6.3\tCDS\t6778\t7335\t52.5\t-\t0\tID=1_6;partial=00;start_type=ATG;rbs_motif=3Base/5BMM;rbs_spacer=13-15bp;gc_cont=0.360;conf=100.00;score=52.49;cscore=53.71;sscore=-1.22;rscore=-2.38;uscore=-1.95;tscore=3.75;\n+NZ_CP043953.1\tProdigal_v2.6.3\tCDS\t7586\t9517\t346.9\t-\t0\tID=1_7;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.419;conf=99.99;score=346.92;cscore=351.91;sscore=-4.99;rscore=-6.71;uscore=-1.38;tscore=3.75;\n+NZ_CP043953.1\tProdigal_v2.6.3\tCDS\t9774\t10778\t127.3\t+\t0\tID=1_8;partial=00;start_type=ATG;rbs_motif=AGGA;rbs_spacer=5-10bp;gc_cont=0.405;conf=100.00;score=127.26;cscore=109.37;sscore=17.89;rscore=11.45;uscore=2.69;tscore=3.75;\n+NZ_CP043953.1\tProdigal_v2.6.3\tCDS\t11034\t12041\t196.3\t+\t0\tID=1_9;partial=00;start_type=ATG;rbs_motif=AGGA;rbs_spacer=5-10bp;gc_cont=0.403;conf=99.99;score=196.29;cscore=182.36;sscore=13.93;rscore=11.45;uscore=-0.61;tscore=3.75;\n+NZ_CP043953.1\tProdigal_v2.6.3\tCDS\t12384\t13388\t179.2\t+\t0\tID=1_10;partial=00;start_type=ATG;rbs_motif=AGGA;rbs_spacer=5-10bp;gc_cont=0.418;conf=99.99;score=179.16;cscore=162.74;sscore=16.41;rscore=11.45;uscore=1.87;tscore=3.75;\n+NZ_CP043953.1\tProdigal_v2.6.3\tCDS\t13513\t13848\t47.9\t+\t0\tID=1_11;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.435;conf=100.00;score=47.88;cscore=31.79;sscore=16.09;rscore=11.73;uscore=0.61;tscore=3.75;\n+NZ_CP043953.1\tProdigal_v2.6.3\tCDS\t13905\t14750\t88.9\t-\t0\tID=1_12;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.371;conf=100.00;score=88.92;cscore=74.85;sscore=14.07;rscore=5.25;uscore=5.06;tscore=3.75;\n+NZ_CP043953.1\tProdigal_v2.6.3\tCDS\t14878\t16005\t199.1\t-\t0\tID=1_13;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.421;conf=99.99;score=199.10;cscore=190.49;sscore=8.61;rscore=5.25;uscore=0.26;tscore=3.75;\n+NZ_CP043953.1\tProdigal_v2.6.3\tCDS\t16085\t17299\t248.0\t+\t0\tID=1_14;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.395;conf=99.99;score=247.97;cscore=237.49;sscore=10.48;rscore=5.25;uscore=1.48;tscore=3.75;\n+NZ_CP043953.1\tProdigal_v2.6.3\tCDS\t22677\t23045\t1.2\t-\t0\tID=1_15;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=11-12bp;gc_cont=0.545;conf=57.05;score=1.23;cscore=0.79;sscore=0.44;rscore=0.12;uscore=-2.78;tscore=3.75;\n+NZ_CP043953.1\tProdigal_v2.6.3\tCDS\t23636\t24235\t81.6\t+\t0\tID=1_16;partial=00;start_type=ATG;rbs_motif=AGxAGG/AGGxGG;rbs_spacer=5-10bp;gc_cont=0.328;conf=100.00;score=81.60;cscore=71.40;sscore=10.20;rscore=1.19;uscore=5.26;tscore=3.75;\n+NZ_CP043953.1\tProdigal_v2.6.3\tCDS\t24293\t24985\t135.2\t-\t0\tID=1_17;partial='..b'=203.41;sscore=-4.70;rscore=-6.71;uscore=-1.75;tscore=3.75;\n+NZ_CP043953.1\tProdigal_v2.6.3\tCDS\t182723\t182854\t0.8\t+\t0\tID=1_161;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.326;conf=54.76;score=0.83;cscore=-2.94;sscore=3.77;rscore=2.71;uscore=-0.37;tscore=1.94;\n+NZ_CP043953.1\tProdigal_v2.6.3\tCDS\t182824\t183126\t43.3\t+\t0\tID=1_162;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.396;conf=100.00;score=43.35;cscore=43.66;sscore=-0.31;rscore=-6.71;uscore=2.64;tscore=3.75;\n+NZ_CP043953.1\tProdigal_v2.6.3\tCDS\t183155\t184213\t255.3\t+\t0\tID=1_163;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.427;conf=99.99;score=255.34;cscore=232.48;sscore=22.87;rscore=11.73;uscore=6.42;tscore=3.75;\n+NZ_CP043953.1\tProdigal_v2.6.3\tCDS\t184382\t185674\t186.7\t+\t0\tID=1_164;partial=00;start_type=TTG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.415;conf=99.99;score=186.70;cscore=183.93;sscore=2.77;rscore=11.73;uscore=2.04;tscore=-11.00;\n+NZ_CP043953.1\tProdigal_v2.6.3\tCDS\t185671\t186378\t113.2\t+\t0\tID=1_165;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.394;conf=100.00;score=113.22;cscore=104.69;sscore=8.54;rscore=-6.71;uscore=3.49;tscore=3.75;\n+NZ_CP043953.1\tProdigal_v2.6.3\tCDS\t186358\t187338\t154.1\t-\t0\tID=1_166;partial=00;start_type=GTG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.384;conf=100.00;score=154.08;cscore=148.88;sscore=5.20;rscore=5.25;uscore=4.53;tscore=-4.58;\n+NZ_CP043953.1\tProdigal_v2.6.3\tCDS\t187451\t188026\t52.1\t-\t0\tID=1_167;partial=00;start_type=ATG;rbs_motif=AGGA;rbs_spacer=5-10bp;gc_cont=0.387;conf=100.00;score=52.06;cscore=37.36;sscore=14.70;rscore=11.45;uscore=0.15;tscore=3.75;\n+NZ_CP043953.1\tProdigal_v2.6.3\tCDS\t188321\t190270\t332.2\t+\t0\tID=1_168;partial=00;start_type=ATG;rbs_motif=AGGA;rbs_spacer=5-10bp;gc_cont=0.448;conf=99.99;score=332.21;cscore=317.79;sscore=14.43;rscore=11.45;uscore=-0.77;tscore=3.75;\n+NZ_CP043953.1\tProdigal_v2.6.3\tCDS\t190317\t190910\t96.0\t-\t0\tID=1_169;partial=00;start_type=TTG;rbs_motif=AGGA/GGAG/GAGG;rbs_spacer=11-12bp;gc_cont=0.357;conf=100.00;score=95.95;cscore=94.57;sscore=1.38;rscore=8.94;uscore=4.10;tscore=-11.00;\n+NZ_CP043953.1\tProdigal_v2.6.3\tCDS\t190965\t191378\t42.6\t+\t0\tID=1_170;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.362;conf=99.99;score=42.62;cscore=48.41;sscore=-5.79;rscore=-6.71;uscore=-2.84;tscore=3.75;\n+NZ_CP043953.1\tProdigal_v2.6.3\tCDS\t191470\t192582\t210.2\t-\t0\tID=1_171;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.425;conf=99.99;score=210.20;cscore=190.78;sscore=19.42;rscore=11.73;uscore=3.14;tscore=3.75;\n+NZ_CP043953.1\tProdigal_v2.6.3\tCDS\t192627\t193364\t140.9\t-\t0\tID=1_172;partial=00;start_type=ATG;rbs_motif=AGGA;rbs_spacer=5-10bp;gc_cont=0.424;conf=100.00;score=140.88;cscore=122.39;sscore=18.49;rscore=11.45;uscore=3.94;tscore=3.75;\n+NZ_CP043953.1\tProdigal_v2.6.3\tCDS\t193741\t194391\t111.3\t+\t0\tID=1_173;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.399;conf=100.00;score=111.29;cscore=113.20;sscore=-1.91;rscore=-6.71;uscore=1.05;tscore=3.75;\n+NZ_CP043953.1\tProdigal_v2.6.3\tCDS\t194434\t195201\t121.3\t-\t0\tID=1_174;partial=00;start_type=ATG;rbs_motif=AGGA;rbs_spacer=5-10bp;gc_cont=0.409;conf=100.00;score=121.34;cscore=106.11;sscore=15.23;rscore=11.45;uscore=0.68;tscore=3.75;\n+NZ_CP043953.1\tProdigal_v2.6.3\tCDS\t195595\t199092\t502.3\t-\t0\tID=1_175;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=3-4bp;gc_cont=0.443;conf=99.99;score=502.28;cscore=508.16;sscore=-5.88;rscore=-6.17;uscore=-2.82;tscore=3.75;\n+NZ_CP043953.1\tProdigal_v2.6.3\tCDS\t199276\t199608\t45.2\t+\t0\tID=1_176;partial=00;start_type=ATG;rbs_motif=AGGAG;rbs_spacer=5-10bp;gc_cont=0.390;conf=100.00;score=45.22;cscore=29.52;sscore=15.70;rscore=13.20;uscore=-1.26;tscore=3.75;\n+NZ_CP043953.1\tProdigal_v2.6.3\tCDS\t199610\t199918\t45.5\t+\t0\tID=1_177;partial=01;start_type=ATG;rbs_motif=AGGA;rbs_spacer=5-10bp;gc_cont=0.447;conf=100.00;score=45.51;cscore=30.66;sscore=14.85;rscore=11.45;uscore=-1.62;tscore=3.75;\n' |
| b |
| diff -r 000000000000 -r 91791b6ecd38 test-data/output.start --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.start Thu Mar 14 16:49:04 2024 +0000 |
| b |
| b'@@ -0,0 +1,7691 @@\n+# Sequence Data: seqnum=1;seqlen=199920;seqhdr="NZ_CP043953.1 Acinetobacter baumannii strain K09-14 chromosome, complete genome"\n+# Run Data: version=Prodigal.v2.6.3;run_type=Single;model="Ab initio";gc_cont=40.29;transl_table=11;uses_sd=1\n+\n+Beg\tEnd\tStd\tTotal\tCodPot\tStrtSc\tCodon\tRBSMot\tSpacer\tRBSScr\tUpsScr\tTypeScr\tGCCont\n+\n+257\t388\t+\t-63.74\t-35.73\t-28.01\tGTG\tNone\tNone\t-13.00\t-5.65\t-8.87\t0.402\n+\n+428\t583\t-\t-49.94\t-20.87\t-29.07\tTTG\tNone\tNone\t-10.96\t0.37\t-17.98\t0.423\n+\n+659\t754\t-\t-16.16\t-19.49\t3.33\tATG\tGGA/GAG/AGG\t5-10bp\t1.95\t0.48\t1.40\t0.302\n+\n+698\t793\t+\t-34.30\t-17.33\t-16.96\tATG\tNone\tNone\t-18.03\t0.17\t1.40\t0.281\n+\n+872\t985\t+\t-52.81\t-21.74\t-31.08\tGTG\tNone\tNone\t-15.11\t-5.16\t-10.31\t0.386\n+875\t985\t+\t-69.70\t-21.37\t-48.33\tTTG\t3Base/5BMM\t13-15bp\t-5.50\t-16.85\t-25.47\t0.378\n+890\t985\t+\t-72.61\t-15.35\t-57.26\tTTG\tNone\tNone\t-18.03\t-9.15\t-29.58\t0.375\n+\n+1115\t1213\t-\t-54.14\t-11.24\t-42.89\tGTG\tNone\tNone\t-17.47\t-13.01\t-11.92\t0.414\n+\n+1\t1398\t+\t219.18\t215.97\t3.22\tEdge\tNone\tNone\t0.00\t3.22\t0.00\t0.399\n+28\t1398\t+\t190.34\t213.83\t-23.49\tTTG\tNone\tNone\t-6.71\t-5.78\t-11.00\t0.398\n+61\t1398\t+\t195.77\t207.50\t-11.73\tATG\tNone\tNone\t-6.71\t-8.78\t3.75\t0.395\n+175\t1398\t+\t148.89\t163.64\t-14.74\tTTG\tGGA/GAG/AGG\t11-12bp\t0.12\t-3.86\t-11.00\t0.397\n+187\t1398\t+\t137.97\t159.12\t-21.15\tTTG\tNone\tNone\t-6.71\t-3.44\t-11.00\t0.397\n+202\t1398\t+\t144.95\t158.05\t-13.10\tGTG\tAGxAG\t5-10bp\t-2.92\t-5.61\t-4.58\t0.394\n+220\t1398\t+\t133.47\t148.19\t-14.72\tTTG\tGGA/GAG/AGG\t5-10bp\t5.25\t-8.97\t-11.00\t0.393\n+247\t1398\t+\t110.44\t134.61\t-24.16\tTTG\tNone\tNone\t-6.71\t-6.45\t-11.00\t0.392\n+436\t1398\t+\t85.59\t90.07\t-4.48\tATG\t3Base/5BMM\t13-15bp\t-2.38\t-5.85\t3.75\t0.395\n+496\t1398\t+\t50.59\t74.06\t-23.48\tTTG\tNone\tNone\t-6.71\t-5.77\t-11.00\t0.394\n+538\t1398\t+\t53.83\t61.77\t-7.95\tATG\t3Base/5BMM\t13-15bp\t-2.38\t-9.32\t3.75\t0.395\n+589\t1398\t+\t41.39\t52.43\t-11.04\tATG\tNone\tNone\t-6.71\t-8.08\t3.75\t0.388\n+595\t1398\t+\t51.91\t50.56\t1.35\tATG\tGGA/GAG/AGG\t5-10bp\t5.25\t-7.65\t3.75\t0.389\n+625\t1398\t+\t25.18\t42.18\t-17.00\tGTG\tNone\tNone\t-6.71\t-5.72\t-4.58\t0.394\n+685\t1398\t+\t11.27\t31.78\t-20.51\tTTG\tNone\tNone\t-6.71\t-2.80\t-11.00\t0.398\n+712\t1398\t+\t3.25\t20.79\t-17.53\tTTG\t3Base/5BMM\t13-15bp\t-2.38\t-4.15\t-11.00\t0.405\n+838\t1398\t+\t-49.50\t-24.94\t-24.55\tTTG\tNone\tNone\t-6.71\t-6.35\t-11.00\t0.422\n+961\t1398\t+\t-81.82\t-59.49\t-22.34\tTTG\tNone\tNone\t-6.71\t-4.13\t-11.00\t0.427\n+1141\t1398\t+\t-143.72\t-126.12\t-17.60\tGTG\tNone\tNone\t-6.71\t-5.81\t-4.58\t0.430\n+1219\t1398\t+\t-186.37\t-149.17\t-37.20\tTTG\tNone\tNone\t-9.47\t-11.69\t-15.54\t0.422\n+1225\t1398\t+\t-170.62\t-150.56\t-20.06\tATG\tNone\tNone\t-9.81\t-12.32\t2.57\t0.414\n+1273\t1398\t+\t-203.15\t-174.35\t-28.80\tATG\tNone\tNone\t-13.63\t-16.52\t1.85\t0.389\n+1303\t1398\t+\t-238.37\t-181.19\t-57.18\tGTG\tNone\tNone\t-18.03\t-26.35\t-12.30\t0.354\n+1306\t1398\t+\t-232.45\t-181.75\t-50.70\tATG\tNone\tNone\t-18.63\t-32.92\t1.35\t0.344\n+\n+1426\t1530\t-\t-60.38\t-5.19\t-55.19\tTTG\tNone\tNone\t-16.44\t-11.28\t-26.97\t0.362\n+\n+1310\t1444\t+\t-45.43\t-28.50\t-16.93\tATG\tNone\tNone\t-12.70\t-5.71\t1.98\t0.341\n+1316\t1444\t+\t-58.79\t-29.30\t-29.48\tGTG\tNone\tNone\t-13.31\t-6.60\t-9.08\t0.341\n+1355\t1444\t+\t-66.27\t-23.48\t-42.79\tTTG\t3Base/5BMM\t13-15bp\t-6.83\t-3.84\t-31.62\t0.300\n+\n+1776\t1943\t-\t-31.62\t-5.99\t-25.63\tTTG\tNone\tNone\t-10.16\t1.70\t-16.67\t0.375\n+\n+2046\t2180\t+\t-55.50\t-32.60\t-22.90\tGTG\tNone\tNone\t-12.70\t-1.03\t-8.67\t0.422\n+2091\t2180\t+\t-91.12\t-27.28\t-63.84\tTTG\tNone\tNone\t-19.27\t-12.45\t-31.62\t0.422\n+\n+2177\t2308\t-\t-38.12\t-26.87\t-11.25\tATG\tNone\tNone\t-13.00\t0.31\t1.94\t0.371\n+2177\t2323\t-\t-34.46\t-26.33\t-8.13\tATG\tNone\tNone\t-11.64\t1.85\t2.16\t0.367\n+2177\t2338\t-\t-60.49\t-28.23\t-32.25\tTTG\tNone\tNone\t-10.55\t-3.91\t-17.30\t0.358\n+\n+2397\t2486\t-\t-28.29\t-7.56\t-20.73\tATG\tNone\tNone\t-19.27\t-2.27\t1.31\t0.389\n+2397\t2498\t-\t-9.10\t-8.32\t-0.78\tATG\tGGA/GAG/AGG\t5-10bp\t2.08\t-3.85\t1.49\t0.373\n+\n+1496\t2644\t+\t225.54\t216.22\t9.32\tGTG\tGGAG/GAGG\t5-10bp\t11.73\t2.17\t-4.58\t0.393\n+1502\t2644\t+\t197.01\t212.65\t-15.64\tTTG\t3Base/5BMM\t13-15bp\t-2.38\t-2.26\t-11.00\t0.391\n+1544\t2644\t+\t190.53\t199.93\t-9.39\tGTG\tNone\tNone\t-6.71\t1.89\t-4.58\t0.395\n+1574\t2644\t+\t163.23\t182.90\t-19.67\tTTG\tNone\tNone\t-6.71\t-1.96\t-11.00\t0.389\n+1724\t2644\t+\t120.13\t141.70\t-21.57\tTTG\tNone\tNone\t-6.71\t-3.86\t-11.00\t0.378\n+1727\t2644\t+\t132.03\t142.2'..b'39\t0.488\n+198090\t198230\t+\t-59.82\t-23.00\t-36.82\tTTG\tNone\tNone\t-12.15\t-4.24\t-19.93\t0.489\n+198123\t198230\t+\t-22.30\t-10.53\t-11.77\tATG\tGGA/GAG/AGG\t5-10bp\t2.20\t-15.05\t1.58\t0.481\n+\n+198367\t198459\t+\t-73.30\t-18.46\t-54.83\tTTG\tNone\tNone\t-18.63\t-5.14\t-30.56\t0.473\n+\n+198363\t198470\t+\t-36.46\t-20.21\t-16.25\tATG\tNone\tNone\t-15.97\t-1.36\t1.58\t0.426\n+\n+198449\t198640\t+\t-51.39\t-27.30\t-24.09\tTTG\t3Base/5BMM\t13-15bp\t-3.14\t-5.90\t-14.55\t0.432\n+198533\t198640\t+\t-51.88\t-38.35\t-13.53\tATG\tNone\tNone\t-15.97\t1.36\t1.58\t0.491\n+\n+198747\t198887\t+\t-39.51\t-22.76\t-16.76\tATG\tNone\tNone\t-12.15\t-6.18\t2.07\t0.461\n+198774\t198887\t+\t-53.30\t-19.65\t-33.66\tGTG\tNone\tNone\t-15.11\t-7.74\t-10.31\t0.465\n+198795\t198887\t+\t-73.94\t-13.32\t-60.62\tTTG\tNone\tNone\t-18.63\t-10.93\t-30.56\t0.430\n+\n+198966\t199073\t-\t-64.16\t-21.10\t-43.06\tTTG\tNone\tNone\t-15.97\t-0.40\t-26.20\t0.407\n+\n+199019\t199126\t-\t-45.98\t-31.99\t-13.99\tATG\tNone\tNone\t-15.97\t0.90\t1.58\t0.361\n+\n+199183\t199284\t-\t-59.69\t-13.26\t-46.43\tTTG\tNone\tNone\t-16.94\t-1.21\t-27.79\t0.324\n+199183\t199290\t-\t-54.84\t-12.03\t-42.81\tTTG\tNone\tNone\t-15.97\t-0.14\t-26.20\t0.333\n+\n+199501\t199590\t-\t-30.63\t-12.94\t-17.69\tATG\tNone\tNone\t-19.27\t0.77\t1.31\t0.411\n+\n+199600\t199716\t-\t-33.33\t-9.34\t-23.98\tGTG\tNone\tNone\t-14.71\t1.26\t-10.03\t0.444\n+199600\t199719\t-\t-49.55\t-9.58\t-39.97\tTTG\tNone\tNone\t-14.33\t-1.63\t-23.51\t0.442\n+199600\t199731\t-\t-22.05\t-11.09\t-10.96\tATG\tNone\tNone\t-13.00\t0.60\t1.94\t0.447\n+199600\t199737\t-\t-26.18\t-15.17\t-11.01\tATG\tNone\tNone\t-12.42\t-0.12\t2.03\t0.442\n+199600\t199746\t-\t-20.99\t-18.65\t-2.34\tATG\t3Base/5BMM\t13-15bp\t-4.13\t0.12\t2.16\t0.429\n+199600\t199776\t-\t-58.98\t-26.91\t-32.07\tTTG\tNone\tNone\t-9.64\t-6.12\t-15.81\t0.407\n+\n+199240\t199608\t+\t22.53\t29.11\t-6.58\tGTG\tNone\tNone\t-6.71\t4.70\t-4.58\t0.398\n+199270\t199608\t+\t11.41\t29.95\t-18.54\tTTG\tNone\tNone\t-6.71\t-0.83\t-11.00\t0.389\n+199276\t199608\t+\t45.22\t29.52\t15.70\tATG\tAGGAG\t5-10bp\t13.20\t-1.26\t3.75\t0.390\n+199327\t199608\t+\t5.86\t11.30\t-5.44\tATG\tNone\tNone\t-6.71\t-2.48\t3.75\t0.401\n+199372\t199608\t+\t16.25\t13.96\t2.29\tATG\t3Base/5BMM\t13-15bp\t-2.54\t1.31\t3.51\t0.401\n+199378\t199608\t+\t-3.17\t10.19\t-13.36\tGTG\tNone\tNone\t-7.35\t-0.99\t-5.02\t0.407\n+199387\t199608\t+\t-6.48\t8.14\t-14.62\tGTG\tNone\tNone\t-7.66\t-1.74\t-5.22\t0.410\n+199396\t199608\t+\t-2.94\t3.93\t-6.88\tATG\tNone\tNone\t-7.98\t-2.04\t3.15\t0.404\n+199405\t199608\t+\t-10.14\t3.11\t-13.25\tGTG\tNone\tNone\t-8.34\t0.78\t-5.69\t0.407\n+199426\t199608\t+\t-33.92\t-0.25\t-33.66\tTTG\tNone\tNone\t-9.32\t-8.57\t-15.28\t0.410\n+199429\t199608\t+\t-17.63\t0.32\t-17.95\tATG\tNone\tNone\t-9.47\t-11.14\t2.66\t0.411\n+199513\t199608\t+\t-63.36\t-26.20\t-37.15\tGTG\tNone\tNone\t-18.03\t-6.32\t-12.30\t0.406\n+\n+199691\t199792\t-\t-57.93\t-1.81\t-56.12\tTTG\tNone\tNone\t-16.94\t-10.89\t-27.79\t0.402\n+199691\t199798\t-\t-52.90\t-1.95\t-50.95\tTTG\tNone\tNone\t-15.97\t-8.28\t-26.20\t0.398\n+199691\t199807\t-\t-45.33\t-3.40\t-41.92\tTTG\tAGxAG\t5-10bp\t-6.40\t-10.90\t-24.13\t0.419\n+199691\t199846\t-\t-37.02\t-5.42\t-31.60\tTTG\tNone\tNone\t-10.96\t-2.16\t-17.98\t0.429\n+\n+199574\t199918\t+\t5.98\t24.72\t-18.74\tTTG\tNone\tNone\t-6.71\t-1.03\t-11.00\t0.443\n+199589\t199918\t+\t21.67\t28.16\t-6.50\tATG\tNone\tNone\t-6.71\t-3.54\t3.75\t0.439\n+199610\t199918\t+\t44.24\t30.66\t13.59\tATG\tAGGA\t5-10bp\t11.45\t-1.62\t3.75\t0.447\n+199643\t199918\t+\t8.02\t27.65\t-19.64\tTTG\tNone\tNone\t-6.71\t-1.93\t-11.00\t0.460\n+199676\t199918\t+\t17.64\t25.35\t-7.70\tATG\tNone\tNone\t-6.71\t-4.75\t3.75\t0.461\n+199736\t199918\t+\t-1.09\t6.50\t-7.60\tATG\tNone\tNone\t-6.71\t-4.64\t3.75\t0.437\n+199763\t199918\t+\t-9.72\t10.20\t-19.92\tTTG\tNone\tNone\t-6.71\t-2.21\t-11.00\t0.455\n+199853\t199918\t+\t-41.93\t-15.47\t-26.46\tTTG\tNone\tNone\t-6.71\t-4.40\t-11.00\t0.455\n+\n+199695\t199919\t+\t-32.41\t-23.25\t-9.17\tGTG\tGGA/GAG/AGG\t5-10bp\t5.25\t-5.49\t-4.58\t0.449\n+199725\t199919\t+\t-30.74\t-18.68\t-12.06\tATG\tNone\tNone\t-6.71\t-4.76\t3.75\t0.431\n+199749\t199919\t+\t-42.98\t-17.15\t-25.83\tTTG\tNone\tNone\t-6.71\t-3.77\t-11.00\t0.450\n+199752\t199919\t+\t-42.06\t-16.55\t-25.51\tTTG\tNone\tNone\t-6.71\t-3.45\t-11.00\t0.452\n+199824\t199919\t+\t-28.80\t-7.70\t-21.10\tGTG\tNone\tNone\t-6.71\t-5.47\t-4.58\t0.469\n+199827\t199919\t+\t-28.19\t-8.58\t-19.61\tGTG\tNone\tNone\t-6.71\t-3.98\t-4.58\t0.462\n+199836\t199919\t+\t-27.98\t-9.54\t-18.44\tGTG\tNone\tNone\t-6.71\t-2.81\t-4.58\t0.452\n+199860\t199919\t+\t-37.69\t-6.33\t-31.36\tTTG\tNone\tNone\t-6.71\t-9.30\t-11.00\t0.433\n+\n' |
| b |
| diff -r 000000000000 -r 91791b6ecd38 test-data/output_c_n_m --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_c_n_m Thu Mar 14 16:49:04 2024 +0000 |
| b |
| b'@@ -0,0 +1,355 @@\n+DEFINITION seqnum=1;seqlen=199920;seqhdr="NZ_CP043953.1 Acinetobacter baumannii strain K09-14 chromosome, complete genome";version=Prodigal.v2.6.3;run_type=Single;model="Ab initio";gc_cont=40.29;transl_table=11;uses_sd=0\n+FEATURES Location/Qualifiers\n+ CDS 1..1398\n+ /note="ID=1_1;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.399;conf=99.99;score=213.00;cscore=215.74;sscore=-2.74;rscore=-6.52;uscore=0.00;tscore=3.78;"\n+ CDS 1496..2644\n+ /note="ID=1_2;partial=00;start_type=GTG;rbs_motif=GAGG;rbs_spacer=8bp;gc_cont=0.393;conf=99.99;score=225.11;cscore=216.25;sscore=8.86;rscore=11.87;uscore=1.89;tscore=-4.90;"\n+ CDS 2659..3741\n+ /note="ID=1_3;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.394;conf=100.00;score=144.76;cscore=148.42;sscore=-3.66;rscore=-6.52;uscore=-2.04;tscore=3.78;"\n+ CDS 3794..6262\n+ /note="ID=1_4;partial=00;start_type=ATG;rbs_motif=GGAG;rbs_spacer=5bp;gc_cont=0.416;conf=99.99;score=517.18;cscore=498.93;sscore=18.25;rscore=11.24;uscore=2.52;tscore=3.78;"\n+ CDS 6300..6692\n+ /note="ID=1_5;partial=00;start_type=ATG;rbs_motif=GGAG;rbs_spacer=5bp;gc_cont=0.384;conf=100.00;score=69.65;cscore=52.88;sscore=16.77;rscore=11.24;uscore=0.87;tscore=3.78;"\n+ CDS complement(6778..7335)\n+ /note="ID=1_6;partial=00;start_type=ATG;rbs_motif=GGA;rbs_spacer=13bp;gc_cont=0.360;conf=100.00;score=54.33;cscore=53.67;sscore=0.66;rscore=-0.41;uscore=-2.06;tscore=3.78;"\n+ CDS complement(7586..9517)\n+ /note="ID=1_7;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.419;conf=99.99;score=347.36;cscore=352.04;sscore=-4.67;rscore=-6.52;uscore=-1.28;tscore=3.78;"\n+ CDS 9774..10778\n+ /note="ID=1_8;partial=00;start_type=ATG;rbs_motif=AGGA;rbs_spacer=7bp;gc_cont=0.405;conf=100.00;score=127.49;cscore=109.43;sscore=18.06;rscore=11.57;uscore=2.71;tscore=3.78;"\n+ CDS 11034..12041\n+ /note="ID=1_9;partial=00;start_type=ATG;rbs_motif=AGGA;rbs_spacer=8bp;gc_cont=0.403;conf=99.99;score=196.31;cscore=182.34;sscore=13.97;rscore=11.57;uscore=-0.73;tscore=3.78;"\n+ CDS 12384..13388\n+ /note="ID=1_10;partial=00;start_type=ATG;rbs_motif=AGGA;rbs_spacer=12bp;gc_cont=0.418;conf=99.99;score=179.07;cscore=162.24;sscore=16.83;rscore=12.10;uscore=1.60;tscore=3.78;"\n+ CDS 13513..13848\n+ /note="ID=1_11;partial=00;start_type=ATG;rbs_motif=GAGG;rbs_spacer=10bp;gc_cont=0.435;conf=100.00;score=47.98;cscore=31.69;sscore=16.28;rscore=11.87;uscore=0.63;tscore=3.78;"\n+ CDS complement(13905..14750)\n+ /note="ID=1_12;partial=00;start_type=ATG;rbs_motif=AGG;rbs_spacer=9bp;gc_cont=0.371;conf=100.00;score=87.46;cscore=74.77;sscore=12.69;rscore=3.54;uscore=5.37;tscore=3.78;"\n+ CDS complement(14878..16005)\n+ /note="ID=1_13;partial=00;start_type=ATG;rbs_motif=GGA;rbs_spacer=8bp;gc_cont=0.421;conf=99.99;score=199.56;cscore=190.39;sscore=9.17;rscore=6.06;uscore=-0.03;tscore=3.78;"\n+ CDS 16085..17299\n+ /note="ID=1_14;partial=00;start_type=ATG;rbs_motif=AGG;rbs_spacer=7bp;gc_cont=0.395;conf=99.99;score=246.51;cscore=237.41;sscore=9.11;rscore=3.54;uscore=1.79;tscore=3.78;"\n+ CDS complement(22677..23045)\n+ /note="ID=1_15;partial=00;start_type=ATG;rbs_motif=AGG;rbs_spacer=12bp;gc_cont=0.545;conf=82.79;score=6.83;cscore=0.83;sscore=6.01;rscore=5.45;uscore=-2.57;tscore=3.78;"\n+ CDS 23636..24235\n+ /note="ID=1_16;partial=00;start_type=ATG;rbs_motif=AGG;rbs_spacer=12bp;gc_cont=0.328;conf=100.00;score=85.40;cscore=71.34;sscore=14.07;rscore=5.45;uscor'..b'type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.421;conf=99.99;score=198.98;cscore=203.40;sscore=-4.41;rscore=-6.52;uscore=-1.68;tscore=3.78;"\n+ CDS 182723..182854\n+ /note="ID=1_161;partial=00;start_type=ATG;rbs_motif=GGA;rbs_spacer=10bp;gc_cont=0.326;conf=55.97;score=1.04;cscore=-2.93;sscore=3.98;rscore=3.13;uscore=-0.60;tscore=1.95;"\n+ CDS 182824..183126\n+ /note="ID=1_162;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.396;conf=100.00;score=43.28;cscore=43.56;sscore=-0.27;rscore=-6.52;uscore=2.46;tscore=3.78;"\n+ CDS 183155..184213\n+ /note="ID=1_163;partial=00;start_type=ATG;rbs_motif=GAGG;rbs_spacer=5bp;gc_cont=0.427;conf=99.99;score=255.63;cscore=232.48;sscore=23.14;rscore=11.87;uscore=6.53;tscore=3.78;"\n+ CDS 184382..185674\n+ /note="ID=1_164;partial=00;start_type=TTG;rbs_motif=GAGG;rbs_spacer=8bp;gc_cont=0.415;conf=99.99;score=187.36;cscore=183.86;sscore=3.50;rscore=11.87;uscore=2.63;tscore=-11.00;"\n+ CDS 185671..186378\n+ /note="ID=1_165;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.394;conf=100.00;score=113.55;cscore=104.89;sscore=8.66;rscore=-6.52;uscore=3.58;tscore=3.78;"\n+ CDS complement(186358..187338)\n+ /note="ID=1_166;partial=00;start_type=GTG;rbs_motif=GAG;rbs_spacer=7bp;gc_cont=0.384;conf=100.00;score=154.40;cscore=149.03;sscore=5.37;rscore=5.38;uscore=4.89;tscore=-4.90;"\n+ CDS complement(187451..188026)\n+ /note="ID=1_167;partial=00;start_type=ATG;rbs_motif=AGGA;rbs_spacer=10bp;gc_cont=0.387;conf=100.00;score=51.83;cscore=37.36;sscore=14.47;rscore=11.57;uscore=-0.22;tscore=3.78;"\n+ CDS 188321..190270\n+ /note="ID=1_168;partial=00;start_type=ATG;rbs_motif=AGGA;rbs_spacer=8bp;gc_cont=0.448;conf=99.99;score=331.82;cscore=317.69;sscore=14.13;rscore=11.57;uscore=-1.22;tscore=3.78;"\n+ CDS complement(190317..190910)\n+ /note="ID=1_169;partial=00;start_type=TTG;rbs_motif=AGGA;rbs_spacer=12bp;gc_cont=0.357;conf=100.00;score=99.44;cscore=94.66;sscore=4.79;rscore=12.10;uscore=4.34;tscore=-11.00;"\n+ CDS 190965..191378\n+ /note="ID=1_170;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.362;conf=99.99;score=42.67;cscore=48.25;sscore=-5.58;rscore=-6.52;uscore=-2.84;tscore=3.78;"\n+ CDS complement(191470..192582)\n+ /note="ID=1_171;partial=00;start_type=ATG;rbs_motif=GGAG;rbs_spacer=8bp;gc_cont=0.425;conf=99.99;score=209.93;cscore=190.86;sscore=19.07;rscore=11.24;uscore=3.25;tscore=3.78;"\n+ CDS complement(192627..193364)\n+ /note="ID=1_172;partial=00;start_type=ATG;rbs_motif=AGGA;rbs_spacer=8bp;gc_cont=0.424;conf=100.00;score=140.91;cscore=122.39;sscore=18.51;rscore=11.57;uscore=3.82;tscore=3.78;"\n+ CDS 193741..194391\n+ /note="ID=1_173;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.399;conf=100.00;score=111.61;cscore=113.22;sscore=-1.62;rscore=-6.52;uscore=1.12;tscore=3.78;"\n+ CDS complement(194434..195201)\n+ /note="ID=1_174;partial=00;start_type=ATG;rbs_motif=AGGA;rbs_spacer=8bp;gc_cont=0.409;conf=100.00;score=121.86;cscore=106.17;sscore=15.68;rscore=11.57;uscore=0.99;tscore=3.78;"\n+ CDS complement(195595..199092)\n+ /note="ID=1_175;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.443;conf=99.99;score=501.67;cscore=507.95;sscore=-6.27;rscore=-6.52;uscore=-2.88;tscore=3.78;"\n+ CDS 199276..199608\n+ /note="ID=1_176;partial=00;start_type=ATG;rbs_motif=AGGA;rbs_spacer=8bp;gc_cont=0.390;conf=100.00;score=43.97;cscore=29.55;sscore=14.42;rscore=11.57;uscore=-0.93;tscore=3.78;"\n+//\n' |
| b |
| diff -r 000000000000 -r 91791b6ecd38 test-data/output_c_n_m.faa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_c_n_m.faa Thu Mar 14 16:49:04 2024 +0000 |
| b |
| b'@@ -0,0 +1,1228 @@\n+>NZ_CP043953.1_1 # 1 # 1398 # 1 # ID=1_1;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.399\n+MLWTDCLTRLRQELSDNVFAMWIRPLVAEEVEGILRLYAPNPYWTRYIQENHLELISILA\n+EQLSEGRVRQVEILVDSRPGSILSSSEQPATTTAALQTAPIPQPAKVKREPEPVANTAVS\n+SKSSKKKLLNPQFTFSLFVEGRSNQMAAETCRKVLTQLGASQHNPLFLYGPTGLGKTHLM\n+QAVGNALLQAKPNARVMYMTSESFVQDFVSSLQKGKVEEFKKNCRSLDLLLVDDIHLLAG\n+KEASLVEFFYTFNALLDESKQIILTSDRYPKELTELDPRLVSRFSWGLSVGVEPPDIETR\n+IEILLKKAENSGVDLPRNCALFIAQQVVANVRELEGALNKVVAISRFKGAPIDLDVVRES\n+LKDVLAIRARTISVENIQRVVSEYFRIPLKELVGPKRTRIYARPRQLAMGLARELTGDSF\n+PEIGMAFGGRDHSTVMHACEKVVSLREEDPIFDEDYKNLLRLLQS*\n+>NZ_CP043953.1_2 # 1496 # 2644 # 1 # ID=1_2;partial=00;start_type=GTG;rbs_motif=GAGG;rbs_spacer=8bp;gc_cont=0.393\n+MRLKIAKESLLNVLSHVVGAVERRHTLNILSNVKIQTNAQALTITGSDLEVELVASTALS\n+EGACLEAGETTVPARKLMEICKSLPTAALIDLQITEDQRCILKSGNSRFVLGTLPAEDYP\n+LLTTENSQGTQVQVTQRELKRLFEKTAFAMAVQDVRFYLTGTLLEIDENQLRAVTTDGHR\n+LALCEILASSTSSQLVQAIVPRKAVGELQRLLSIEDEQLTLLIGRELLNVTINTPSRDKE\n+QGDITVRFTTKLIDGKFPDYRRVIPRGGDKHVLIGHDVFKQSLQRVAILSNEKLRGVFLN\n+FNQDSLQLRANNPEQDEAIEDLAIQYQSAPLEMSFNAQYLLDVLGVLDGDDVNMSMTEAN\n+QSVLVQDPAHPDQTYVVMPMRV*\n+>NZ_CP043953.1_3 # 2659 # 3741 # 1 # ID=1_3;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.394\n+MHLTRLNIERVRNLKTVALHGLQPFNVFYGANGSGKTSILEAIHLLATGRSFRTHIPKNY\n+IQYEADDAIVFAQSATEKIGMQKLASGEQLMKVNGDTVATQGQLAKLLPLQHIDPQSTDI\n+IDHGAKPRRQLLDWLMFHVEPEFYFAWQYYSRALKQRNTLLKTRRNLSLADLEPWNKMLS\n+DYGEILHSQRLSIVEQWNVYFQNDLSQLLPDLEIELEYSPGFHTEQGLMQDLLNQHQKDI\n+ERRYTEYGPHRADLRLKTPFGHADDVLSRGQKKLLIIALKLSQIAMLHASNKETVVLLDD\n+LTAELDLTAQQRLIERLSQLGSQVFMTTLDHASVKKHLHDLSISYQLFSVESGQVSLAAP\n+*\n+>NZ_CP043953.1_4 # 3794 # 6262 # 1 # ID=1_4;partial=00;start_type=ATG;rbs_motif=GGAG;rbs_spacer=5bp;gc_cont=0.416\n+MSSESQSASQTEQTNEKAYDSSSIKVLRGLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDN\n+AIDEALAGHCDEIIVTIHEDESVSVSDNGRGIPTDIHPEEGVSAAEVILTILHAGGKFDD\n+NSYKVSGGLHGVGVSVVNALSSKLHLTIYRAGQIHEQEYHHGDPQYPLRVIGETDNTGTT\n+VRFWPSAETFSQTIFNVEILARRLRELSFLNAGVRIVLRDERINLEHVYDYEGGLSEFVK\n+YINEGKNHLNEIFHFTADADNGITVEVALQWNDSYQENVRCFTNNIPQKDGGTHLAGFRA\n+ALTRGLNQYLENENILKKEKVNVTGDDAREGLTAIISVKVPDPKFSSQTKEKLVSSEVKP\n+AVEQAMNKEFSAYLLENPQAAKSIAGKIIDAARARDAARKAREMTRRKSALDIAGLPGKL\n+ADCQEKDPALSELYLVEGDSAGGSAKQGRNRKMQAILPLKGKILNVERARFDKMISSQEV\n+GTLITALGCGIGREEYNPDKLRYHKIIIMTDADVDGSHIRTLLLTFFFRQMPELVERGHI\n+YIAQPPLYKLKKGKQEQYIKDNDALETYLISNAIDELALHISADAPAITGEALAKVIQDY\n+QVSQKSLQRLTLRYPASLLDALLEVDAFKADQNHDQAYVQQWADQVREAVEKLQPSLRPE\n+ITLETFERENAQGEKSAHYWPRVTVYVHNLPHAYLLDAGLLNSAEYARLLKNSKSWFKLI\n+EDGAYLQKGDRRIQVANFHQVWQHILQDSRRGMMIQRYKGLGEMNAEQLWETTMDPENRN\n+MLQVTIDDAIEADRMFSCLMGDDVEPRRAFIEENALNADIDA*\n+>NZ_CP043953.1_5 # 6300 # 6692 # 1 # ID=1_5;partial=00;start_type=ATG;rbs_motif=GGAG;rbs_spacer=5bp;gc_cont=0.384\n+MMSQKILASMLISCAALVSHSAFAADLEADMKTLAKSTKAFAEAKDIDNAKQQLVIMRQA\n+ALSSKLSLPHKLEGLPPENVQVKEYQAGLDQLVAEIDRVTVFVDKGQLDQAKTEAINLVN\n+IRNENHKKFR*\n+>NZ_CP043953.1_6 # 6778 # 7335 # -1 # ID=1_6;partial=00;start_type=ATG;rbs_motif=GGA;rbs_spacer=13bp;gc_cont=0.360\n+MNFIDFITNFEQFLPILIQEYGAWVYAILFLIIFSETAFVFMFFLPGDSLLLTVGALCSV\n+VELMHLGYMITLLTIAATLGYIVNYSIGRHFGNRIFEAKSRFIKKEYLNKTNRYFLQHGG\n+KTILLARFIPFARSFAPLAAGSSNMSYGKFLIYNVAGAILWICILLTAGYLFGHALIQVT\n+DFVEN*\n+>NZ_CP043953.1_7 # 7586 # 9517 # -1 # ID=1_7;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.419\n+MIQFDQVSLRRGGRVLFQKASMQLHPGWKIGLTGVNGAGKSTLFAALLGSLGADEGSLTR\n+PSVWTVAHMAQEVKALDMPAIDFVLSGDEEYWDIQNKLAQPEQLTDSDLAKLHGRFDEIH\n+GYSAPSKAAQLMAGLGFLEHQLRLNVASFSGGWRMRLNLARTLMSRSDLLLLDEPTNHLD\n+LDAILWLEDWLKAYEGTLILISHDRDFLDAITDHILHIENQELTLYTGNYSTFETTRSER\n+LAQQQQAFEKQQEARAHLQKFIDRFKAKATKARQAQSRIKQLERMQQLAPAHVDTPFTFS\n+FREPTKMSSPLLTLENASIGYGDKKIAEKIKLQITPNSRIGLLGMNGAGKSTLIKSLVGD\n+LPLLAGERKASELLNIGYFAQHQMDALDGQASPMLQLARIADKQISEATLRSFLGSFGFS\n+GERMDTPCESFSGGERARLALALIVWQRPNVLILDEPTNHLDLDMRHALSMALQDFEGAV\n+VLVSHERQLIASVCDELLLVHGGKCTEFEGDLQDYAKWLREARQQQINAQTAVAQNNSSS\n+AAPTPAKVDKEAQRKEAARRREQTRPIRKNIEKVESQIEQLQPRLAEIEEALADTSLYEA\n+NRKDDLLKLMNEQTELKAKLEQYEEQLLELMMELEEMEASFEN*\n+>NZ_CP043953.1_8 # 9774 # 10778 # 1 # ID=1_8;partial=00;start_type=ATG'..b'EGAAEGNLVIKDSWPGQMRTIWGDPD\n+RFIEAYFSTFKNTYFTGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVSHESV\n+AEAAVVGMPHDIKGQGICTFVTLQAGVPESEELRKELISWVRKVLGPVASPDALHWAPAL\n+PKTRSGKIMRRILRKIAANELDSLGDTSTLAEPAVVDQLIATVYPDRQK*\n+>NZ_CP043953.1_169 # 190317 # 190910 # -1 # ID=1_169;partial=00;start_type=TTG;rbs_motif=AGGA;rbs_spacer=12bp;gc_cont=0.357\n+MWAENNLVLSYTNKSILMKQALLVIDVQNDYFKNGKMELVGPDQALDKIKQLEQYFNEKD\n+LSIIYVQHINPPQASFFQENTEGVLLHPELSAGGDSLIVTKHYPNSFLETNLKELLKAHQ\n+IEQLVITGMMTHICIDSGTRAAKELGYQPILIGDATATRDLSHNGKTVKAEDVQTAFLAA\n+LGMFASVQNTADFLAKS*\n+>NZ_CP043953.1_170 # 190965 # 191378 # 1 # ID=1_170;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.362\n+MNIELDPIDLKIIALLKQDSRLTNKEIGQRVHRTGQAVGARIAQLMDAGVIKNYTIAVQY\n+RHKQFIHLHLNEQRSFEEIENLVKQYEQIDECFKVMGNACYMIVSHFEPAELNAFIEVLS\n+KWCRYSVETVIREVEKA*\n+>NZ_CP043953.1_171 # 191470 # 192582 # -1 # ID=1_171;partial=00;start_type=ATG;rbs_motif=GGAG;rbs_spacer=8bp;gc_cont=0.425\n+MTQLQQPIKFAYWVPNVSGGLVVSNIEQRTDWSYDYNVRLAQAAENNGFEYALTQIRFTA\n+GYGAENQHESVSFSHALLAKTEKLKVIAAILPGPWKPALAAKQLATIDYLTQGRIAINVV\n+SGWFRGEFDAIGEEWPEHDERYVRSEEFIRTLKGIWTTDNYSFDGKYYQFQNYTLKPKPL\n+QKPHIEVFQGGSSRAARDMASRVSDWYFTNGNTVEEIQKQVEDIRAKAKANNHQVKIGVN\n+AFIIARDTEEEAKAVLQEIIDKANTEAVNAFGDATREAGAASPEQEGNWAKSTFEDLVQY\n+NDGFKTNLIGTPQQIAERIVALKNVGVDLVLSGFLHFIEEVEYFGEKVLPLVRQLELQQE\n+KEVEIQAKSA*\n+>NZ_CP043953.1_172 # 192627 # 193364 # -1 # ID=1_172;partial=00;start_type=ATG;rbs_motif=AGGA;rbs_spacer=8bp;gc_cont=0.424\n+MTGITSSKPLNIVAVSGGLNTPSKTESLVQAILDELSEAIDIKVHFIKLSEIGPLLGGAF\n+YRNQLPQRVQDDLAAVEAADALIVGTPVYRASFTGLFKHFFDFVEQTALVDVPVLLAASG\n+GSDRHALVLEHQLRPLFSFFQAQTLPIGVYATDRDFTPEYTVKSEQLSDRITLAVARALP\n+ILEWAPAKGKRAEVVKPKSQQANQELGINKQIEQEEVLPSAAVPNLDAAESRLHHKSGKS\n+LTHVA*\n+>NZ_CP043953.1_173 # 193741 # 194391 # 1 # ID=1_173;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.399\n+MNILIVDDHPLFRHALIQAVRYSLPQAQIHETASVDEFYERLENGAEPDLVLLDLNLPGA\n+SGFSALVYVRAQYPSIPIIVVSAHEEASIIQRAIAHGAMGYIPKSAHPSHIGEAIRQVLD\n+GEIWLPPNLPSNINLDPRAADETALAERIQSLTPQQFRVLMMVAEGLLNKQIAYELDVSE\n+ATIKAHVTAIFRKLGVQNRTQAVLAISALNIEDKKI*\n+>NZ_CP043953.1_174 # 194434 # 195201 # -1 # ID=1_174;partial=00;start_type=ATG;rbs_motif=AGGA;rbs_spacer=8bp;gc_cont=0.409\n+MNISDNTPQGQLSSQQFYRQYSANALLPELDWQSIFPHSKLSEAHIKALNTIYQCAVPLA\n+LNVFHDLNFDVFAPAAYHPQGLGLFDKLAQQEENFLKVLTAESENLDHETRHQIWSMLLR\n+GGAVLVFKAWLGHVKLGENQLDMTQFDELSDLLFIKTPPHQLAERLHVDEKAKLDHIFLM\n+YGNDIFLDRFNSLETAALFVDLGVYDAAFLSLRDDRVAEYLKSKGYVTQEQIDDLQCALN\n+PLYCDSLTPKQDCLA*\n+>NZ_CP043953.1_175 # 195595 # 199092 # -1 # ID=1_175;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.443\n+MNSWLIIGVLTLYIALLFVCAFFGEKHASRLSTRGRMFLFSLTLGVYCSSWTFYGATGAA\n+VREGVIFLPIYLGPLLFVWFGYDIWRRLGRVRQHHAISSIADFVAARYGKSGVLASLVTI\n+LAVIAIIPYLALQLRAIALSTSVIMEQSSHIHTTTNSVLLLTSVLAILAMIFGTRQIANT\n+EQHGGLMLAVAFESFVKLFALLCVALFFIFESPANLSQMTSDVNQTFQEVQLFGVPETFW\n+IQTLLAGLAIICLPRQFHVAVVELRDEKHIRGARKWFAVYLILTILAIIPIASWALHAAP\n+KFLTVPDVAVLSLPLSYNQEWLALLAFLGGFSASTGMLLVSSVALSIMLSNDLIMPALWR\n+FKLLSRHDKHLPKVLKFSRRISIVAVMLLGFLFFHFFNDINQLSVFGLLAFSAVAQFAPA\n+LIGGLYWRGGSRQGVYAGLIIGFLMWSYTLLFPTILRSLPEAYQETAQSILLFGPFGINA\n+LRPESLFGFESFAPLTHGVIWSLGLNIVLYIWISKIYRPSVAEQIQAESFFYYETKPLPS\n+PHTSTDLTYLPHDAARLKVGDLFALAKRITGEQPTTQAFENFCEQNHLTLNPNSIANGMW\n+WRFTEQYLAGIIGAASARTLLTTAMINNGLALGQVANILDQASQWQRFNQNLLMTMIDHM\n+TQGVSVVDKNMCLVAWNNQYLKLFGYPKDLVYVGCPIADLIRYNAERGECGPGSVEEHVR\n+KRLHWMKVGSAHEFERIRKDGRVIQMRGNPIAGGGFVTTFADITAFRANEAVLEARVKDR\n+TQQLADALTEQQLAREQADMANMSKSRFIAAASHDLLQPMHAARLFSTVLEQSISTEEDR\n+QTLQQLDRALYGAESMLSALLDIARLEGGTIQPKRQPYPLHDLLSDLELQFKSIAAQRNI\n+SLKVHDVSFWIDTDPQWIRRIIQNFVSNALRYTAKGRVVVGVLRSAQQSGHIRIGVWDTG\n+PGIAEEQRIKLFQEFERCGHLSPWGEQGLGLGLAIVQRMTGLLNYPVHVYSELGKGSCFM\n+IEVPIVEPPKVATPAVQAVPLKTKAYRILCLDNDETILEGMSSLLGRWGYQVFKATEPEQ\n+ALEIIQKENIQVWLIDQHLNHNQLGVDFITQNRQEDVPVALITADSHPELPQQLKELNIV\n+LLKKPLKPASLRAWLSGLKIASTTD*\n+>NZ_CP043953.1_176 # 199276 # 199608 # 1 # ID=1_176;partial=00;start_type=ATG;rbs_motif=AGGA;rbs_spacer=8bp;gc_cont=0.390\n+MDQSQVEQILRNPKFQKMVKKKSALSWTLTIIMLVLYVGFMLLVGYNKEFLMSSFSGGVT\n+TWGIPLGLGIIVLSFLLCGVYSYIANNTLDQLSEEALKEVEAITHEKGLH*\n' |
| b |
| diff -r 000000000000 -r 91791b6ecd38 test-data/output_c_n_m.fnn --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_c_n_m.fnn Thu Mar 14 16:49:04 2024 +0000 |
| b |
| b'@@ -0,0 +1,2732 @@\n+>NZ_CP043953.1_1 # 1 # 1398 # 1 # ID=1_1;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.399\n+ATGCTTTGGACAGACTGCTTAACTCGCTTGCGACAAGAGCTCTCTGATAACGTCTTTGCGATGTGGATTC\n+GCCCTTTAGTAGCTGAAGAAGTAGAGGGGATACTACGTCTCTATGCTCCTAATCCTTATTGGACGCGTTA\n+TATTCAAGAGAATCATTTAGAGTTAATTTCTATATTGGCTGAACAATTGTCAGAAGGGCGGGTGCGTCAG\n+GTTGAAATCTTGGTAGATTCTCGTCCTGGTAGTATTTTGTCTTCTAGTGAACAGCCTGCAACAACTACAG\n+CAGCTTTACAAACTGCCCCTATACCTCAACCTGCTAAGGTTAAAAGAGAACCGGAACCTGTTGCTAATAC\n+TGCAGTTAGTTCTAAGAGTTCAAAAAAGAAACTATTAAATCCACAATTTACTTTTTCACTATTTGTTGAA\n+GGCCGTTCTAACCAAATGGCAGCAGAAACCTGTAGAAAAGTATTAACACAGTTAGGTGCTTCTCAACATA\n+ACCCTTTGTTTTTATATGGTCCGACAGGTCTAGGTAAGACTCACTTAATGCAAGCAGTTGGTAATGCCCT\n+ACTGCAAGCGAAGCCGAATGCAAGAGTCATGTATATGACTTCAGAAAGTTTTGTACAAGATTTTGTGAGC\n+TCATTACAAAAAGGAAAGGTAGAAGAGTTTAAGAAAAATTGCCGTTCTTTAGACTTGTTATTAGTAGATG\n+ATATTCATCTTTTGGCAGGAAAAGAAGCAAGTCTCGTTGAATTCTTCTATACATTTAATGCCTTACTTGA\n+TGAATCTAAACAAATTATTTTAACGTCTGATCGATATCCTAAAGAATTAACAGAACTTGATCCTCGATTG\n+GTTTCTCGTTTTTCCTGGGGGCTATCAGTAGGTGTTGAACCACCTGATATTGAAACTCGAATCGAAATTC\n+TGCTTAAAAAAGCTGAAAATAGTGGCGTTGATTTACCTAGAAACTGTGCGTTGTTTATTGCCCAACAAGT\n+CGTAGCGAACGTACGTGAACTTGAGGGCGCACTGAATAAAGTTGTCGCAATTTCACGTTTTAAAGGTGCT\n+CCAATTGACCTGGATGTCGTACGGGAATCTTTAAAAGATGTTTTAGCGATCCGTGCTCGTACAATTAGTG\n+TAGAAAATATCCAGCGTGTAGTGAGTGAATATTTCCGAATTCCATTAAAAGAGCTGGTAGGTCCAAAGCG\n+TACCCGAATTTATGCTCGACCACGTCAGTTGGCGATGGGGCTTGCCCGTGAATTAACGGGGGATAGTTTT\n+CCTGAAATTGGAATGGCTTTTGGTGGGCGTGATCACAGTACAGTGATGCATGCTTGTGAAAAAGTCGTCA\n+GTTTACGGGAAGAAGACCCAATCTTTGATGAAGATTATAAGAACTTATTACGTTTGCTTCAAAGTTAA\n+>NZ_CP043953.1_2 # 1496 # 2644 # 1 # ID=1_2;partial=00;start_type=GTG;rbs_motif=GAGG;rbs_spacer=8bp;gc_cont=0.393\n+GTGCGTTTGAAAATCGCTAAAGAAAGTTTACTCAATGTTTTATCGCATGTGGTCGGTGCGGTAGAACGTC\n+GTCATACCTTGAATATTCTTTCAAACGTCAAAATTCAGACTAATGCTCAAGCGCTCACTATTACGGGTTC\n+CGATTTAGAAGTTGAACTCGTAGCGAGCACCGCTTTATCAGAAGGGGCGTGCCTTGAGGCAGGCGAGACA\n+ACTGTTCCTGCTCGTAAATTGATGGAAATTTGTAAATCTTTGCCTACAGCTGCATTGATTGATTTACAAA\n+TTACTGAAGATCAAAGATGTATTTTAAAATCTGGTAATAGCCGTTTTGTGCTAGGTACACTACCGGCTGA\n+AGATTATCCATTGTTAACCACTGAGAATAGCCAGGGTACGCAAGTACAGGTGACTCAACGTGAATTAAAG\n+CGTTTATTTGAAAAAACTGCTTTTGCAATGGCTGTACAAGATGTACGTTTTTACCTCACTGGTACTTTAT\n+TAGAAATTGATGAAAATCAATTGCGTGCAGTAACAACTGATGGTCACCGTTTAGCACTTTGTGAAATTTT\n+GGCTTCCTCTACTTCATCTCAGTTGGTACAAGCGATTGTGCCTCGTAAAGCTGTGGGCGAATTGCAACGT\n+TTACTCAGCATTGAAGATGAACAGCTCACATTGCTTATTGGCCGTGAATTATTAAATGTAACGATTAATA\n+CGCCAAGCCGTGATAAAGAACAAGGTGATATTACAGTTCGTTTTACAACTAAATTGATTGATGGGAAATT\n+CCCTGATTATCGCCGTGTTATTCCACGTGGTGGTGATAAACATGTTTTGATTGGTCATGACGTATTTAAA\n+CAATCATTACAACGTGTAGCAATTTTAAGTAATGAAAAATTGCGTGGTGTTTTCCTAAATTTCAATCAGG\n+ATTCTTTACAGCTTCGTGCAAATAACCCTGAACAAGATGAAGCAATTGAAGATTTAGCGATCCAATATCA\n+AAGTGCCCCATTAGAAATGTCATTTAATGCTCAATACCTACTCGATGTATTGGGTGTATTAGATGGTGAT\n+GATGTAAATATGAGCATGACTGAGGCGAATCAGTCTGTATTGGTTCAAGATCCGGCTCATCCTGACCAGA\n+CCTATGTGGTTATGCCGATGCGTGTTTAA\n+>NZ_CP043953.1_3 # 2659 # 3741 # 1 # ID=1_3;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.394\n+ATGCATCTTACGCGCTTAAATATTGAACGTGTGCGTAATTTAAAAACGGTTGCACTCCATGGGTTGCAAC\n+CGTTTAATGTCTTTTATGGCGCAAACGGTTCAGGTAAAACATCAATTTTAGAAGCGATCCATTTGCTTGC\n+AACAGGTCGCTCATTCCGTACACATATACCCAAAAATTATATTCAATATGAAGCTGACGACGCGATTGTA\n+TTTGCTCAGTCAGCAACTGAAAAAATTGGTATGCAGAAACTCGCTTCTGGTGAGCAACTCATGAAAGTGA\n+ATGGCGATACCGTTGCGACTCAAGGTCAGCTCGCAAAGTTACTTCCTTTACAGCATATTGATCCACAAAG\n+TACGGATATTATTGATCATGGTGCCAAGCCAAGAAGACAACTTTTAGATTGGCTTATGTTCCACGTGGAA\n+CCTGAATTTTATTTTGCGTGGCAATATTACTCTCGTGCGCTAAAGCAGCGTAATACCTTACTCAAAACAC\n+GGCGTAATCTTTCATTAGCTGATTTAGAACCGTGGAACAAAATGTTGAGTGATTATGGCGAGATTTTGCA\n+CTCACAGCGTTTAAGTATTGTCGAGCAATGGAATGTTTATTTCCAAAATGACTTAAGCCAATTACTCCCT\n+GATTTGGAGATTGAACTGGAATATAGCCCAGGTTTTCATACAGAGCAGGGGCTTATGCAAGACTTGTTGA\n+ATCAGCATCAAAAAGACATCGAGAGACGTTATACCGAGTATGGTCCGCATCGGGCAGATTTGCGCTTAAA\n+AACGCCATTTGGACATGCTGATGATGTTTTATCAAGAGGTCAGAAAAAACTCTTGATTATTGCCTTAAAA\n+CTGTCACAAATTGCAATGTTGCATGCGAGTAATAAGGAAACTGTGGTATTATTAGATGATCTGACAGCAG\n+AATTAGACTTAACCGCACAACAACGTTTAATTGAACGATTAAGCCAACTTGGTAGCCAGGTTTTTATGAC\n+AACTTT'..b'TTTTTG\n+GTGAGAAGCATGCCAGTCGTCTTAGCACGCGTGGCCGTATGTTTTTATTTAGCTTAACTTTAGGTGTCTA\n+TTGTTCCTCTTGGACATTCTATGGCGCAACTGGGGCTGCCGTACGTGAAGGCGTTATCTTCTTACCTATT\n+TATTTAGGTCCACTGTTATTTGTCTGGTTTGGTTATGATATCTGGCGGCGTCTAGGTCGAGTTCGTCAGC\n+ATCATGCGATTTCGTCAATCGCTGACTTTGTCGCGGCACGCTATGGTAAAAGTGGTGTACTCGCATCGTT\n+GGTGACTATTCTTGCCGTTATTGCAATTATCCCCTACCTCGCGTTACAGCTGCGTGCGATTGCTTTAAGT\n+ACCTCGGTCATTATGGAGCAAAGCTCGCATATTCATACGACGACCAACAGCGTGTTATTGCTCACCAGTG\n+TGCTTGCGATTTTAGCTATGATTTTTGGTACACGGCAGATTGCAAACACGGAGCAACACGGCGGCCTCAT\n+GCTTGCGGTTGCATTTGAATCATTTGTGAAGTTATTTGCCTTACTTTGTGTCGCTTTATTTTTTATTTTT\n+GAATCACCGGCCAACCTGAGCCAAATGACCTCTGATGTAAACCAGACTTTTCAGGAAGTTCAGCTCTTTG\n+GTGTACCCGAAACCTTCTGGATTCAAACATTATTGGCGGGTTTAGCCATTATTTGCTTACCACGTCAGTT\n+CCACGTGGCGGTGGTCGAGCTACGCGATGAGAAGCATATTCGCGGTGCCCGTAAATGGTTCGCGGTTTAT\n+CTCATTTTAACTATTCTTGCCATTATTCCGATTGCAAGCTGGGCTTTACATGCTGCACCGAAGTTTCTGA\n+CCGTGCCTGATGTGGCTGTGCTGTCATTGCCTTTAAGTTATAACCAAGAGTGGCTGGCATTACTGGCCTT\n+TTTAGGCGGGTTCTCTGCCTCAACAGGCATGTTACTGGTGTCATCAGTAGCATTGTCTATTATGCTCAGT\n+AACGACTTGATTATGCCTGCTCTATGGCGATTTAAGTTGCTGTCACGTCACGATAAGCACTTACCTAAAG\n+TTCTTAAATTTAGCCGCCGTATTAGTATTGTTGCAGTGATGCTACTTGGCTTTTTATTCTTCCATTTCTT\n+TAATGACATTAACCAACTTTCAGTTTTCGGCTTATTGGCCTTTAGTGCTGTAGCACAGTTTGCACCTGCA\n+CTGATTGGTGGTTTGTATTGGCGTGGCGGAAGCCGTCAAGGCGTCTATGCAGGACTTATTATTGGATTTT\n+TAATGTGGAGTTATACATTACTATTTCCAACTATTTTGCGTAGCTTGCCTGAAGCCTATCAGGAAACTGC\n+TCAAAGTATTTTACTTTTCGGTCCTTTCGGCATTAATGCCCTACGCCCGGAATCTTTATTTGGTTTTGAG\n+TCATTTGCACCTTTAACTCACGGTGTTATTTGGTCACTCGGCTTAAATATTGTTTTATATATCTGGATTT\n+CAAAAATTTATCGGCCAAGCGTCGCTGAACAAATTCAGGCAGAAAGCTTCTTCTACTATGAAACTAAGCC\n+TTTACCATCACCGCACACATCTACTGATTTAACCTATCTTCCTCATGATGCGGCCCGCTTAAAAGTGGGT\n+GATTTATTTGCCCTAGCCAAAAGAATTACGGGTGAGCAACCCACTACGCAAGCGTTCGAAAATTTTTGTG\n+AGCAAAATCACCTCACCCTCAACCCAAATAGTATTGCCAATGGCATGTGGTGGCGTTTTACCGAGCAATA\n+TCTGGCCGGTATTATCGGTGCCGCTTCTGCACGTACGTTGCTCACAACAGCAATGATTAATAACGGCCTC\n+GCTTTAGGGCAAGTGGCTAATATTTTAGACCAAGCATCGCAGTGGCAACGTTTTAATCAGAACCTTCTTA\n+TGACCATGATTGACCACATGACCCAAGGGGTAAGCGTGGTTGATAAAAATATGTGTTTGGTCGCATGGAA\n+CAATCAATATTTAAAACTGTTTGGTTACCCAAAAGACCTCGTTTATGTGGGCTGCCCAATTGCCGACCTC\n+ATTCGTTATAACGCCGAACGCGGTGAATGTGGTCCCGGTTCAGTTGAAGAACATGTGCGTAAACGCCTTC\n+ACTGGATGAAAGTGGGAAGTGCTCACGAATTTGAACGTATTCGTAAAGATGGCCGTGTAATTCAAATGCG\n+AGGAAATCCAATCGCAGGTGGAGGCTTTGTAACGACATTTGCCGATATTACGGCCTTCCGTGCGAACGAA\n+GCCGTGCTTGAAGCCCGCGTAAAAGATAGAACTCAACAGCTTGCCGATGCCTTAACTGAGCAACAGCTTG\n+CACGTGAACAAGCCGATATGGCCAATATGTCAAAGAGTCGATTTATTGCCGCGGCAAGTCACGATCTATT\n+ACAGCCTATGCATGCTGCTCGTCTGTTTAGTACCGTTCTTGAGCAAAGTATTTCGACCGAAGAAGACCGC\n+CAGACCCTACAACAGCTTGACCGAGCACTCTATGGTGCAGAAAGTATGCTCTCTGCCCTACTCGATATTG\n+CACGTTTGGAAGGCGGTACCATACAGCCAAAGAGACAACCTTATCCGTTGCATGATTTGCTCAGTGATCT\n+TGAGTTGCAGTTTAAATCGATCGCTGCTCAGCGAAATATCTCACTGAAAGTCCACGATGTGTCTTTCTGG\n+ATCGATACCGACCCGCAGTGGATTCGTCGTATTATTCAGAACTTTGTCAGTAATGCTTTGCGTTATACCG\n+CTAAAGGTCGAGTGGTGGTAGGTGTACTCCGCTCTGCGCAGCAGTCTGGACATATTCGAATTGGGGTTTG\n+GGATACTGGACCTGGTATTGCCGAAGAACAACGGATTAAGCTATTCCAAGAGTTTGAGCGCTGTGGGCAT\n+TTATCACCTTGGGGTGAACAAGGTTTAGGGCTAGGACTTGCCATCGTACAACGTATGACAGGTTTGCTAA\n+ATTACCCTGTTCATGTTTACTCAGAGTTGGGCAAAGGCTCATGCTTTATGATTGAAGTACCTATTGTCGA\n+GCCACCAAAAGTTGCAACACCAGCTGTACAAGCCGTACCTTTAAAAACTAAAGCCTACCGTATTTTGTGC\n+CTAGACAATGATGAAACTATTCTTGAAGGAATGAGTAGTTTATTAGGACGATGGGGTTATCAAGTTTTCA\n+AAGCGACTGAACCTGAACAGGCGCTAGAAATTATTCAAAAAGAGAATATTCAGGTTTGGCTCATTGACCA\n+GCACTTAAACCACAATCAACTTGGCGTTGATTTTATTACTCAAAATCGTCAAGAAGATGTTCCTGTTGCC\n+TTAATTACAGCGGACTCGCACCCTGAATTACCGCAGCAATTAAAAGAACTGAATATTGTTTTACTCAAAA\n+AACCGTTAAAACCTGCTTCATTAAGAGCATGGTTATCTGGGCTTAAAATTGCCAGCACGACAGACTAA\n+>NZ_CP043953.1_176 # 199276 # 199608 # 1 # ID=1_176;partial=00;start_type=ATG;rbs_motif=AGGA;rbs_spacer=8bp;gc_cont=0.390\n+ATGGATCAAAGCCAAGTAGAACAGATTCTACGTAATCCAAAGTTTCAAAAAATGGTCAAGAAAAAAAGTG\n+CATTAAGCTGGACGCTCACAATCATCATGTTAGTGCTTTATGTGGGCTTTATGCTACTTGTGGGCTACAA\n+CAAAGAATTTTTGATGAGTTCCTTTAGTGGTGGTGTAACGACATGGGGGATCCCGCTAGGTTTAGGAATT\n+ATTGTTTTATCTTTCCTACTTTGTGGTGTGTATTCCTATATCGCAAATAATACCCTTGACCAATTGAGTG\n+AAGAAGCGTTGAAGGAAGTTGAAGCCATCACGCATGAGAAAGGACTACACTAA\n' |
| b |
| diff -r 000000000000 -r 91791b6ecd38 test-data/output_c_n_m.start --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_c_n_m.start Thu Mar 14 16:49:04 2024 +0000 |
| b |
| b'@@ -0,0 +1,7673 @@\n+# Sequence Data: seqnum=1;seqlen=199920;seqhdr="NZ_CP043953.1 Acinetobacter baumannii strain K09-14 chromosome, complete genome"\n+# Run Data: version=Prodigal.v2.6.3;run_type=Single;model="Ab initio";gc_cont=40.29;transl_table=11;uses_sd=0\n+\n+Beg\tEnd\tStd\tTotal\tCodPot\tStrtSc\tCodon\tRBSMot\tSpacer\tRBSScr\tUpsScr\tTypeScr\tGCCont\n+\n+257\t388\t+\t-64.41\t-35.79\t-28.61\tGTG\tNone\tNone\t-12.63\t-5.99\t-9.49\t0.402\n+\n+428\t583\t-\t-49.78\t-20.95\t-28.83\tTTG\tNone\tNone\t-10.65\t0.30\t-17.98\t0.423\n+\n+659\t754\t-\t-16.84\t-19.48\t2.64\tATG\tAGG\t6bp\t1.32\t0.41\t1.41\t0.302\n+\n+698\t793\t+\t-33.85\t-17.33\t-16.52\tATG\tNone\tNone\t-17.52\t0.09\t1.41\t0.281\n+\n+872\t985\t+\t-52.10\t-21.76\t-30.34\tGTG\tNone\tNone\t-14.68\t-4.12\t-11.03\t0.386\n+875\t985\t+\t-79.22\t-21.40\t-57.83\tTTG\tNone\tNone\t-15.09\t-16.77\t-25.47\t0.378\n+890\t985\t+\t-72.30\t-15.37\t-56.93\tTTG\tNone\tNone\t-17.52\t-9.33\t-29.57\t0.375\n+\n+1115\t1213\t-\t-51.92\t-11.24\t-40.69\tGTG\tNone\tNone\t-16.98\t-10.46\t-12.75\t0.414\n+\n+1\t1398\t+\t213.00\t215.74\t-2.74\tATG\tNone\tNone\t-6.52\t0.00\t3.78\t0.399\n+28\t1398\t+\t194.39\t213.60\t-19.21\tTTG\tNone\tNone\t-6.52\t-1.69\t-11.00\t0.398\n+61\t1398\t+\t200.27\t207.27\t-7.00\tATG\tNone\tNone\t-6.52\t-4.26\t3.78\t0.395\n+175\t1398\t+\t150.23\t163.38\t-13.15\tTTG\tGAG\t12bp\t-2.55\t0.40\t-11.00\t0.397\n+187\t1398\t+\t142.01\t158.86\t-16.85\tTTG\tNone\tNone\t-6.52\t0.67\t-11.00\t0.397\n+202\t1398\t+\t145.30\t158.05\t-12.75\tGTG\tNone\tNone\t-6.52\t-1.34\t-4.90\t0.394\n+220\t1398\t+\t136.06\t148.19\t-12.13\tTTG\tAGG\t8bp\t3.54\t-4.67\t-11.00\t0.393\n+247\t1398\t+\t115.26\t134.70\t-19.44\tTTG\tNone\tNone\t-6.52\t-1.92\t-11.00\t0.392\n+436\t1398\t+\t85.38\t90.13\t-4.75\tATG\tNone\tNone\t-6.52\t-2.02\t3.78\t0.395\n+496\t1398\t+\t54.61\t74.04\t-19.43\tTTG\tNone\tNone\t-6.52\t-1.91\t-11.00\t0.394\n+538\t1398\t+\t53.97\t61.74\t-7.78\tATG\tNone\tNone\t-6.52\t-5.04\t3.78\t0.395\n+589\t1398\t+\t45.90\t52.47\t-6.56\tATG\tNone\tNone\t-6.52\t-3.83\t3.78\t0.388\n+595\t1398\t+\t56.46\t50.60\t5.86\tATG\tGAG\t8bp\t5.38\t-3.30\t3.78\t0.389\n+625\t1398\t+\t29.69\t42.22\t-12.53\tGTG\tNone\tNone\t-6.52\t-1.11\t-4.90\t0.394\n+685\t1398\t+\t15.80\t31.80\t-16.01\tTTG\tNone\tNone\t-6.52\t1.51\t-11.00\t0.398\n+712\t1398\t+\t3.54\t20.81\t-17.27\tTTG\tNone\tNone\t-6.52\t0.25\t-11.00\t0.405\n+838\t1398\t+\t-45.01\t-24.68\t-20.33\tTTG\tNone\tNone\t-6.52\t-2.31\t-11.00\t0.422\n+961\t1398\t+\t-76.92\t-59.24\t-17.68\tTTG\tNone\tNone\t-6.52\t0.34\t-11.00\t0.427\n+1141\t1398\t+\t-139.47\t-125.85\t-13.63\tGTG\tNone\tNone\t-6.52\t-1.71\t-4.90\t0.430\n+1219\t1398\t+\t-180.25\t-148.91\t-31.34\tTTG\tNone\tNone\t-9.21\t-6.09\t-15.54\t0.422\n+1225\t1398\t+\t-164.46\t-150.31\t-14.15\tATG\tNone\tNone\t-9.53\t-6.71\t2.59\t0.414\n+1273\t1398\t+\t-193.46\t-174.10\t-19.36\tATG\tNone\tNone\t-13.25\t-7.47\t1.86\t0.389\n+1303\t1398\t+\t-227.42\t-180.95\t-46.47\tGTG\tNone\tNone\t-17.52\t-15.28\t-13.17\t0.354\n+1306\t1398\t+\t-220.08\t-181.51\t-38.57\tATG\tNone\tNone\t-18.11\t-21.32\t1.36\t0.344\n+\n+1426\t1530\t-\t-59.91\t-5.18\t-54.73\tTTG\tNone\tNone\t-15.98\t-11.29\t-26.96\t0.362\n+\n+1310\t1444\t+\t-45.41\t-28.49\t-16.92\tATG\tNone\tNone\t-12.35\t-6.07\t2.00\t0.341\n+1316\t1444\t+\t-59.05\t-29.29\t-29.76\tGTG\tNone\tNone\t-12.93\t-6.61\t-9.72\t0.341\n+1355\t1444\t+\t-61.51\t-23.47\t-38.04\tTTG\tGGA\t14bp\t-1.17\t-4.76\t-31.61\t0.300\n+\n+1776\t1943\t-\t-31.57\t-5.98\t-25.60\tTTG\tNone\tNone\t-9.88\t1.45\t-16.67\t0.375\n+\n+2046\t2180\t+\t-55.25\t-32.72\t-22.53\tGTG\tNone\tNone\t-12.35\t-0.41\t-9.28\t0.422\n+2091\t2180\t+\t-91.09\t-27.27\t-63.81\tTTG\tNone\tNone\t-18.73\t-12.97\t-31.61\t0.422\n+\n+2177\t2308\t-\t-37.78\t-26.81\t-10.97\tATG\tNone\tNone\t-12.63\t0.21\t1.95\t0.371\n+2177\t2323\t-\t-33.97\t-26.26\t-7.70\tATG\tNone\tNone\t-11.32\t1.94\t2.18\t0.367\n+2177\t2338\t-\t-60.13\t-28.17\t-31.96\tTTG\tNone\tNone\t-10.25\t-3.91\t-17.30\t0.358\n+\n+2397\t2486\t-\t-27.96\t-7.55\t-20.41\tATG\tNone\tNone\t-18.73\t-2.50\t1.32\t0.389\n+2397\t2498\t-\t-9.41\t-8.31\t-1.10\tATG\tGAG\t6bp\t2.13\t-4.23\t1.50\t0.373\n+\n+1496\t2644\t+\t225.11\t216.25\t8.86\tGTG\tGAGG\t8bp\t11.87\t1.89\t-4.90\t0.393\n+1502\t2644\t+\t198.83\t212.68\t-13.84\tTTG\tGGA\t13bp\t-0.41\t-2.43\t-11.00\t0.391\n+1544\t2644\t+\t190.64\t199.94\t-9.31\tGTG\tNone\tNone\t-6.52\t2.11\t-4.90\t0.395\n+1574\t2644\t+\t163.41\t182.98\t-19.57\tTTG\tNone\tNone\t-6.52\t-2.05\t-11.00\t0.389\n+1724\t2644\t+\t120.37\t141.75\t-21.38\tTTG\tNone\tNone\t-6.52\t-3.86\t-11.00\t0.378\n+1727\t2644\t+\t132.85\t142.26\t-9.41\tATG\tNone\tNone\t-6.52\t-6.67\t3.78\t0.378\n+1745\t2644\t+\t129.17\t140.86\t-11.69\tTTG\tGGA\t13bp\t-0.41\t-0.28\t-11.00\t0.381\n+1760\t2644\t+\t'..b'\t0.467\n+196842\t196994\t+\t-37.89\t-6.28\t-31.60\tTTG\tNone\tNone\t-10.87\t-1.90\t-18.34\t0.458\n+\n+197004\t197135\t+\t-37.59\t-15.56\t-22.03\tTTG\tGAGG\t7bp\t6.12\t-6.34\t-21.32\t0.409\n+197031\t197135\t+\t-47.39\t-13.63\t-33.77\tTTG\tGAG\t5bp\t2.19\t-8.50\t-26.96\t0.381\n+\n+197056\t197178\t+\t-56.37\t-13.19\t-43.18\tTTG\tNone\tNone\t-13.58\t-6.18\t-22.92\t0.423\n+\n+197217\t197309\t-\t-70.36\t-10.04\t-60.31\tTTG\tNone\tNone\t-18.11\t-11.14\t-30.56\t0.516\n+197217\t197345\t-\t-47.98\t-14.97\t-33.01\tGTG\tNone\tNone\t-12.93\t-9.86\t-9.72\t0.496\n+197217\t197381\t-\t-44.51\t-15.37\t-29.14\tGTG\tNone\tNone\t-10.06\t-11.02\t-7.56\t0.497\n+\n+197228\t197335\t+\t-64.89\t-28.88\t-36.01\tGTG\tNone\tNone\t-15.52\t-8.33\t-11.66\t0.519\n+\n+197275\t197400\t+\t-41.72\t2.45\t-44.16\tTTG\tNone\tNone\t-13.25\t-8.55\t-22.36\t0.460\n+\n+197451\t197573\t-\t-70.44\t-27.06\t-43.39\tTTG\tNone\tNone\t-13.58\t-6.39\t-22.92\t0.366\n+\n+197720\t197815\t-\t-88.53\t-29.99\t-58.54\tTTG\tNone\tNone\t-17.52\t-10.94\t-29.57\t0.385\n+\n+197894\t197995\t+\t-54.16\t-27.91\t-26.25\tATG\tNone\tNone\t-16.46\t-10.79\t1.50\t0.343\n+\n+198041\t198133\t-\t-65.14\t-20.04\t-45.10\tGTG\tNone\tNone\t-18.11\t-12.89\t-13.61\t0.473\n+\n+198173\t198268\t-\t-41.29\t-19.20\t-22.09\tATG\tNone\tNone\t-17.52\t-5.47\t1.41\t0.427\n+\n+198060\t198230\t+\t-45.16\t-31.18\t-13.98\tATG\tGAG\t11bp\t-3.79\t-12.22\t2.54\t0.485\n+198069\t198230\t+\t-40.90\t-31.09\t-9.81\tATG\tNone\tNone\t-10.25\t-1.47\t2.40\t0.488\n+198090\t198230\t+\t-59.75\t-22.99\t-36.77\tTTG\tNone\tNone\t-11.81\t-4.53\t-19.93\t0.489\n+198123\t198230\t+\t-22.53\t-10.52\t-12.01\tATG\tAGG\t6bp\t1.49\t-14.58\t1.59\t0.481\n+\n+198367\t198459\t+\t-72.99\t-18.46\t-54.53\tTTG\tNone\tNone\t-18.11\t-5.36\t-30.56\t0.473\n+\n+198363\t198470\t+\t-35.22\t-20.20\t-15.02\tATG\tNone\tNone\t-15.52\t-0.59\t1.59\t0.426\n+\n+198449\t198640\t+\t-56.90\t-27.28\t-29.62\tTTG\tNone\tNone\t-8.62\t-5.95\t-14.55\t0.432\n+198533\t198640\t+\t-51.31\t-38.35\t-12.96\tATG\tNone\tNone\t-15.52\t1.47\t1.59\t0.491\n+\n+198747\t198887\t+\t-39.40\t-22.88\t-16.52\tATG\tNone\tNone\t-11.81\t-6.30\t2.09\t0.461\n+198774\t198887\t+\t-55.07\t-19.77\t-35.30\tGTG\tNone\tNone\t-14.68\t-9.08\t-11.03\t0.465\n+198795\t198887\t+\t-74.00\t-13.31\t-60.69\tTTG\tNone\tNone\t-18.11\t-11.53\t-30.56\t0.430\n+\n+198966\t199073\t-\t-65.02\t-21.09\t-43.92\tTTG\tNone\tNone\t-15.52\t-1.71\t-26.19\t0.407\n+\n+199019\t199126\t-\t-45.47\t-31.98\t-13.49\tATG\tNone\tNone\t-15.52\t0.95\t1.59\t0.361\n+\n+199183\t199284\t-\t-59.32\t-13.26\t-46.06\tTTG\tNone\tNone\t-16.46\t-1.32\t-27.78\t0.324\n+199183\t199290\t-\t-54.79\t-12.02\t-42.77\tTTG\tNone\tNone\t-15.52\t-0.56\t-26.19\t0.333\n+\n+199501\t199590\t-\t-30.10\t-12.93\t-17.17\tATG\tNone\tNone\t-18.73\t0.75\t1.32\t0.411\n+\n+199600\t199716\t-\t-33.68\t-9.38\t-24.30\tGTG\tNone\tNone\t-14.30\t1.24\t-10.74\t0.444\n+199600\t199719\t-\t-50.04\t-9.62\t-40.42\tTTG\tNone\tNone\t-13.93\t-2.48\t-23.51\t0.442\n+199600\t199731\t-\t-21.74\t-11.13\t-10.61\tATG\tNone\tNone\t-12.63\t0.57\t1.95\t0.447\n+199600\t199737\t-\t-25.88\t-15.20\t-10.67\tATG\tNone\tNone\t-12.07\t-0.14\t2.04\t0.442\n+199600\t199746\t-\t-28.09\t-18.69\t-9.40\tATG\tNone\tNone\t-11.32\t0.24\t2.18\t0.429\n+199600\t199776\t-\t-58.33\t-27.00\t-31.33\tTTG\tNone\tNone\t-9.37\t-5.66\t-15.81\t0.407\n+\n+199240\t199608\t+\t22.59\t29.14\t-6.55\tGTG\tNone\tNone\t-6.52\t4.86\t-4.90\t0.398\n+199270\t199608\t+\t11.64\t29.98\t-18.34\tTTG\tNone\tNone\t-6.52\t-0.82\t-11.00\t0.389\n+199276\t199608\t+\t43.97\t29.55\t14.42\tATG\tAGGA\t8bp\t11.57\t-0.93\t3.78\t0.390\n+199327\t199608\t+\t6.00\t11.32\t-5.31\tATG\tNone\tNone\t-6.52\t-2.58\t3.78\t0.401\n+199372\t199608\t+\t18.45\t13.97\t4.48\tATG\tGGA\t14bp\t-0.44\t1.37\t3.54\t0.401\n+199378\t199608\t+\t-3.04\t10.20\t-13.24\tGTG\tNone\tNone\t-7.15\t-0.73\t-5.37\t0.407\n+199387\t199608\t+\t-6.96\t8.15\t-15.11\tGTG\tNone\tNone\t-7.44\t-2.08\t-5.59\t0.410\n+199396\t199608\t+\t-2.65\t3.94\t-6.59\tATG\tNone\tNone\t-7.76\t-2.00\t3.18\t0.404\n+199405\t199608\t+\t-10.35\t3.11\t-13.46\tGTG\tNone\tNone\t-8.11\t0.74\t-6.09\t0.407\n+199426\t199608\t+\t-33.72\t-0.25\t-33.47\tTTG\tNone\tNone\t-9.05\t-8.63\t-15.28\t0.410\n+199429\t199608\t+\t-17.12\t0.33\t-17.45\tATG\tNone\tNone\t-9.21\t-10.92\t2.68\t0.411\n+199513\t199608\t+\t-63.95\t-26.22\t-37.74\tGTG\tNone\tNone\t-17.52\t-6.55\t-13.17\t0.406\n+\n+199691\t199792\t-\t-56.24\t-1.80\t-54.44\tTTG\tNone\tNone\t-16.46\t-9.70\t-27.78\t0.402\n+199691\t199798\t-\t-53.04\t-1.94\t-51.10\tTTG\tNone\tNone\t-15.52\t-8.89\t-26.19\t0.398\n+199691\t199807\t-\t-53.79\t-3.53\t-50.26\tTTG\tNone\tNone\t-14.30\t-11.34\t-24.13\t0.419\n+199691\t199846\t-\t-35.01\t-3.88\t-31.14\tTTG\tNone\tNone\t-10.65\t-2.01\t-17.98\t0.429\n+\n' |
| b |
| diff -r 000000000000 -r 91791b6ecd38 test-data/output_train --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_train Thu Mar 14 16:49:04 2024 +0000 |
| b |
| b'@@ -0,0 +1,353 @@\n+DEFINITION seqnum=1;seqlen=199920;seqhdr="NZ_CP043953.1 Acinetobacter baumannii strain K09-14 chromosome, complete genome";version=Prodigal.v2.6.3;run_type=Single;model="Ab initio";gc_cont=38.99;transl_table=11;uses_sd=1\n+FEATURES Location/Qualifiers\n+ CDS <1..1398\n+ /note="ID=1_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.399;conf=99.99;score=210.23;cscore=207.01;sscore=3.22;rscore=0.00;uscore=3.22;tscore=0.00;"\n+ CDS 1496..2644\n+ /note="ID=1_2;partial=00;start_type=GTG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.393;conf=99.99;score=215.73;cscore=211.69;sscore=4.04;rscore=11.34;uscore=-0.58;tscore=-6.72;"\n+ CDS 2659..3741\n+ /note="ID=1_3;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.394;conf=100.00;score=141.92;cscore=144.06;sscore=-2.14;rscore=-6.04;uscore=-1.16;tscore=3.94;"\n+ CDS 3794..6262\n+ /note="ID=1_4;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.416;conf=99.99;score=484.11;cscore=465.80;sscore=18.32;rscore=11.34;uscore=2.33;tscore=3.94;"\n+ CDS 6300..6692\n+ /note="ID=1_5;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.384;conf=100.00;score=67.45;cscore=50.96;sscore=16.48;rscore=11.34;uscore=0.33;tscore=3.94;"\n+ CDS complement(6778..7335)\n+ /note="ID=1_6;partial=00;start_type=ATG;rbs_motif=3Base/5BMM;rbs_spacer=13-15bp;gc_cont=0.360;conf=100.00;score=45.48;cscore=49.57;sscore=-4.09;rscore=-5.27;uscore=-2.11;tscore=3.94;"\n+ CDS complement(7586..9517)\n+ /note="ID=1_7;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.419;conf=99.99;score=338.94;cscore=342.40;sscore=-3.46;rscore=-6.04;uscore=-0.71;tscore=3.94;"\n+ CDS 9774..10778\n+ /note="ID=1_8;partial=00;start_type=ATG;rbs_motif=AGGA;rbs_spacer=5-10bp;gc_cont=0.405;conf=100.00;score=124.40;cscore=106.86;sscore=17.53;rscore=11.57;uscore=2.02;tscore=3.94;"\n+ CDS 11034..12041\n+ /note="ID=1_9;partial=00;start_type=ATG;rbs_motif=AGGA;rbs_spacer=5-10bp;gc_cont=0.403;conf=99.99;score=194.49;cscore=180.04;sscore=14.44;rscore=11.57;uscore=-0.42;tscore=3.94;"\n+ CDS 12384..13388\n+ /note="ID=1_10;partial=00;start_type=ATG;rbs_motif=AGGA;rbs_spacer=5-10bp;gc_cont=0.418;conf=100.00;score=171.08;cscore=153.57;sscore=17.51;rscore=11.57;uscore=2.65;tscore=3.94;"\n+ CDS 13513..13848\n+ /note="ID=1_11;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.435;conf=100.00;score=46.25;cscore=29.63;sscore=16.62;rscore=11.34;uscore=1.34;tscore=3.94;"\n+ CDS complement(13905..14750)\n+ /note="ID=1_12;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.371;conf=100.00;score=87.53;cscore=74.84;sscore=12.69;rscore=4.87;uscore=3.88;tscore=3.94;"\n+ CDS complement(14878..16005)\n+ /note="ID=1_13;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.421;conf=99.99;score=196.50;cscore=189.76;sscore=6.74;rscore=4.87;uscore=-1.41;tscore=3.94;"\n+ CDS 16085..17299\n+ /note="ID=1_14;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.395;conf=99.99;score=239.80;cscore=231.35;sscore=8.45;rscore=4.87;uscore=-0.36;tscore=3.94;"\n+ CDS 23636..24235\n+ /note="ID=1_15;partial=00;start_type=ATG;rbs_motif=AGxAGG/AGGxGG;rbs_spacer=5-10bp;gc_cont=0.328;conf=100.00;score=78.48;cscore=67.71;sscore=10.77;rscore=3.35;uscore=4.13;tscore=3.94;"\n+ CDS complement(24293..24985)\n+ /note="ID=1_16;partial=00;start_type=ATG;rbs_motif='..b'core=192.60;cscore=195.64;sscore=-3.04;rscore=-6.04;uscore=-0.94;tscore=3.94;"\n+ CDS 182824..183126\n+ /note="ID=1_160;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.396;conf=99.98;score=36.56;cscore=37.74;sscore=-1.17;rscore=-6.04;uscore=0.93;tscore=3.94;"\n+ CDS 183155..184213\n+ /note="ID=1_161;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.427;conf=99.99;score=246.04;cscore=226.33;sscore=19.71;rscore=11.34;uscore=3.46;tscore=3.94;"\n+ CDS 184382..185674\n+ /note="ID=1_162;partial=00;start_type=TTG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.415;conf=100.00;score=166.79;cscore=169.40;sscore=-2.61;rscore=11.34;uscore=0.99;tscore=-14.94;"\n+ CDS 185671..186378\n+ /note="ID=1_163;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.394;conf=100.00;score=106.88;cscore=101.42;sscore=5.47;rscore=-6.04;uscore=0.23;tscore=3.94;"\n+ CDS complement(186358..187338)\n+ /note="ID=1_164;partial=00;start_type=GTG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.384;conf=100.00;score=143.26;cscore=144.02;sscore=-0.76;rscore=4.87;uscore=1.09;tscore=-6.72;"\n+ CDS complement(187451..188026)\n+ /note="ID=1_165;partial=00;start_type=ATG;rbs_motif=AGGA;rbs_spacer=5-10bp;gc_cont=0.387;conf=100.00;score=45.40;cscore=31.96;sscore=13.44;rscore=11.57;uscore=-1.42;tscore=3.94;"\n+ CDS 188321..190270\n+ /note="ID=1_166;partial=00;start_type=ATG;rbs_motif=AGGA;rbs_spacer=5-10bp;gc_cont=0.448;conf=99.99;score=318.23;cscore=305.29;sscore=12.94;rscore=11.57;uscore=-2.58;tscore=3.94;"\n+ CDS complement(190317..190859)\n+ /note="ID=1_167;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.359;conf=100.00;score=90.00;cscore=80.64;sscore=9.36;rscore=4.87;uscore=1.21;tscore=3.94;"\n+ CDS 190965..191378\n+ /note="ID=1_168;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.362;conf=100.00;score=43.18;cscore=46.60;sscore=-3.42;rscore=-6.04;uscore=-1.32;tscore=3.94;"\n+ CDS complement(191470..192582)\n+ /note="ID=1_169;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.425;conf=99.99;score=204.45;cscore=185.31;sscore=19.14;rscore=11.34;uscore=3.07;tscore=3.94;"\n+ CDS complement(192627..193364)\n+ /note="ID=1_170;partial=00;start_type=ATG;rbs_motif=AGGA;rbs_spacer=5-10bp;gc_cont=0.424;conf=100.00;score=134.79;cscore=119.04;sscore=15.76;rscore=11.57;uscore=0.89;tscore=3.94;"\n+ CDS 193741..194391\n+ /note="ID=1_171;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.399;conf=100.00;score=110.75;cscore=111.89;sscore=-1.14;rscore=-6.04;uscore=0.97;tscore=3.94;"\n+ CDS complement(194434..195201)\n+ /note="ID=1_172;partial=00;start_type=ATG;rbs_motif=AGGA;rbs_spacer=5-10bp;gc_cont=0.409;conf=100.00;score=111.35;cscore=97.04;sscore=14.32;rscore=11.57;uscore=-0.55;tscore=3.94;"\n+ CDS complement(195595..199092)\n+ /note="ID=1_173;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.443;conf=99.99;score=454.33;cscore=458.08;sscore=-3.75;rscore=-6.04;uscore=-1.00;tscore=3.94;"\n+ CDS 199276..199608\n+ /note="ID=1_174;partial=00;start_type=ATG;rbs_motif=AGGAG;rbs_spacer=5-10bp;gc_cont=0.390;conf=99.98;score=36.72;cscore=20.29;sscore=16.43;rscore=13.64;uscore=-1.15;tscore=3.94;"\n+ CDS 199610..>199918\n+ /note="ID=1_175;partial=01;start_type=ATG;rbs_motif=AGGA;rbs_spacer=5-10bp;gc_cont=0.447;conf=100.00;score=48.17;cscore=34.06;sscore=14.11;rscore=11.57;uscore=-2.67;tscore=3.94;"\n+//\n' |
| b |
| diff -r 000000000000 -r 91791b6ecd38 test-data/output_train.faa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_train.faa Thu Mar 14 16:49:04 2024 +0000 |
| b |
| b'@@ -0,0 +1,1225 @@\n+>NZ_CP043953.1_1 # 1 # 1398 # 1 # ID=1_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.399\n+MLWTDCLTRLRQELSDNVFAMWIRPLVAEEVEGILRLYAPNPYWTRYIQENHLELISILA\n+EQLSEGRVRQVEILVDSRPGSILSSSEQPATTTAALQTAPIPQPAKVKREPEPVANTAVS\n+SKSSKKKLLNPQFTFSLFVEGRSNQMAAETCRKVLTQLGASQHNPLFLYGPTGLGKTHLM\n+QAVGNALLQAKPNARVMYMTSESFVQDFVSSLQKGKVEEFKKNCRSLDLLLVDDIHLLAG\n+KEASLVEFFYTFNALLDESKQIILTSDRYPKELTELDPRLVSRFSWGLSVGVEPPDIETR\n+IEILLKKAENSGVDLPRNCALFIAQQVVANVRELEGALNKVVAISRFKGAPIDLDVVRES\n+LKDVLAIRARTISVENIQRVVSEYFRIPLKELVGPKRTRIYARPRQLAMGLARELTGDSF\n+PEIGMAFGGRDHSTVMHACEKVVSLREEDPIFDEDYKNLLRLLQS*\n+>NZ_CP043953.1_2 # 1496 # 2644 # 1 # ID=1_2;partial=00;start_type=GTG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.393\n+MRLKIAKESLLNVLSHVVGAVERRHTLNILSNVKIQTNAQALTITGSDLEVELVASTALS\n+EGACLEAGETTVPARKLMEICKSLPTAALIDLQITEDQRCILKSGNSRFVLGTLPAEDYP\n+LLTTENSQGTQVQVTQRELKRLFEKTAFAMAVQDVRFYLTGTLLEIDENQLRAVTTDGHR\n+LALCEILASSTSSQLVQAIVPRKAVGELQRLLSIEDEQLTLLIGRELLNVTINTPSRDKE\n+QGDITVRFTTKLIDGKFPDYRRVIPRGGDKHVLIGHDVFKQSLQRVAILSNEKLRGVFLN\n+FNQDSLQLRANNPEQDEAIEDLAIQYQSAPLEMSFNAQYLLDVLGVLDGDDVNMSMTEAN\n+QSVLVQDPAHPDQTYVVMPMRV*\n+>NZ_CP043953.1_3 # 2659 # 3741 # 1 # ID=1_3;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.394\n+MHLTRLNIERVRNLKTVALHGLQPFNVFYGANGSGKTSILEAIHLLATGRSFRTHIPKNY\n+IQYEADDAIVFAQSATEKIGMQKLASGEQLMKVNGDTVATQGQLAKLLPLQHIDPQSTDI\n+IDHGAKPRRQLLDWLMFHVEPEFYFAWQYYSRALKQRNTLLKTRRNLSLADLEPWNKMLS\n+DYGEILHSQRLSIVEQWNVYFQNDLSQLLPDLEIELEYSPGFHTEQGLMQDLLNQHQKDI\n+ERRYTEYGPHRADLRLKTPFGHADDVLSRGQKKLLIIALKLSQIAMLHASNKETVVLLDD\n+LTAELDLTAQQRLIERLSQLGSQVFMTTLDHASVKKHLHDLSISYQLFSVESGQVSLAAP\n+*\n+>NZ_CP043953.1_4 # 3794 # 6262 # 1 # ID=1_4;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.416\n+MSSESQSASQTEQTNEKAYDSSSIKVLRGLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDN\n+AIDEALAGHCDEIIVTIHEDESVSVSDNGRGIPTDIHPEEGVSAAEVILTILHAGGKFDD\n+NSYKVSGGLHGVGVSVVNALSSKLHLTIYRAGQIHEQEYHHGDPQYPLRVIGETDNTGTT\n+VRFWPSAETFSQTIFNVEILARRLRELSFLNAGVRIVLRDERINLEHVYDYEGGLSEFVK\n+YINEGKNHLNEIFHFTADADNGITVEVALQWNDSYQENVRCFTNNIPQKDGGTHLAGFRA\n+ALTRGLNQYLENENILKKEKVNVTGDDAREGLTAIISVKVPDPKFSSQTKEKLVSSEVKP\n+AVEQAMNKEFSAYLLENPQAAKSIAGKIIDAARARDAARKAREMTRRKSALDIAGLPGKL\n+ADCQEKDPALSELYLVEGDSAGGSAKQGRNRKMQAILPLKGKILNVERARFDKMISSQEV\n+GTLITALGCGIGREEYNPDKLRYHKIIIMTDADVDGSHIRTLLLTFFFRQMPELVERGHI\n+YIAQPPLYKLKKGKQEQYIKDNDALETYLISNAIDELALHISADAPAITGEALAKVIQDY\n+QVSQKSLQRLTLRYPASLLDALLEVDAFKADQNHDQAYVQQWADQVREAVEKLQPSLRPE\n+ITLETFERENAQGEKSAHYWPRVTVYVHNLPHAYLLDAGLLNSAEYARLLKNSKSWFKLI\n+EDGAYLQKGDRRIQVANFHQVWQHILQDSRRGMMIQRYKGLGEMNAEQLWETTMDPENRN\n+MLQVTIDDAIEADRMFSCLMGDDVEPRRAFIEENALNADIDA*\n+>NZ_CP043953.1_5 # 6300 # 6692 # 1 # ID=1_5;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.384\n+MMSQKILASMLISCAALVSHSAFAADLEADMKTLAKSTKAFAEAKDIDNAKQQLVIMRQA\n+ALSSKLSLPHKLEGLPPENVQVKEYQAGLDQLVAEIDRVTVFVDKGQLDQAKTEAINLVN\n+IRNENHKKFR*\n+>NZ_CP043953.1_6 # 6778 # 7335 # -1 # ID=1_6;partial=00;start_type=ATG;rbs_motif=3Base/5BMM;rbs_spacer=13-15bp;gc_cont=0.360\n+MNFIDFITNFEQFLPILIQEYGAWVYAILFLIIFSETAFVFMFFLPGDSLLLTVGALCSV\n+VELMHLGYMITLLTIAATLGYIVNYSIGRHFGNRIFEAKSRFIKKEYLNKTNRYFLQHGG\n+KTILLARFIPFARSFAPLAAGSSNMSYGKFLIYNVAGAILWICILLTAGYLFGHALIQVT\n+DFVEN*\n+>NZ_CP043953.1_7 # 7586 # 9517 # -1 # ID=1_7;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.419\n+MIQFDQVSLRRGGRVLFQKASMQLHPGWKIGLTGVNGAGKSTLFAALLGSLGADEGSLTR\n+PSVWTVAHMAQEVKALDMPAIDFVLSGDEEYWDIQNKLAQPEQLTDSDLAKLHGRFDEIH\n+GYSAPSKAAQLMAGLGFLEHQLRLNVASFSGGWRMRLNLARTLMSRSDLLLLDEPTNHLD\n+LDAILWLEDWLKAYEGTLILISHDRDFLDAITDHILHIENQELTLYTGNYSTFETTRSER\n+LAQQQQAFEKQQEARAHLQKFIDRFKAKATKARQAQSRIKQLERMQQLAPAHVDTPFTFS\n+FREPTKMSSPLLTLENASIGYGDKKIAEKIKLQITPNSRIGLLGMNGAGKSTLIKSLVGD\n+LPLLAGERKASELLNIGYFAQHQMDALDGQASPMLQLARIADKQISEATLRSFLGSFGFS\n+GERMDTPCESFSGGERARLALALIVWQRPNVLILDEPTNHLDLDMRHALSMALQDFEGAV\n+VLVSHERQLIASVCDELLLVHGGKCTEFEGDLQDYAKWLREARQQQINAQTAVAQNNSSS\n+AAPTPAKVDKEAQRKEAARRREQTRPIRKNIEKVESQIEQLQPRLAEIEEALADTSLYEA\n+NRKDDLLKLMNEQTELKAKLEQYEEQLLELMMELEEMEASFEN*\n+>NZ_CP043953.1_8 # 9774 # 10778 # 1'..b'-1 # ID=1_167;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.359\n+MKQALLVIDVQNDYFKNGKMELVGPDQALDKIKQLEQYFNEKDLSIIYVQHINPPQASFF\n+QENTEGVLLHPELSAGGDSLIVTKHYPNSFLETNLKELLKAHQIEQLVITGMMTHICIDS\n+GTRAAKELGYQPILIGDATATRDLSHNGKTVKAEDVQTAFLAALGMFASVQNTADFLAKS\n+*\n+>NZ_CP043953.1_168 # 190965 # 191378 # 1 # ID=1_168;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.362\n+MNIELDPIDLKIIALLKQDSRLTNKEIGQRVHRTGQAVGARIAQLMDAGVIKNYTIAVQY\n+RHKQFIHLHLNEQRSFEEIENLVKQYEQIDECFKVMGNACYMIVSHFEPAELNAFIEVLS\n+KWCRYSVETVIREVEKA*\n+>NZ_CP043953.1_169 # 191470 # 192582 # -1 # ID=1_169;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.425\n+MTQLQQPIKFAYWVPNVSGGLVVSNIEQRTDWSYDYNVRLAQAAENNGFEYALTQIRFTA\n+GYGAENQHESVSFSHALLAKTEKLKVIAAILPGPWKPALAAKQLATIDYLTQGRIAINVV\n+SGWFRGEFDAIGEEWPEHDERYVRSEEFIRTLKGIWTTDNYSFDGKYYQFQNYTLKPKPL\n+QKPHIEVFQGGSSRAARDMASRVSDWYFTNGNTVEEIQKQVEDIRAKAKANNHQVKIGVN\n+AFIIARDTEEEAKAVLQEIIDKANTEAVNAFGDATREAGAASPEQEGNWAKSTFEDLVQY\n+NDGFKTNLIGTPQQIAERIVALKNVGVDLVLSGFLHFIEEVEYFGEKVLPLVRQLELQQE\n+KEVEIQAKSA*\n+>NZ_CP043953.1_170 # 192627 # 193364 # -1 # ID=1_170;partial=00;start_type=ATG;rbs_motif=AGGA;rbs_spacer=5-10bp;gc_cont=0.424\n+MTGITSSKPLNIVAVSGGLNTPSKTESLVQAILDELSEAIDIKVHFIKLSEIGPLLGGAF\n+YRNQLPQRVQDDLAAVEAADALIVGTPVYRASFTGLFKHFFDFVEQTALVDVPVLLAASG\n+GSDRHALVLEHQLRPLFSFFQAQTLPIGVYATDRDFTPEYTVKSEQLSDRITLAVARALP\n+ILEWAPAKGKRAEVVKPKSQQANQELGINKQIEQEEVLPSAAVPNLDAAESRLHHKSGKS\n+LTHVA*\n+>NZ_CP043953.1_171 # 193741 # 194391 # 1 # ID=1_171;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.399\n+MNILIVDDHPLFRHALIQAVRYSLPQAQIHETASVDEFYERLENGAEPDLVLLDLNLPGA\n+SGFSALVYVRAQYPSIPIIVVSAHEEASIIQRAIAHGAMGYIPKSAHPSHIGEAIRQVLD\n+GEIWLPPNLPSNINLDPRAADETALAERIQSLTPQQFRVLMMVAEGLLNKQIAYELDVSE\n+ATIKAHVTAIFRKLGVQNRTQAVLAISALNIEDKKI*\n+>NZ_CP043953.1_172 # 194434 # 195201 # -1 # ID=1_172;partial=00;start_type=ATG;rbs_motif=AGGA;rbs_spacer=5-10bp;gc_cont=0.409\n+MNISDNTPQGQLSSQQFYRQYSANALLPELDWQSIFPHSKLSEAHIKALNTIYQCAVPLA\n+LNVFHDLNFDVFAPAAYHPQGLGLFDKLAQQEENFLKVLTAESENLDHETRHQIWSMLLR\n+GGAVLVFKAWLGHVKLGENQLDMTQFDELSDLLFIKTPPHQLAERLHVDEKAKLDHIFLM\n+YGNDIFLDRFNSLETAALFVDLGVYDAAFLSLRDDRVAEYLKSKGYVTQEQIDDLQCALN\n+PLYCDSLTPKQDCLA*\n+>NZ_CP043953.1_173 # 195595 # 199092 # -1 # ID=1_173;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.443\n+MNSWLIIGVLTLYIALLFVCAFFGEKHASRLSTRGRMFLFSLTLGVYCSSWTFYGATGAA\n+VREGVIFLPIYLGPLLFVWFGYDIWRRLGRVRQHHAISSIADFVAARYGKSGVLASLVTI\n+LAVIAIIPYLALQLRAIALSTSVIMEQSSHIHTTTNSVLLLTSVLAILAMIFGTRQIANT\n+EQHGGLMLAVAFESFVKLFALLCVALFFIFESPANLSQMTSDVNQTFQEVQLFGVPETFW\n+IQTLLAGLAIICLPRQFHVAVVELRDEKHIRGARKWFAVYLILTILAIIPIASWALHAAP\n+KFLTVPDVAVLSLPLSYNQEWLALLAFLGGFSASTGMLLVSSVALSIMLSNDLIMPALWR\n+FKLLSRHDKHLPKVLKFSRRISIVAVMLLGFLFFHFFNDINQLSVFGLLAFSAVAQFAPA\n+LIGGLYWRGGSRQGVYAGLIIGFLMWSYTLLFPTILRSLPEAYQETAQSILLFGPFGINA\n+LRPESLFGFESFAPLTHGVIWSLGLNIVLYIWISKIYRPSVAEQIQAESFFYYETKPLPS\n+PHTSTDLTYLPHDAARLKVGDLFALAKRITGEQPTTQAFENFCEQNHLTLNPNSIANGMW\n+WRFTEQYLAGIIGAASARTLLTTAMINNGLALGQVANILDQASQWQRFNQNLLMTMIDHM\n+TQGVSVVDKNMCLVAWNNQYLKLFGYPKDLVYVGCPIADLIRYNAERGECGPGSVEEHVR\n+KRLHWMKVGSAHEFERIRKDGRVIQMRGNPIAGGGFVTTFADITAFRANEAVLEARVKDR\n+TQQLADALTEQQLAREQADMANMSKSRFIAAASHDLLQPMHAARLFSTVLEQSISTEEDR\n+QTLQQLDRALYGAESMLSALLDIARLEGGTIQPKRQPYPLHDLLSDLELQFKSIAAQRNI\n+SLKVHDVSFWIDTDPQWIRRIIQNFVSNALRYTAKGRVVVGVLRSAQQSGHIRIGVWDTG\n+PGIAEEQRIKLFQEFERCGHLSPWGEQGLGLGLAIVQRMTGLLNYPVHVYSELGKGSCFM\n+IEVPIVEPPKVATPAVQAVPLKTKAYRILCLDNDETILEGMSSLLGRWGYQVFKATEPEQ\n+ALEIIQKENIQVWLIDQHLNHNQLGVDFITQNRQEDVPVALITADSHPELPQQLKELNIV\n+LLKKPLKPASLRAWLSGLKIASTTD*\n+>NZ_CP043953.1_174 # 199276 # 199608 # 1 # ID=1_174;partial=00;start_type=ATG;rbs_motif=AGGAG;rbs_spacer=5-10bp;gc_cont=0.390\n+MDQSQVEQILRNPKFQKMVKKKSALSWTLTIIMLVLYVGFMLLVGYNKEFLMSSFSGGVT\n+TWGIPLGLGIIVLSFLLCGVYSYIANNTLDQLSEEALKEVEAITHEKGLH*\n+>NZ_CP043953.1_175 # 199610 # 199918 # 1 # ID=1_175;partial=01;start_type=ATG;rbs_motif=AGGA;rbs_spacer=5-10bp;gc_cont=0.447\n+MKWNSFKAKALLAAASLYSTVAMASPDLGEAEQQATNWHAIIMFIIFVGFTLFITKWAAK\n+QTQSAQDFYTAGGGISGFQNGLAIAGDYMSAASFLGISAMVFS\n' |
| b |
| diff -r 000000000000 -r 91791b6ecd38 test-data/output_train.fnn --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_train.fnn Thu Mar 14 16:49:04 2024 +0000 |
| b |
| b'@@ -0,0 +1,2727 @@\n+>NZ_CP043953.1_1 # 1 # 1398 # 1 # ID=1_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.399\n+ATGCTTTGGACAGACTGCTTAACTCGCTTGCGACAAGAGCTCTCTGATAACGTCTTTGCGATGTGGATTC\n+GCCCTTTAGTAGCTGAAGAAGTAGAGGGGATACTACGTCTCTATGCTCCTAATCCTTATTGGACGCGTTA\n+TATTCAAGAGAATCATTTAGAGTTAATTTCTATATTGGCTGAACAATTGTCAGAAGGGCGGGTGCGTCAG\n+GTTGAAATCTTGGTAGATTCTCGTCCTGGTAGTATTTTGTCTTCTAGTGAACAGCCTGCAACAACTACAG\n+CAGCTTTACAAACTGCCCCTATACCTCAACCTGCTAAGGTTAAAAGAGAACCGGAACCTGTTGCTAATAC\n+TGCAGTTAGTTCTAAGAGTTCAAAAAAGAAACTATTAAATCCACAATTTACTTTTTCACTATTTGTTGAA\n+GGCCGTTCTAACCAAATGGCAGCAGAAACCTGTAGAAAAGTATTAACACAGTTAGGTGCTTCTCAACATA\n+ACCCTTTGTTTTTATATGGTCCGACAGGTCTAGGTAAGACTCACTTAATGCAAGCAGTTGGTAATGCCCT\n+ACTGCAAGCGAAGCCGAATGCAAGAGTCATGTATATGACTTCAGAAAGTTTTGTACAAGATTTTGTGAGC\n+TCATTACAAAAAGGAAAGGTAGAAGAGTTTAAGAAAAATTGCCGTTCTTTAGACTTGTTATTAGTAGATG\n+ATATTCATCTTTTGGCAGGAAAAGAAGCAAGTCTCGTTGAATTCTTCTATACATTTAATGCCTTACTTGA\n+TGAATCTAAACAAATTATTTTAACGTCTGATCGATATCCTAAAGAATTAACAGAACTTGATCCTCGATTG\n+GTTTCTCGTTTTTCCTGGGGGCTATCAGTAGGTGTTGAACCACCTGATATTGAAACTCGAATCGAAATTC\n+TGCTTAAAAAAGCTGAAAATAGTGGCGTTGATTTACCTAGAAACTGTGCGTTGTTTATTGCCCAACAAGT\n+CGTAGCGAACGTACGTGAACTTGAGGGCGCACTGAATAAAGTTGTCGCAATTTCACGTTTTAAAGGTGCT\n+CCAATTGACCTGGATGTCGTACGGGAATCTTTAAAAGATGTTTTAGCGATCCGTGCTCGTACAATTAGTG\n+TAGAAAATATCCAGCGTGTAGTGAGTGAATATTTCCGAATTCCATTAAAAGAGCTGGTAGGTCCAAAGCG\n+TACCCGAATTTATGCTCGACCACGTCAGTTGGCGATGGGGCTTGCCCGTGAATTAACGGGGGATAGTTTT\n+CCTGAAATTGGAATGGCTTTTGGTGGGCGTGATCACAGTACAGTGATGCATGCTTGTGAAAAAGTCGTCA\n+GTTTACGGGAAGAAGACCCAATCTTTGATGAAGATTATAAGAACTTATTACGTTTGCTTCAAAGTTAA\n+>NZ_CP043953.1_2 # 1496 # 2644 # 1 # ID=1_2;partial=00;start_type=GTG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.393\n+GTGCGTTTGAAAATCGCTAAAGAAAGTTTACTCAATGTTTTATCGCATGTGGTCGGTGCGGTAGAACGTC\n+GTCATACCTTGAATATTCTTTCAAACGTCAAAATTCAGACTAATGCTCAAGCGCTCACTATTACGGGTTC\n+CGATTTAGAAGTTGAACTCGTAGCGAGCACCGCTTTATCAGAAGGGGCGTGCCTTGAGGCAGGCGAGACA\n+ACTGTTCCTGCTCGTAAATTGATGGAAATTTGTAAATCTTTGCCTACAGCTGCATTGATTGATTTACAAA\n+TTACTGAAGATCAAAGATGTATTTTAAAATCTGGTAATAGCCGTTTTGTGCTAGGTACACTACCGGCTGA\n+AGATTATCCATTGTTAACCACTGAGAATAGCCAGGGTACGCAAGTACAGGTGACTCAACGTGAATTAAAG\n+CGTTTATTTGAAAAAACTGCTTTTGCAATGGCTGTACAAGATGTACGTTTTTACCTCACTGGTACTTTAT\n+TAGAAATTGATGAAAATCAATTGCGTGCAGTAACAACTGATGGTCACCGTTTAGCACTTTGTGAAATTTT\n+GGCTTCCTCTACTTCATCTCAGTTGGTACAAGCGATTGTGCCTCGTAAAGCTGTGGGCGAATTGCAACGT\n+TTACTCAGCATTGAAGATGAACAGCTCACATTGCTTATTGGCCGTGAATTATTAAATGTAACGATTAATA\n+CGCCAAGCCGTGATAAAGAACAAGGTGATATTACAGTTCGTTTTACAACTAAATTGATTGATGGGAAATT\n+CCCTGATTATCGCCGTGTTATTCCACGTGGTGGTGATAAACATGTTTTGATTGGTCATGACGTATTTAAA\n+CAATCATTACAACGTGTAGCAATTTTAAGTAATGAAAAATTGCGTGGTGTTTTCCTAAATTTCAATCAGG\n+ATTCTTTACAGCTTCGTGCAAATAACCCTGAACAAGATGAAGCAATTGAAGATTTAGCGATCCAATATCA\n+AAGTGCCCCATTAGAAATGTCATTTAATGCTCAATACCTACTCGATGTATTGGGTGTATTAGATGGTGAT\n+GATGTAAATATGAGCATGACTGAGGCGAATCAGTCTGTATTGGTTCAAGATCCGGCTCATCCTGACCAGA\n+CCTATGTGGTTATGCCGATGCGTGTTTAA\n+>NZ_CP043953.1_3 # 2659 # 3741 # 1 # ID=1_3;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.394\n+ATGCATCTTACGCGCTTAAATATTGAACGTGTGCGTAATTTAAAAACGGTTGCACTCCATGGGTTGCAAC\n+CGTTTAATGTCTTTTATGGCGCAAACGGTTCAGGTAAAACATCAATTTTAGAAGCGATCCATTTGCTTGC\n+AACAGGTCGCTCATTCCGTACACATATACCCAAAAATTATATTCAATATGAAGCTGACGACGCGATTGTA\n+TTTGCTCAGTCAGCAACTGAAAAAATTGGTATGCAGAAACTCGCTTCTGGTGAGCAACTCATGAAAGTGA\n+ATGGCGATACCGTTGCGACTCAAGGTCAGCTCGCAAAGTTACTTCCTTTACAGCATATTGATCCACAAAG\n+TACGGATATTATTGATCATGGTGCCAAGCCAAGAAGACAACTTTTAGATTGGCTTATGTTCCACGTGGAA\n+CCTGAATTTTATTTTGCGTGGCAATATTACTCTCGTGCGCTAAAGCAGCGTAATACCTTACTCAAAACAC\n+GGCGTAATCTTTCATTAGCTGATTTAGAACCGTGGAACAAAATGTTGAGTGATTATGGCGAGATTTTGCA\n+CTCACAGCGTTTAAGTATTGTCGAGCAATGGAATGTTTATTTCCAAAATGACTTAAGCCAATTACTCCCT\n+GATTTGGAGATTGAACTGGAATATAGCCCAGGTTTTCATACAGAGCAGGGGCTTATGCAAGACTTGTTGA\n+ATCAGCATCAAAAAGACATCGAGAGACGTTATACCGAGTATGGTCCGCATCGGGCAGATTTGCGCTTAAA\n+AACGCCATTTGGACATGCTGATGATGTTTTATCAAGAGGTCAGAAAAAACTCTTGATTATTGCCTTAAAA\n+CTGTCACAAATTGCAATGTTGCATGCGAGTAATAAGGAAACTGTGGTATTATTAGATGATCTGACAGCAG\n+AATTAGACTTAACCGCACAACAACGTTTAATTGAACGATTAAGCCAACTTGGTAGCCAGGTTTTTATGA'..b'TTTTAGCTATGATTTTTGGTACACGGCAGATTGCAAACACGGAGCAACACGGCGGCCTCAT\n+GCTTGCGGTTGCATTTGAATCATTTGTGAAGTTATTTGCCTTACTTTGTGTCGCTTTATTTTTTATTTTT\n+GAATCACCGGCCAACCTGAGCCAAATGACCTCTGATGTAAACCAGACTTTTCAGGAAGTTCAGCTCTTTG\n+GTGTACCCGAAACCTTCTGGATTCAAACATTATTGGCGGGTTTAGCCATTATTTGCTTACCACGTCAGTT\n+CCACGTGGCGGTGGTCGAGCTACGCGATGAGAAGCATATTCGCGGTGCCCGTAAATGGTTCGCGGTTTAT\n+CTCATTTTAACTATTCTTGCCATTATTCCGATTGCAAGCTGGGCTTTACATGCTGCACCGAAGTTTCTGA\n+CCGTGCCTGATGTGGCTGTGCTGTCATTGCCTTTAAGTTATAACCAAGAGTGGCTGGCATTACTGGCCTT\n+TTTAGGCGGGTTCTCTGCCTCAACAGGCATGTTACTGGTGTCATCAGTAGCATTGTCTATTATGCTCAGT\n+AACGACTTGATTATGCCTGCTCTATGGCGATTTAAGTTGCTGTCACGTCACGATAAGCACTTACCTAAAG\n+TTCTTAAATTTAGCCGCCGTATTAGTATTGTTGCAGTGATGCTACTTGGCTTTTTATTCTTCCATTTCTT\n+TAATGACATTAACCAACTTTCAGTTTTCGGCTTATTGGCCTTTAGTGCTGTAGCACAGTTTGCACCTGCA\n+CTGATTGGTGGTTTGTATTGGCGTGGCGGAAGCCGTCAAGGCGTCTATGCAGGACTTATTATTGGATTTT\n+TAATGTGGAGTTATACATTACTATTTCCAACTATTTTGCGTAGCTTGCCTGAAGCCTATCAGGAAACTGC\n+TCAAAGTATTTTACTTTTCGGTCCTTTCGGCATTAATGCCCTACGCCCGGAATCTTTATTTGGTTTTGAG\n+TCATTTGCACCTTTAACTCACGGTGTTATTTGGTCACTCGGCTTAAATATTGTTTTATATATCTGGATTT\n+CAAAAATTTATCGGCCAAGCGTCGCTGAACAAATTCAGGCAGAAAGCTTCTTCTACTATGAAACTAAGCC\n+TTTACCATCACCGCACACATCTACTGATTTAACCTATCTTCCTCATGATGCGGCCCGCTTAAAAGTGGGT\n+GATTTATTTGCCCTAGCCAAAAGAATTACGGGTGAGCAACCCACTACGCAAGCGTTCGAAAATTTTTGTG\n+AGCAAAATCACCTCACCCTCAACCCAAATAGTATTGCCAATGGCATGTGGTGGCGTTTTACCGAGCAATA\n+TCTGGCCGGTATTATCGGTGCCGCTTCTGCACGTACGTTGCTCACAACAGCAATGATTAATAACGGCCTC\n+GCTTTAGGGCAAGTGGCTAATATTTTAGACCAAGCATCGCAGTGGCAACGTTTTAATCAGAACCTTCTTA\n+TGACCATGATTGACCACATGACCCAAGGGGTAAGCGTGGTTGATAAAAATATGTGTTTGGTCGCATGGAA\n+CAATCAATATTTAAAACTGTTTGGTTACCCAAAAGACCTCGTTTATGTGGGCTGCCCAATTGCCGACCTC\n+ATTCGTTATAACGCCGAACGCGGTGAATGTGGTCCCGGTTCAGTTGAAGAACATGTGCGTAAACGCCTTC\n+ACTGGATGAAAGTGGGAAGTGCTCACGAATTTGAACGTATTCGTAAAGATGGCCGTGTAATTCAAATGCG\n+AGGAAATCCAATCGCAGGTGGAGGCTTTGTAACGACATTTGCCGATATTACGGCCTTCCGTGCGAACGAA\n+GCCGTGCTTGAAGCCCGCGTAAAAGATAGAACTCAACAGCTTGCCGATGCCTTAACTGAGCAACAGCTTG\n+CACGTGAACAAGCCGATATGGCCAATATGTCAAAGAGTCGATTTATTGCCGCGGCAAGTCACGATCTATT\n+ACAGCCTATGCATGCTGCTCGTCTGTTTAGTACCGTTCTTGAGCAAAGTATTTCGACCGAAGAAGACCGC\n+CAGACCCTACAACAGCTTGACCGAGCACTCTATGGTGCAGAAAGTATGCTCTCTGCCCTACTCGATATTG\n+CACGTTTGGAAGGCGGTACCATACAGCCAAAGAGACAACCTTATCCGTTGCATGATTTGCTCAGTGATCT\n+TGAGTTGCAGTTTAAATCGATCGCTGCTCAGCGAAATATCTCACTGAAAGTCCACGATGTGTCTTTCTGG\n+ATCGATACCGACCCGCAGTGGATTCGTCGTATTATTCAGAACTTTGTCAGTAATGCTTTGCGTTATACCG\n+CTAAAGGTCGAGTGGTGGTAGGTGTACTCCGCTCTGCGCAGCAGTCTGGACATATTCGAATTGGGGTTTG\n+GGATACTGGACCTGGTATTGCCGAAGAACAACGGATTAAGCTATTCCAAGAGTTTGAGCGCTGTGGGCAT\n+TTATCACCTTGGGGTGAACAAGGTTTAGGGCTAGGACTTGCCATCGTACAACGTATGACAGGTTTGCTAA\n+ATTACCCTGTTCATGTTTACTCAGAGTTGGGCAAAGGCTCATGCTTTATGATTGAAGTACCTATTGTCGA\n+GCCACCAAAAGTTGCAACACCAGCTGTACAAGCCGTACCTTTAAAAACTAAAGCCTACCGTATTTTGTGC\n+CTAGACAATGATGAAACTATTCTTGAAGGAATGAGTAGTTTATTAGGACGATGGGGTTATCAAGTTTTCA\n+AAGCGACTGAACCTGAACAGGCGCTAGAAATTATTCAAAAAGAGAATATTCAGGTTTGGCTCATTGACCA\n+GCACTTAAACCACAATCAACTTGGCGTTGATTTTATTACTCAAAATCGTCAAGAAGATGTTCCTGTTGCC\n+TTAATTACAGCGGACTCGCACCCTGAATTACCGCAGCAATTAAAAGAACTGAATATTGTTTTACTCAAAA\n+AACCGTTAAAACCTGCTTCATTAAGAGCATGGTTATCTGGGCTTAAAATTGCCAGCACGACAGACTAA\n+>NZ_CP043953.1_174 # 199276 # 199608 # 1 # ID=1_174;partial=00;start_type=ATG;rbs_motif=AGGAG;rbs_spacer=5-10bp;gc_cont=0.390\n+ATGGATCAAAGCCAAGTAGAACAGATTCTACGTAATCCAAAGTTTCAAAAAATGGTCAAGAAAAAAAGTG\n+CATTAAGCTGGACGCTCACAATCATCATGTTAGTGCTTTATGTGGGCTTTATGCTACTTGTGGGCTACAA\n+CAAAGAATTTTTGATGAGTTCCTTTAGTGGTGGTGTAACGACATGGGGGATCCCGCTAGGTTTAGGAATT\n+ATTGTTTTATCTTTCCTACTTTGTGGTGTGTATTCCTATATCGCAAATAATACCCTTGACCAATTGAGTG\n+AAGAAGCGTTGAAGGAAGTTGAAGCCATCACGCATGAGAAAGGACTACACTAA\n+>NZ_CP043953.1_175 # 199610 # 199918 # 1 # ID=1_175;partial=01;start_type=ATG;rbs_motif=AGGA;rbs_spacer=5-10bp;gc_cont=0.447\n+ATGAAATGGAATTCATTCAAAGCGAAAGCCTTATTGGCAGCAGCATCGCTATATTCAACTGTTGCTATGG\n+CAAGCCCGGACTTAGGTGAAGCAGAACAGCAAGCCACCAACTGGCATGCCATTATCATGTTTATCATCTT\n+TGTTGGCTTTACCTTGTTTATTACCAAATGGGCGGCTAAACAAACTCAATCGGCGCAAGACTTCTATACT\n+GCTGGTGGTGGGATCAGTGGTTTCCAAAACGGTTTGGCGATTGCGGGTGACTATATGTCAGCAGCGTCAT\n+TTCTTGGTATTTCTGCAATGGTGTTTAGC\n' |
| b |
| diff -r 000000000000 -r 91791b6ecd38 test-data/output_train.start --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_train.start Thu Mar 14 16:49:04 2024 +0000 |
| b |
| b'@@ -0,0 +1,7691 @@\n+# Sequence Data: seqnum=1;seqlen=199920;seqhdr="NZ_CP043953.1 Acinetobacter baumannii strain K09-14 chromosome, complete genome"\n+# Run Data: version=Prodigal.v2.6.3;run_type=Single;model="Ab initio";gc_cont=38.99;transl_table=11;uses_sd=1\n+\n+Beg\tEnd\tStd\tTotal\tCodPot\tStrtSc\tCodon\tRBSMot\tSpacer\tRBSScr\tUpsScr\tTypeScr\tGCCont\n+\n+257\t388\t+\t-56.05\t-25.50\t-30.56\tGTG\tNone\tNone\t-11.71\t-5.33\t-13.02\t0.402\n+\n+428\t583\t-\t-49.57\t-15.57\t-34.00\tTTG\tNone\tNone\t-9.87\t0.78\t-24.41\t0.423\n+\n+659\t754\t-\t-12.10\t-15.19\t3.08\tATG\tGGA/GAG/AGG\t5-10bp\t1.81\t0.31\t1.47\t0.302\n+\n+698\t793\t+\t-33.00\t-16.24\t-16.76\tATG\tNone\tNone\t-16.24\t-1.48\t1.47\t0.281\n+\n+872\t985\t+\t-52.32\t-22.26\t-30.06\tGTG\tGGxGG\t5-10bp\t-6.92\t-7.52\t-15.13\t0.386\n+875\t985\t+\t-79.94\t-22.12\t-57.82\tTTG\t3Base/5BMM\t13-15bp\t-12.20\t-10.54\t-34.59\t0.378\n+890\t985\t+\t-81.08\t-16.39\t-64.69\tTTG\tNone\tNone\t-16.24\t-7.79\t-40.16\t0.375\n+\n+1115\t1213\t-\t-52.92\t-9.55\t-43.37\tGTG\tNone\tNone\t-15.73\t-9.64\t-17.49\t0.414\n+\n+1\t1398\t+\t210.23\t207.01\t3.22\tEdge\tNone\tNone\t0.00\t3.22\t0.00\t0.399\n+28\t1398\t+\t178.73\t206.14\t-27.41\tTTG\tNone\tNone\t-6.04\t-6.42\t-14.94\t0.398\n+61\t1398\t+\t188.45\t199.08\t-10.63\tATG\tNone\tNone\t-6.04\t-8.52\t3.94\t0.395\n+175\t1398\t+\t138.58\t158.20\t-19.63\tTTG\tGGA/GAG/AGG\t11-12bp\t-0.62\t-4.07\t-14.94\t0.397\n+187\t1398\t+\t128.26\t152.53\t-24.27\tTTG\tNone\tNone\t-6.04\t-3.29\t-14.94\t0.397\n+202\t1398\t+\t142.29\t152.16\t-9.87\tGTG\tAGxAGG/AGGxGG\t3-4bp\t2.13\t-5.28\t-6.72\t0.394\n+220\t1398\t+\t124.29\t143.65\t-19.36\tTTG\tGGA/GAG/AGG\t5-10bp\t4.87\t-9.28\t-14.94\t0.393\n+247\t1398\t+\t101.95\t129.37\t-27.42\tTTG\tNone\tNone\t-6.04\t-6.44\t-14.94\t0.392\n+436\t1398\t+\t74.81\t79.32\t-4.50\tATG\t3Base/5BMM\t13-15bp\t-5.27\t-3.17\t3.94\t0.395\n+496\t1398\t+\t37.39\t63.16\t-25.77\tTTG\tNone\tNone\t-6.04\t-4.79\t-14.94\t0.394\n+538\t1398\t+\t42.76\t49.71\t-6.96\tATG\t3Base/5BMM\t13-15bp\t-5.27\t-5.63\t3.94\t0.395\n+589\t1398\t+\t30.59\t40.01\t-9.41\tATG\tNone\tNone\t-6.04\t-7.31\t3.94\t0.388\n+595\t1398\t+\t40.19\t38.45\t1.74\tATG\tGGA/GAG/AGG\t5-10bp\t4.87\t-7.07\t3.94\t0.389\n+625\t1398\t+\t13.65\t29.81\t-16.15\tGTG\tNone\tNone\t-6.04\t-3.40\t-6.72\t0.394\n+685\t1398\t+\t0.06\t22.82\t-22.76\tTTG\tNone\tNone\t-6.04\t-1.78\t-14.94\t0.398\n+712\t1398\t+\t-9.06\t14.40\t-23.46\tTTG\t3Base/5BMM\t13-15bp\t-5.27\t-3.25\t-14.94\t0.405\n+838\t1398\t+\t-55.34\t-29.02\t-26.32\tTTG\tNone\tNone\t-6.04\t-4.84\t-14.94\t0.422\n+961\t1398\t+\t-80.84\t-53.92\t-26.92\tTTG\tNone\tNone\t-6.04\t-5.44\t-14.94\t0.427\n+1141\t1398\t+\t-138.24\t-120.26\t-17.99\tGTG\tNone\tNone\t-6.04\t-4.73\t-6.72\t0.430\n+1219\t1398\t+\t-176.55\t-137.97\t-38.57\tTTG\tNone\tNone\t-8.53\t-8.44\t-21.10\t0.422\n+1225\t1398\t+\t-157.37\t-139.42\t-17.95\tATG\tNone\tNone\t-8.83\t-11.31\t2.69\t0.414\n+1273\t1398\t+\t-189.05\t-161.71\t-27.34\tATG\tNone\tNone\t-12.28\t-16.50\t1.94\t0.389\n+1303\t1398\t+\t-228.44\t-171.88\t-56.56\tGTG\tNone\tNone\t-16.24\t-21.77\t-18.06\t0.354\n+1306\t1398\t+\t-214.78\t-172.55\t-42.23\tATG\tNone\tNone\t-16.78\t-26.37\t1.42\t0.344\n+\n+1426\t1530\t-\t-66.78\t-5.05\t-61.74\tTTG\tNone\tNone\t-14.81\t-9.81\t-36.62\t0.362\n+\n+1310\t1444\t+\t-45.64\t-27.61\t-18.03\tATG\tNone\tNone\t-11.44\t-8.16\t2.08\t0.341\n+1316\t1444\t+\t-58.65\t-27.74\t-30.92\tGTG\tNone\tNone\t-11.99\t-5.10\t-13.33\t0.341\n+1355\t1444\t+\t-80.71\t-22.76\t-57.95\tTTG\tAGxAG\t5-10bp\t-9.34\t-5.17\t-42.93\t0.300\n+\n+1776\t1943\t-\t-33.07\t-0.79\t-32.27\tTTG\tNone\tNone\t-9.15\t0.02\t-22.64\t0.375\n+\n+2046\t2180\t+\t-57.71\t-29.64\t-28.07\tGTG\tNone\tNone\t-11.44\t-3.41\t-12.72\t0.422\n+2091\t2180\t+\t-92.28\t-24.74\t-67.54\tTTG\tNone\tNone\t-17.36\t-6.75\t-42.93\t0.422\n+\n+2177\t2308\t-\t-34.91\t-25.24\t-9.67\tATG\tNone\tNone\t-11.71\t0.51\t2.03\t0.371\n+2177\t2323\t-\t-31.27\t-23.80\t-7.48\tATG\tNone\tNone\t-10.49\t1.24\t2.27\t0.367\n+2177\t2338\t-\t-58.41\t-24.56\t-33.85\tTTG\tNone\tNone\t-9.50\t-0.36\t-23.49\t0.358\n+\n+2397\t2486\t-\t-26.33\t-6.49\t-19.84\tATG\tNone\tNone\t-17.36\t-3.35\t1.37\t0.389\n+2397\t2498\t-\t-4.42\t-7.04\t2.62\tATG\tGGA/GAG/AGG\t5-10bp\t1.93\t-0.37\t1.56\t0.373\n+\n+1496\t2644\t+\t215.73\t211.69\t4.04\tGTG\tGGAG/GAGG\t5-10bp\t11.34\t-0.58\t-6.72\t0.393\n+1502\t2644\t+\t187.97\t208.67\t-20.69\tTTG\t4Base/6BMM\t13-15bp\t-3.62\t-2.13\t-14.94\t0.391\n+1544\t2644\t+\t185.76\t197.25\t-11.49\tGTG\tNone\tNone\t-6.04\t1.27\t-6.72\t0.395\n+1574\t2644\t+\t158.00\t181.92\t-23.93\tTTG\tNone\tNone\t-6.04\t-2.95\t-14.94\t0.389\n+1724\t2644\t+\t113.80\t139.19\t-25.39\tTTG\tNone\tNone\t-6.04\t-4.41\t-14.94\t0.378\n+1727\t2644\t+\t132.63\t140.00\t'..b'5\t2.51\t0.488\n+198090\t198230\t+\t-61.18\t-17.69\t-43.49\tTTG\tNone\tNone\t-10.94\t-4.98\t-27.07\t0.489\n+198123\t198230\t+\t-16.10\t-8.65\t-7.45\tATG\tGGA/GAG/AGG\t5-10bp\t2.04\t-10.65\t1.65\t0.481\n+\n+198367\t198459\t+\t-72.45\t-12.04\t-60.41\tTTG\tNone\tNone\t-16.78\t-1.63\t-41.50\t0.473\n+\n+198363\t198470\t+\t-28.15\t-11.42\t-16.73\tATG\tNone\tNone\t-14.38\t-3.50\t1.65\t0.426\n+\n+198449\t198640\t+\t-47.24\t-17.44\t-29.80\tTTG\t4Base/6BMM\t13-15bp\t-4.79\t-4.74\t-19.76\t0.432\n+198533\t198640\t+\t-42.64\t-29.74\t-12.91\tATG\tNone\tNone\t-14.38\t0.32\t1.65\t0.491\n+\n+198747\t198887\t+\t-28.67\t-14.90\t-13.77\tATG\tNone\tNone\t-10.94\t-4.50\t2.17\t0.461\n+198774\t198887\t+\t-47.13\t-11.15\t-35.98\tGTG\tNone\tNone\t-13.61\t-6.75\t-15.13\t0.465\n+198795\t198887\t+\t-83.24\t-9.36\t-73.88\tTTG\tNone\tNone\t-16.78\t-15.10\t-41.50\t0.430\n+\n+198966\t199073\t-\t-66.71\t-16.35\t-50.37\tTTG\tNone\tNone\t-14.38\t0.09\t-35.57\t0.407\n+\n+199019\t199126\t-\t-35.51\t-23.35\t-12.16\tATG\tNone\tNone\t-14.38\t1.07\t1.65\t0.361\n+\n+199183\t199284\t-\t-64.85\t-11.58\t-53.27\tTTG\tNone\tNone\t-15.26\t0.22\t-37.73\t0.324\n+199183\t199290\t-\t-59.78\t-9.67\t-50.10\tTTG\tNone\tNone\t-14.38\t0.35\t-35.57\t0.333\n+\n+199501\t199590\t-\t-27.13\t-11.25\t-15.88\tATG\tNone\tNone\t-17.36\t0.61\t1.37\t0.411\n+\n+199600\t199716\t-\t-36.62\t-8.24\t-28.38\tGTG\tNone\tNone\t-13.25\t0.10\t-14.73\t0.444\n+199600\t199719\t-\t-55.67\t-8.51\t-47.17\tTTG\tNone\tNone\t-12.91\t-1.83\t-31.93\t0.442\n+199600\t199731\t-\t-20.39\t-10.38\t-10.01\tATG\tNone\tNone\t-11.71\t0.17\t2.03\t0.447\n+199600\t199737\t-\t-21.85\t-12.42\t-9.43\tATG\tNone\tNone\t-11.19\t0.13\t2.13\t0.442\n+199600\t199746\t-\t-24.62\t-14.43\t-10.19\tATG\t3Base/5BMM\t13-15bp\t-9.15\t-2.81\t2.27\t0.429\n+199600\t199776\t-\t-53.45\t-21.17\t-32.28\tTTG\tNone\tNone\t-8.68\t-1.63\t-21.47\t0.407\n+\n+199240\t199608\t+\t10.84\t20.46\t-9.62\tGTG\tNone\tNone\t-6.04\t3.14\t-6.72\t0.398\n+199270\t199608\t+\t-2.46\t21.18\t-23.64\tTTG\tNone\tNone\t-6.04\t-2.66\t-14.94\t0.389\n+199276\t199608\t+\t36.72\t20.29\t16.43\tATG\tAGGAG\t5-10bp\t13.64\t-1.15\t3.94\t0.390\n+199327\t199608\t+\t3.69\t6.14\t-2.45\tATG\tNone\tNone\t-6.04\t-0.35\t3.94\t0.401\n+199372\t199608\t+\t6.18\t8.01\t-1.83\tATG\t3Base/5BMM\t13-15bp\t-5.63\t0.11\t3.69\t0.401\n+199378\t199608\t+\t-11.20\t5.35\t-16.55\tGTG\tNone\tNone\t-6.62\t-2.56\t-7.37\t0.407\n+199387\t199608\t+\t-12.41\t3.41\t-15.81\tGTG\tNone\tNone\t-6.90\t-1.25\t-7.67\t0.410\n+199396\t199608\t+\t-5.73\t0.80\t-6.52\tATG\tNone\tNone\t-7.19\t-2.64\t3.31\t0.404\n+199405\t199608\t+\t-16.99\t0.12\t-17.10\tGTG\tNone\tNone\t-7.51\t-1.23\t-8.36\t0.407\n+199426\t199608\t+\t-34.94\t-1.79\t-33.15\tTTG\tNone\tNone\t-8.39\t-3.51\t-20.75\t0.410\n+199429\t199608\t+\t-12.48\t-0.91\t-11.57\tATG\tNone\tNone\t-8.53\t-5.33\t2.79\t0.411\n+199513\t199608\t+\t-57.29\t-22.02\t-35.27\tGTG\tNone\tNone\t-16.24\t-0.47\t-18.06\t0.406\n+\n+199691\t199792\t-\t-62.71\t-3.38\t-59.32\tTTG\tNone\tNone\t-15.26\t-5.84\t-37.73\t0.402\n+199691\t199798\t-\t-60.47\t-3.92\t-56.55\tTTG\tNone\tNone\t-14.38\t-6.10\t-35.57\t0.398\n+199691\t199807\t-\t-51.31\t-5.90\t-45.42\tTTG\tAGxAG\t5-10bp\t-7.13\t-5.02\t-32.77\t0.419\n+199691\t199846\t-\t-44.08\t-6.62\t-37.46\tTTG\tNone\tNone\t-9.87\t-2.67\t-24.41\t0.429\n+\n+199574\t199918\t+\t8.39\t32.05\t-23.66\tTTG\tNone\tNone\t-6.04\t-2.68\t-14.94\t0.443\n+199589\t199918\t+\t27.59\t33.53\t-5.95\tATG\tNone\tNone\t-6.04\t-3.85\t3.94\t0.439\n+199610\t199918\t+\t46.91\t34.06\t12.85\tATG\tAGGA\t5-10bp\t11.57\t-2.67\t3.94\t0.447\n+199643\t199918\t+\t8.85\t30.46\t-21.61\tTTG\tNone\tNone\t-6.04\t-0.63\t-14.94\t0.460\n+199676\t199918\t+\t19.24\t25.46\t-6.22\tATG\tNone\tNone\t-6.04\t-4.12\t3.94\t0.461\n+199736\t199918\t+\t0.67\t5.59\t-4.93\tATG\tNone\tNone\t-6.04\t-2.82\t3.94\t0.437\n+199763\t199918\t+\t-14.88\t7.36\t-22.24\tTTG\tNone\tNone\t-6.04\t-1.25\t-14.94\t0.455\n+199853\t199918\t+\t-50.44\t-19.76\t-30.67\tTTG\tNone\tNone\t-6.04\t-5.34\t-14.94\t0.455\n+\n+199695\t199919\t+\t-33.34\t-22.27\t-11.07\tGTG\tGGA/GAG/AGG\t5-10bp\t4.87\t-4.87\t-6.72\t0.449\n+199725\t199919\t+\t-31.12\t-19.80\t-11.31\tATG\tNone\tNone\t-6.04\t-4.86\t3.94\t0.431\n+199749\t199919\t+\t-47.82\t-18.98\t-28.84\tTTG\tNone\tNone\t-6.04\t-3.51\t-14.94\t0.450\n+199752\t199919\t+\t-47.67\t-18.33\t-29.35\tTTG\tNone\tNone\t-6.04\t-4.01\t-14.94\t0.452\n+199824\t199919\t+\t-33.33\t-11.09\t-22.24\tGTG\tNone\tNone\t-6.04\t-5.13\t-6.72\t0.469\n+199827\t199919\t+\t-33.52\t-11.56\t-21.96\tGTG\tNone\tNone\t-6.04\t-4.85\t-6.72\t0.462\n+199836\t199919\t+\t-29.61\t-11.56\t-18.06\tGTG\tGGxGG\t5-10bp\t-3.07\t-3.92\t-6.72\t0.452\n+199860\t199919\t+\t-41.21\t-8.69\t-32.51\tTTG\tNone\tNone\t-6.04\t-7.18\t-14.94\t0.433\n+\n' |
| b |
| diff -r 000000000000 -r 91791b6ecd38 test-data/output_tt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_tt Thu Mar 14 16:49:04 2024 +0000 |
| b |
| b'@@ -0,0 +1,353 @@\n+DEFINITION seqnum=1;seqlen=199920;seqhdr="NZ_CP043953.1 Acinetobacter baumannii strain K09-14 chromosome, complete genome";version=Prodigal.v2.6.3;run_type=Single;model="Ab initio";gc_cont=40.29;transl_table=4;uses_sd=1\n+FEATURES Location/Qualifiers\n+ CDS <1..1398\n+ /note="ID=1_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.399;conf=99.99;score=210.07;cscore=206.85;sscore=3.22;rscore=0.00;uscore=3.22;tscore=0.00;"\n+ CDS 1496..2644\n+ /note="ID=1_2;partial=00;start_type=GTG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.393;conf=99.99;score=217.17;cscore=206.94;sscore=10.23;rscore=11.96;uscore=2.64;tscore=-4.37;"\n+ CDS 2659..3741\n+ /note="ID=1_3;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.394;conf=100.00;score=138.30;cscore=142.02;sscore=-3.72;rscore=-6.78;uscore=-1.93;tscore=3.87;"\n+ CDS 3794..6262\n+ /note="ID=1_4;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.416;conf=99.99;score=485.83;cscore=467.34;sscore=18.48;rscore=11.96;uscore=1.95;tscore=3.87;"\n+ CDS 6300..6692\n+ /note="ID=1_5;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.384;conf=100.00;score=68.77;cscore=50.71;sscore=18.05;rscore=11.96;uscore=1.36;tscore=3.87;"\n+ CDS complement(6778..7335)\n+ /note="ID=1_6;partial=00;start_type=ATG;rbs_motif=3Base/5BMM;rbs_spacer=13-15bp;gc_cont=0.360;conf=100.00;score=46.62;cscore=47.71;sscore=-1.09;rscore=-2.22;uscore=-2.08;tscore=3.87;"\n+ CDS complement(7586..9517)\n+ /note="ID=1_7;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.419;conf=99.99;score=325.08;cscore=330.06;sscore=-4.98;rscore=-6.78;uscore=-1.42;tscore=3.87;"\n+ CDS 9774..10778\n+ /note="ID=1_8;partial=00;start_type=ATG;rbs_motif=AGGA;rbs_spacer=5-10bp;gc_cont=0.405;conf=100.00;score=121.68;cscore=103.69;sscore=17.99;rscore=11.85;uscore=2.27;tscore=3.87;"\n+ CDS 11034..12041\n+ /note="ID=1_9;partial=00;start_type=ATG;rbs_motif=AGGA;rbs_spacer=5-10bp;gc_cont=0.403;conf=99.99;score=187.93;cscore=173.28;sscore=14.65;rscore=11.85;uscore=-0.42;tscore=3.87;"\n+ CDS 12384..13388\n+ /note="ID=1_10;partial=00;start_type=ATG;rbs_motif=AGGA;rbs_spacer=5-10bp;gc_cont=0.418;conf=100.00;score=167.77;cscore=150.72;sscore=17.05;rscore=11.85;uscore=1.98;tscore=3.87;"\n+ CDS 13513..13848\n+ /note="ID=1_11;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.435;conf=99.98;score=38.27;cscore=21.15;sscore=17.13;rscore=11.96;uscore=1.30;tscore=3.87;"\n+ CDS complement(13905..14750)\n+ /note="ID=1_12;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.371;conf=100.00;score=88.27;cscore=73.66;sscore=14.61;rscore=5.20;uscore=5.54;tscore=3.87;"\n+ CDS complement(14878..16005)\n+ /note="ID=1_13;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.421;conf=99.99;score=186.58;cscore=177.05;sscore=9.53;rscore=5.20;uscore=1.11;tscore=3.87;"\n+ CDS 16085..17299\n+ /note="ID=1_14;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.395;conf=99.99;score=236.39;cscore=226.19;sscore=10.20;rscore=5.20;uscore=1.13;tscore=3.87;"\n+ CDS 18152..18376\n+ /note="ID=1_15;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.516;conf=61.06;score=1.96;cscore=-0.31;sscore=2.27;rscore=4.62;uscore=-4.63;tscore=3.43;"\n+ CDS 23636..24235\n+ /note="ID=1_16;partial=00;start_type=ATG;rbs_motif=AGxAGG/AGGxGG;rbs_s'..b'2.95;cscore=-1.16;sscore=4.11;rscore=2.68;uscore=-0.07;tscore=2.00;"\n+ CDS 182824..183126\n+ /note="ID=1_160;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.396;conf=99.99;score=39.72;cscore=40.60;sscore=-0.88;rscore=-6.78;uscore=2.03;tscore=3.87;"\n+ CDS 183155..184213\n+ /note="ID=1_161;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.427;conf=99.99;score=243.24;cscore=220.12;sscore=23.13;rscore=11.96;uscore=6.33;tscore=3.87;"\n+ CDS 184382..185689\n+ /note="ID=1_162;partial=00;start_type=TTG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.413;conf=100.00;score=172.81;cscore=170.47;sscore=2.34;rscore=11.96;uscore=1.46;tscore=-11.08;"\n+ CDS 185671..186393\n+ /note="ID=1_163;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.393;conf=100.00;score=95.42;cscore=94.41;sscore=1.01;rscore=-6.78;uscore=3.92;tscore=3.87;"\n+ CDS complement(186358..187338)\n+ /note="ID=1_164;partial=00;start_type=GTG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.384;conf=100.00;score=145.08;cscore=139.93;sscore=5.16;rscore=5.20;uscore=4.32;tscore=-4.37;"\n+ CDS complement(187451..188026)\n+ /note="ID=1_165;partial=00;start_type=ATG;rbs_motif=AGGA;rbs_spacer=5-10bp;gc_cont=0.387;conf=100.00;score=49.64;cscore=34.67;sscore=14.97;rscore=11.85;uscore=-0.10;tscore=3.87;"\n+ CDS 188321..190270\n+ /note="ID=1_166;partial=00;start_type=ATG;rbs_motif=AGGA;rbs_spacer=5-10bp;gc_cont=0.448;conf=99.99;score=314.00;cscore=298.62;sscore=15.37;rscore=11.85;uscore=-0.35;tscore=3.87;"\n+ CDS complement(190317..190910)\n+ /note="ID=1_167;partial=00;start_type=TTG;rbs_motif=AGGA/GGAG/GAGG;rbs_spacer=11-12bp;gc_cont=0.357;conf=100.00;score=90.83;cscore=89.54;sscore=1.29;rscore=8.80;uscore=4.22;tscore=-11.08;"\n+ CDS 190965..191378\n+ /note="ID=1_168;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.362;conf=99.99;score=40.31;cscore=46.20;sscore=-5.89;rscore=-6.78;uscore=-2.98;tscore=3.87;"\n+ CDS complement(191470..192582)\n+ /note="ID=1_169;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.425;conf=99.99;score=197.94;cscore=178.67;sscore=19.27;rscore=11.96;uscore=2.66;tscore=3.87;"\n+ CDS complement(192627..193364)\n+ /note="ID=1_170;partial=00;start_type=ATG;rbs_motif=AGGA;rbs_spacer=5-10bp;gc_cont=0.424;conf=100.00;score=133.88;cscore=115.37;sscore=18.50;rscore=11.85;uscore=3.44;tscore=3.87;"\n+ CDS 193741..194391\n+ /note="ID=1_171;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.399;conf=100.00;score=107.30;cscore=108.93;sscore=-1.62;rscore=-6.78;uscore=1.29;tscore=3.87;"\n+ CDS complement(194434..195201)\n+ /note="ID=1_172;partial=00;start_type=ATG;rbs_motif=AGGA;rbs_spacer=5-10bp;gc_cont=0.409;conf=100.00;score=117.04;cscore=101.34;sscore=15.70;rscore=11.85;uscore=0.63;tscore=3.87;"\n+ CDS complement(195595..199092)\n+ /note="ID=1_173;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=3-4bp;gc_cont=0.443;conf=99.99;score=470.07;cscore=474.88;sscore=-4.80;rscore=-5.57;uscore=-2.45;tscore=3.87;"\n+ CDS 199276..199608\n+ /note="ID=1_174;partial=00;start_type=ATG;rbs_motif=AGGAG;rbs_spacer=5-10bp;gc_cont=0.390;conf=100.00;score=46.23;cscore=30.52;sscore=15.70;rscore=13.73;uscore=-1.89;tscore=3.87;"\n+ CDS 199610..>199918\n+ /note="ID=1_175;partial=01;start_type=ATG;rbs_motif=AGGA;rbs_spacer=5-10bp;gc_cont=0.447;conf=100.00;score=45.97;cscore=30.24;sscore=15.73;rscore=11.85;uscore=-1.25;tscore=3.87;"\n+//\n' |
| b |
| diff -r 000000000000 -r 91791b6ecd38 test-data/output_tt.faa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_tt.faa Thu Mar 14 16:49:04 2024 +0000 |
| b |
| b'@@ -0,0 +1,1224 @@\n+>NZ_CP043953.1_1 # 1 # 1398 # 1 # ID=1_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.399\n+MLWTDCLTRLRQELSDNVFAMWIRPLVAEEVEGILRLYAPNPYWTRYIQENHLELISILA\n+EQLSEGRVRQVEILVDSRPGSILSSSEQPATTTAALQTAPIPQPAKVKREPEPVANTAVS\n+SKSSKKKLLNPQFTFSLFVEGRSNQMAAETCRKVLTQLGASQHNPLFLYGPTGLGKTHLM\n+QAVGNALLQAKPNARVMYMTSESFVQDFVSSLQKGKVEEFKKNCRSLDLLLVDDIHLLAG\n+KEASLVEFFYTFNALLDESKQIILTSDRYPKELTELDPRLVSRFSWGLSVGVEPPDIETR\n+IEILLKKAENSGVDLPRNCALFIAQQVVANVRELEGALNKVVAISRFKGAPIDLDVVRES\n+LKDVLAIRARTISVENIQRVVSEYFRIPLKELVGPKRTRIYARPRQLAMGLARELTGDSF\n+PEIGMAFGGRDHSTVMHACEKVVSLREEDPIFDEDYKNLLRLLQS*\n+>NZ_CP043953.1_2 # 1496 # 2644 # 1 # ID=1_2;partial=00;start_type=GTG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.393\n+MRLKIAKESLLNVLSHVVGAVERRHTLNILSNVKIQTNAQALTITGSDLEVELVASTALS\n+EGACLEAGETTVPARKLMEICKSLPTAALIDLQITEDQRCILKSGNSRFVLGTLPAEDYP\n+LLTTENSQGTQVQVTQRELKRLFEKTAFAMAVQDVRFYLTGTLLEIDENQLRAVTTDGHR\n+LALCEILASSTSSQLVQAIVPRKAVGELQRLLSIEDEQLTLLIGRELLNVTINTPSRDKE\n+QGDITVRFTTKLIDGKFPDYRRVIPRGGDKHVLIGHDVFKQSLQRVAILSNEKLRGVFLN\n+FNQDSLQLRANNPEQDEAIEDLAIQYQSAPLEMSFNAQYLLDVLGVLDGDDVNMSMTEAN\n+QSVLVQDPAHPDQTYVVMPMRV*\n+>NZ_CP043953.1_3 # 2659 # 3741 # 1 # ID=1_3;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.394\n+MHLTRLNIERVRNLKTVALHGLQPFNVFYGANGSGKTSILEAIHLLATGRSFRTHIPKNY\n+IQYEADDAIVFAQSATEKIGMQKLASGEQLMKVNGDTVATQGQLAKLLPLQHIDPQSTDI\n+IDHGAKPRRQLLDWLMFHVEPEFYFAWQYYSRALKQRNTLLKTRRNLSLADLEPWNKMLS\n+DYGEILHSQRLSIVEQWNVYFQNDLSQLLPDLEIELEYSPGFHTEQGLMQDLLNQHQKDI\n+ERRYTEYGPHRADLRLKTPFGHADDVLSRGQKKLLIIALKLSQIAMLHASNKETVVLLDD\n+LTAELDLTAQQRLIERLSQLGSQVFMTTLDHASVKKHLHDLSISYQLFSVESGQVSLAAP\n+*\n+>NZ_CP043953.1_4 # 3794 # 6262 # 1 # ID=1_4;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.416\n+MSSESQSASQTEQTNEKAYDSSSIKVLRGLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDN\n+AIDEALAGHCDEIIVTIHEDESVSVSDNGRGIPTDIHPEEGVSAAEVILTILHAGGKFDD\n+NSYKVSGGLHGVGVSVVNALSSKLHLTIYRAGQIHEQEYHHGDPQYPLRVIGETDNTGTT\n+VRFWPSAETFSQTIFNVEILARRLRELSFLNAGVRIVLRDERINLEHVYDYEGGLSEFVK\n+YINEGKNHLNEIFHFTADADNGITVEVALQWNDSYQENVRCFTNNIPQKDGGTHLAGFRA\n+ALTRGLNQYLENENILKKEKVNVTGDDAREGLTAIISVKVPDPKFSSQTKEKLVSSEVKP\n+AVEQAMNKEFSAYLLENPQAAKSIAGKIIDAARARDAARKAREMTRRKSALDIAGLPGKL\n+ADCQEKDPALSELYLVEGDSAGGSAKQGRNRKMQAILPLKGKILNVERARFDKMISSQEV\n+GTLITALGCGIGREEYNPDKLRYHKIIIMTDADVDGSHIRTLLLTFFFRQMPELVERGHI\n+YIAQPPLYKLKKGKQEQYIKDNDALETYLISNAIDELALHISADAPAITGEALAKVIQDY\n+QVSQKSLQRLTLRYPASLLDALLEVDAFKADQNHDQAYVQQWADQVREAVEKLQPSLRPE\n+ITLETFERENAQGEKSAHYWPRVTVYVHNLPHAYLLDAGLLNSAEYARLLKNSKSWFKLI\n+EDGAYLQKGDRRIQVANFHQVWQHILQDSRRGMMIQRYKGLGEMNAEQLWETTMDPENRN\n+MLQVTIDDAIEADRMFSCLMGDDVEPRRAFIEENALNADIDA*\n+>NZ_CP043953.1_5 # 6300 # 6692 # 1 # ID=1_5;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.384\n+MMSQKILASMLISCAALVSHSAFAADLEADMKTLAKSTKAFAEAKDIDNAKQQLVIMRQA\n+ALSSKLSLPHKLEGLPPENVQVKEYQAGLDQLVAEIDRVTVFVDKGQLDQAKTEAINLVN\n+IRNENHKKFR*\n+>NZ_CP043953.1_6 # 6778 # 7335 # -1 # ID=1_6;partial=00;start_type=ATG;rbs_motif=3Base/5BMM;rbs_spacer=13-15bp;gc_cont=0.360\n+MNFIDFITNFEQFLPILIQEYGAWVYAILFLIIFSETAFVFMFFLPGDSLLLTVGALCSV\n+VELMHLGYMITLLTIAATLGYIVNYSIGRHFGNRIFEAKSRFIKKEYLNKTNRYFLQHGG\n+KTILLARFIPFARSFAPLAAGSSNMSYGKFLIYNVAGAILWICILLTAGYLFGHALIQVT\n+DFVEN*\n+>NZ_CP043953.1_7 # 7586 # 9517 # -1 # ID=1_7;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.419\n+MIQFDQVSLRRGGRVLFQKASMQLHPGWKIGLTGVNGAGKSTLFAALLGSLGADEGSLTR\n+PSVWTVAHMAQEVKALDMPAIDFVLSGDEEYWDIQNKLAQPEQLTDSDLAKLHGRFDEIH\n+GYSAPSKAAQLMAGLGFLEHQLRLNVASFSGGWRMRLNLARTLMSRSDLLLLDEPTNHLD\n+LDAILWLEDWLKAYEGTLILISHDRDFLDAITDHILHIENQELTLYTGNYSTFETTRSER\n+LAQQQQAFEKQQEARAHLQKFIDRFKAKATKARQAQSRIKQLERMQQLAPAHVDTPFTFS\n+FREPTKMSSPLLTLENASIGYGDKKIAEKIKLQITPNSRIGLLGMNGAGKSTLIKSLVGD\n+LPLLAGERKASELLNIGYFAQHQMDALDGQASPMLQLARIADKQISEATLRSFLGSFGFS\n+GERMDTPCESFSGGERARLALALIVWQRPNVLILDEPTNHLDLDMRHALSMALQDFEGAV\n+VLVSHERQLIASVCDELLLVHGGKCTEFEGDLQDYAKWLREARQQQINAQTAVAQNNSSS\n+AAPTPAKVDKEAQRKEAARRREQTRPIRKNIEKVESQIEQLQPRLAEIEEALADTSLYEA\n+NRKDDLLKLMNEQTELKAKLEQYEEQLLELMMELEEMEASFEN*\n+>NZ_CP043953.1_8 # 9774 # 10778 # 1'..b't_type=TTG;rbs_motif=AGGA/GGAG/GAGG;rbs_spacer=11-12bp;gc_cont=0.357\n+MWAENNLVLSYTNKSILMKQALLVIDVQNDYFKNGKMELVGPDQALDKIKQLEQYFNEKD\n+LSIIYVQHINPPQASFFQENTEGVLLHPELSAGGDSLIVTKHYPNSFLETNLKELLKAHQ\n+IEQLVITGMMTHICIDSGTRAAKELGYQPILIGDATATRDLSHNGKTVKAEDVQTAFLAA\n+LGMFASVQNTADFLAKS*\n+>NZ_CP043953.1_168 # 190965 # 191378 # 1 # ID=1_168;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.362\n+MNIELDPIDLKIIALLKQDSRLTNKEIGQRVHRTGQAVGARIAQLMDAGVIKNYTIAVQY\n+RHKQFIHLHLNEQRSFEEIENLVKQYEQIDECFKVMGNACYMIVSHFEPAELNAFIEVLS\n+KWCRYSVETVIREVEKA*\n+>NZ_CP043953.1_169 # 191470 # 192582 # -1 # ID=1_169;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.425\n+MTQLQQPIKFAYWVPNVSGGLVVSNIEQRTDWSYDYNVRLAQAAENNGFEYALTQIRFTA\n+GYGAENQHESVSFSHALLAKTEKLKVIAAILPGPWKPALAAKQLATIDYLTQGRIAINVV\n+SGWFRGEFDAIGEEWPEHDERYVRSEEFIRTLKGIWTTDNYSFDGKYYQFQNYTLKPKPL\n+QKPHIEVFQGGSSRAARDMASRVSDWYFTNGNTVEEIQKQVEDIRAKAKANNHQVKIGVN\n+AFIIARDTEEEAKAVLQEIIDKANTEAVNAFGDATREAGAASPEQEGNWAKSTFEDLVQY\n+NDGFKTNLIGTPQQIAERIVALKNVGVDLVLSGFLHFIEEVEYFGEKVLPLVRQLELQQE\n+KEVEIQAKSA*\n+>NZ_CP043953.1_170 # 192627 # 193364 # -1 # ID=1_170;partial=00;start_type=ATG;rbs_motif=AGGA;rbs_spacer=5-10bp;gc_cont=0.424\n+MTGITSSKPLNIVAVSGGLNTPSKTESLVQAILDELSEAIDIKVHFIKLSEIGPLLGGAF\n+YRNQLPQRVQDDLAAVEAADALIVGTPVYRASFTGLFKHFFDFVEQTALVDVPVLLAASG\n+GSDRHALVLEHQLRPLFSFFQAQTLPIGVYATDRDFTPEYTVKSEQLSDRITLAVARALP\n+ILEWAPAKGKRAEVVKPKSQQANQELGINKQIEQEEVLPSAAVPNLDAAESRLHHKSGKS\n+LTHVA*\n+>NZ_CP043953.1_171 # 193741 # 194391 # 1 # ID=1_171;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.399\n+MNILIVDDHPLFRHALIQAVRYSLPQAQIHETASVDEFYERLENGAEPDLVLLDLNLPGA\n+SGFSALVYVRAQYPSIPIIVVSAHEEASIIQRAIAHGAMGYIPKSAHPSHIGEAIRQVLD\n+GEIWLPPNLPSNINLDPRAADETALAERIQSLTPQQFRVLMMVAEGLLNKQIAYELDVSE\n+ATIKAHVTAIFRKLGVQNRTQAVLAISALNIEDKKI*\n+>NZ_CP043953.1_172 # 194434 # 195201 # -1 # ID=1_172;partial=00;start_type=ATG;rbs_motif=AGGA;rbs_spacer=5-10bp;gc_cont=0.409\n+MNISDNTPQGQLSSQQFYRQYSANALLPELDWQSIFPHSKLSEAHIKALNTIYQCAVPLA\n+LNVFHDLNFDVFAPAAYHPQGLGLFDKLAQQEENFLKVLTAESENLDHETRHQIWSMLLR\n+GGAVLVFKAWLGHVKLGENQLDMTQFDELSDLLFIKTPPHQLAERLHVDEKAKLDHIFLM\n+YGNDIFLDRFNSLETAALFVDLGVYDAAFLSLRDDRVAEYLKSKGYVTQEQIDDLQCALN\n+PLYCDSLTPKQDCLA*\n+>NZ_CP043953.1_173 # 195595 # 199092 # -1 # ID=1_173;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=3-4bp;gc_cont=0.443\n+MNSWLIIGVLTLYIALLFVCAFFGEKHASRLSTRGRMFLFSLTLGVYCSSWTFYGATGAA\n+VREGVIFLPIYLGPLLFVWFGYDIWRRLGRVRQHHAISSIADFVAARYGKSGVLASLVTI\n+LAVIAIIPYLALQLRAIALSTSVIMEQSSHIHTTTNSVLLLTSVLAILAMIFGTRQIANT\n+EQHGGLMLAVAFESFVKLFALLCVALFFIFESPANLSQMTSDVNQTFQEVQLFGVPETFW\n+IQTLLAGLAIICLPRQFHVAVVELRDEKHIRGARKWFAVYLILTILAIIPIASWALHAAP\n+KFLTVPDVAVLSLPLSYNQEWLALLAFLGGFSASTGMLLVSSVALSIMLSNDLIMPALWR\n+FKLLSRHDKHLPKVLKFSRRISIVAVMLLGFLFFHFFNDINQLSVFGLLAFSAVAQFAPA\n+LIGGLYWRGGSRQGVYAGLIIGFLMWSYTLLFPTILRSLPEAYQETAQSILLFGPFGINA\n+LRPESLFGFESFAPLTHGVIWSLGLNIVLYIWISKIYRPSVAEQIQAESFFYYETKPLPS\n+PHTSTDLTYLPHDAARLKVGDLFALAKRITGEQPTTQAFENFCEQNHLTLNPNSIANGMW\n+WRFTEQYLAGIIGAASARTLLTTAMINNGLALGQVANILDQASQWQRFNQNLLMTMIDHM\n+TQGVSVVDKNMCLVAWNNQYLKLFGYPKDLVYVGCPIADLIRYNAERGECGPGSVEEHVR\n+KRLHWMKVGSAHEFERIRKDGRVIQMRGNPIAGGGFVTTFADITAFRANEAVLEARVKDR\n+TQQLADALTEQQLAREQADMANMSKSRFIAAASHDLLQPMHAARLFSTVLEQSISTEEDR\n+QTLQQLDRALYGAESMLSALLDIARLEGGTIQPKRQPYPLHDLLSDLELQFKSIAAQRNI\n+SLKVHDVSFWIDTDPQWIRRIIQNFVSNALRYTAKGRVVVGVLRSAQQSGHIRIGVWDTG\n+PGIAEEQRIKLFQEFERCGHLSPWGEQGLGLGLAIVQRMTGLLNYPVHVYSELGKGSCFM\n+IEVPIVEPPKVATPAVQAVPLKTKAYRILCLDNDETILEGMSSLLGRWGYQVFKATEPEQ\n+ALEIIQKENIQVWLIDQHLNHNQLGVDFITQNRQEDVPVALITADSHPELPQQLKELNIV\n+LLKKPLKPASLRAWLSGLKIASTTD*\n+>NZ_CP043953.1_174 # 199276 # 199608 # 1 # ID=1_174;partial=00;start_type=ATG;rbs_motif=AGGAG;rbs_spacer=5-10bp;gc_cont=0.390\n+MDQSQVEQILRNPKFQKMVKKKSALSWTLTIIMLVLYVGFMLLVGYNKEFLMSSFSGGVT\n+TWGIPLGLGIIVLSFLLCGVYSYIANNTLDQLSEEALKEVEAITHEKGLH*\n+>NZ_CP043953.1_175 # 199610 # 199918 # 1 # ID=1_175;partial=01;start_type=ATG;rbs_motif=AGGA;rbs_spacer=5-10bp;gc_cont=0.447\n+MKWNSFKAKALLAAASLYSTVAMASPDLGEAEQQATNWHAIIMFIIFVGFTLFITKWAAK\n+QTQSAQDFYTAGGGISGFQNGLAIAGDYMSAASFLGISAMVFS\n' |
| b |
| diff -r 000000000000 -r 91791b6ecd38 test-data/output_tt.fnn --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_tt.fnn Thu Mar 14 16:49:04 2024 +0000 |
| b |
| b'@@ -0,0 +1,2737 @@\n+>NZ_CP043953.1_1 # 1 # 1398 # 1 # ID=1_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.399\n+ATGCTTTGGACAGACTGCTTAACTCGCTTGCGACAAGAGCTCTCTGATAACGTCTTTGCGATGTGGATTC\n+GCCCTTTAGTAGCTGAAGAAGTAGAGGGGATACTACGTCTCTATGCTCCTAATCCTTATTGGACGCGTTA\n+TATTCAAGAGAATCATTTAGAGTTAATTTCTATATTGGCTGAACAATTGTCAGAAGGGCGGGTGCGTCAG\n+GTTGAAATCTTGGTAGATTCTCGTCCTGGTAGTATTTTGTCTTCTAGTGAACAGCCTGCAACAACTACAG\n+CAGCTTTACAAACTGCCCCTATACCTCAACCTGCTAAGGTTAAAAGAGAACCGGAACCTGTTGCTAATAC\n+TGCAGTTAGTTCTAAGAGTTCAAAAAAGAAACTATTAAATCCACAATTTACTTTTTCACTATTTGTTGAA\n+GGCCGTTCTAACCAAATGGCAGCAGAAACCTGTAGAAAAGTATTAACACAGTTAGGTGCTTCTCAACATA\n+ACCCTTTGTTTTTATATGGTCCGACAGGTCTAGGTAAGACTCACTTAATGCAAGCAGTTGGTAATGCCCT\n+ACTGCAAGCGAAGCCGAATGCAAGAGTCATGTATATGACTTCAGAAAGTTTTGTACAAGATTTTGTGAGC\n+TCATTACAAAAAGGAAAGGTAGAAGAGTTTAAGAAAAATTGCCGTTCTTTAGACTTGTTATTAGTAGATG\n+ATATTCATCTTTTGGCAGGAAAAGAAGCAAGTCTCGTTGAATTCTTCTATACATTTAATGCCTTACTTGA\n+TGAATCTAAACAAATTATTTTAACGTCTGATCGATATCCTAAAGAATTAACAGAACTTGATCCTCGATTG\n+GTTTCTCGTTTTTCCTGGGGGCTATCAGTAGGTGTTGAACCACCTGATATTGAAACTCGAATCGAAATTC\n+TGCTTAAAAAAGCTGAAAATAGTGGCGTTGATTTACCTAGAAACTGTGCGTTGTTTATTGCCCAACAAGT\n+CGTAGCGAACGTACGTGAACTTGAGGGCGCACTGAATAAAGTTGTCGCAATTTCACGTTTTAAAGGTGCT\n+CCAATTGACCTGGATGTCGTACGGGAATCTTTAAAAGATGTTTTAGCGATCCGTGCTCGTACAATTAGTG\n+TAGAAAATATCCAGCGTGTAGTGAGTGAATATTTCCGAATTCCATTAAAAGAGCTGGTAGGTCCAAAGCG\n+TACCCGAATTTATGCTCGACCACGTCAGTTGGCGATGGGGCTTGCCCGTGAATTAACGGGGGATAGTTTT\n+CCTGAAATTGGAATGGCTTTTGGTGGGCGTGATCACAGTACAGTGATGCATGCTTGTGAAAAAGTCGTCA\n+GTTTACGGGAAGAAGACCCAATCTTTGATGAAGATTATAAGAACTTATTACGTTTGCTTCAAAGTTAA\n+>NZ_CP043953.1_2 # 1496 # 2644 # 1 # ID=1_2;partial=00;start_type=GTG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.393\n+GTGCGTTTGAAAATCGCTAAAGAAAGTTTACTCAATGTTTTATCGCATGTGGTCGGTGCGGTAGAACGTC\n+GTCATACCTTGAATATTCTTTCAAACGTCAAAATTCAGACTAATGCTCAAGCGCTCACTATTACGGGTTC\n+CGATTTAGAAGTTGAACTCGTAGCGAGCACCGCTTTATCAGAAGGGGCGTGCCTTGAGGCAGGCGAGACA\n+ACTGTTCCTGCTCGTAAATTGATGGAAATTTGTAAATCTTTGCCTACAGCTGCATTGATTGATTTACAAA\n+TTACTGAAGATCAAAGATGTATTTTAAAATCTGGTAATAGCCGTTTTGTGCTAGGTACACTACCGGCTGA\n+AGATTATCCATTGTTAACCACTGAGAATAGCCAGGGTACGCAAGTACAGGTGACTCAACGTGAATTAAAG\n+CGTTTATTTGAAAAAACTGCTTTTGCAATGGCTGTACAAGATGTACGTTTTTACCTCACTGGTACTTTAT\n+TAGAAATTGATGAAAATCAATTGCGTGCAGTAACAACTGATGGTCACCGTTTAGCACTTTGTGAAATTTT\n+GGCTTCCTCTACTTCATCTCAGTTGGTACAAGCGATTGTGCCTCGTAAAGCTGTGGGCGAATTGCAACGT\n+TTACTCAGCATTGAAGATGAACAGCTCACATTGCTTATTGGCCGTGAATTATTAAATGTAACGATTAATA\n+CGCCAAGCCGTGATAAAGAACAAGGTGATATTACAGTTCGTTTTACAACTAAATTGATTGATGGGAAATT\n+CCCTGATTATCGCCGTGTTATTCCACGTGGTGGTGATAAACATGTTTTGATTGGTCATGACGTATTTAAA\n+CAATCATTACAACGTGTAGCAATTTTAAGTAATGAAAAATTGCGTGGTGTTTTCCTAAATTTCAATCAGG\n+ATTCTTTACAGCTTCGTGCAAATAACCCTGAACAAGATGAAGCAATTGAAGATTTAGCGATCCAATATCA\n+AAGTGCCCCATTAGAAATGTCATTTAATGCTCAATACCTACTCGATGTATTGGGTGTATTAGATGGTGAT\n+GATGTAAATATGAGCATGACTGAGGCGAATCAGTCTGTATTGGTTCAAGATCCGGCTCATCCTGACCAGA\n+CCTATGTGGTTATGCCGATGCGTGTTTAA\n+>NZ_CP043953.1_3 # 2659 # 3741 # 1 # ID=1_3;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.394\n+ATGCATCTTACGCGCTTAAATATTGAACGTGTGCGTAATTTAAAAACGGTTGCACTCCATGGGTTGCAAC\n+CGTTTAATGTCTTTTATGGCGCAAACGGTTCAGGTAAAACATCAATTTTAGAAGCGATCCATTTGCTTGC\n+AACAGGTCGCTCATTCCGTACACATATACCCAAAAATTATATTCAATATGAAGCTGACGACGCGATTGTA\n+TTTGCTCAGTCAGCAACTGAAAAAATTGGTATGCAGAAACTCGCTTCTGGTGAGCAACTCATGAAAGTGA\n+ATGGCGATACCGTTGCGACTCAAGGTCAGCTCGCAAAGTTACTTCCTTTACAGCATATTGATCCACAAAG\n+TACGGATATTATTGATCATGGTGCCAAGCCAAGAAGACAACTTTTAGATTGGCTTATGTTCCACGTGGAA\n+CCTGAATTTTATTTTGCGTGGCAATATTACTCTCGTGCGCTAAAGCAGCGTAATACCTTACTCAAAACAC\n+GGCGTAATCTTTCATTAGCTGATTTAGAACCGTGGAACAAAATGTTGAGTGATTATGGCGAGATTTTGCA\n+CTCACAGCGTTTAAGTATTGTCGAGCAATGGAATGTTTATTTCCAAAATGACTTAAGCCAATTACTCCCT\n+GATTTGGAGATTGAACTGGAATATAGCCCAGGTTTTCATACAGAGCAGGGGCTTATGCAAGACTTGTTGA\n+ATCAGCATCAAAAAGACATCGAGAGACGTTATACCGAGTATGGTCCGCATCGGGCAGATTTGCGCTTAAA\n+AACGCCATTTGGACATGCTGATGATGTTTTATCAAGAGGTCAGAAAAAACTCTTGATTATTGCCTTAAAA\n+CTGTCACAAATTGCAATGTTGCATGCGAGTAATAAGGAAACTGTGGTATTATTAGATGATCTGACAGCAG\n+AATTAGACTTAACCGCACAACAACGTTTAATTGAACGATTAAGCCAACTTGGTAGCCAGGTTTTTATGA'..b'TTTTAGCTATGATTTTTGGTACACGGCAGATTGCAAACACGGAGCAACACGGCGGCCTCAT\n+GCTTGCGGTTGCATTTGAATCATTTGTGAAGTTATTTGCCTTACTTTGTGTCGCTTTATTTTTTATTTTT\n+GAATCACCGGCCAACCTGAGCCAAATGACCTCTGATGTAAACCAGACTTTTCAGGAAGTTCAGCTCTTTG\n+GTGTACCCGAAACCTTCTGGATTCAAACATTATTGGCGGGTTTAGCCATTATTTGCTTACCACGTCAGTT\n+CCACGTGGCGGTGGTCGAGCTACGCGATGAGAAGCATATTCGCGGTGCCCGTAAATGGTTCGCGGTTTAT\n+CTCATTTTAACTATTCTTGCCATTATTCCGATTGCAAGCTGGGCTTTACATGCTGCACCGAAGTTTCTGA\n+CCGTGCCTGATGTGGCTGTGCTGTCATTGCCTTTAAGTTATAACCAAGAGTGGCTGGCATTACTGGCCTT\n+TTTAGGCGGGTTCTCTGCCTCAACAGGCATGTTACTGGTGTCATCAGTAGCATTGTCTATTATGCTCAGT\n+AACGACTTGATTATGCCTGCTCTATGGCGATTTAAGTTGCTGTCACGTCACGATAAGCACTTACCTAAAG\n+TTCTTAAATTTAGCCGCCGTATTAGTATTGTTGCAGTGATGCTACTTGGCTTTTTATTCTTCCATTTCTT\n+TAATGACATTAACCAACTTTCAGTTTTCGGCTTATTGGCCTTTAGTGCTGTAGCACAGTTTGCACCTGCA\n+CTGATTGGTGGTTTGTATTGGCGTGGCGGAAGCCGTCAAGGCGTCTATGCAGGACTTATTATTGGATTTT\n+TAATGTGGAGTTATACATTACTATTTCCAACTATTTTGCGTAGCTTGCCTGAAGCCTATCAGGAAACTGC\n+TCAAAGTATTTTACTTTTCGGTCCTTTCGGCATTAATGCCCTACGCCCGGAATCTTTATTTGGTTTTGAG\n+TCATTTGCACCTTTAACTCACGGTGTTATTTGGTCACTCGGCTTAAATATTGTTTTATATATCTGGATTT\n+CAAAAATTTATCGGCCAAGCGTCGCTGAACAAATTCAGGCAGAAAGCTTCTTCTACTATGAAACTAAGCC\n+TTTACCATCACCGCACACATCTACTGATTTAACCTATCTTCCTCATGATGCGGCCCGCTTAAAAGTGGGT\n+GATTTATTTGCCCTAGCCAAAAGAATTACGGGTGAGCAACCCACTACGCAAGCGTTCGAAAATTTTTGTG\n+AGCAAAATCACCTCACCCTCAACCCAAATAGTATTGCCAATGGCATGTGGTGGCGTTTTACCGAGCAATA\n+TCTGGCCGGTATTATCGGTGCCGCTTCTGCACGTACGTTGCTCACAACAGCAATGATTAATAACGGCCTC\n+GCTTTAGGGCAAGTGGCTAATATTTTAGACCAAGCATCGCAGTGGCAACGTTTTAATCAGAACCTTCTTA\n+TGACCATGATTGACCACATGACCCAAGGGGTAAGCGTGGTTGATAAAAATATGTGTTTGGTCGCATGGAA\n+CAATCAATATTTAAAACTGTTTGGTTACCCAAAAGACCTCGTTTATGTGGGCTGCCCAATTGCCGACCTC\n+ATTCGTTATAACGCCGAACGCGGTGAATGTGGTCCCGGTTCAGTTGAAGAACATGTGCGTAAACGCCTTC\n+ACTGGATGAAAGTGGGAAGTGCTCACGAATTTGAACGTATTCGTAAAGATGGCCGTGTAATTCAAATGCG\n+AGGAAATCCAATCGCAGGTGGAGGCTTTGTAACGACATTTGCCGATATTACGGCCTTCCGTGCGAACGAA\n+GCCGTGCTTGAAGCCCGCGTAAAAGATAGAACTCAACAGCTTGCCGATGCCTTAACTGAGCAACAGCTTG\n+CACGTGAACAAGCCGATATGGCCAATATGTCAAAGAGTCGATTTATTGCCGCGGCAAGTCACGATCTATT\n+ACAGCCTATGCATGCTGCTCGTCTGTTTAGTACCGTTCTTGAGCAAAGTATTTCGACCGAAGAAGACCGC\n+CAGACCCTACAACAGCTTGACCGAGCACTCTATGGTGCAGAAAGTATGCTCTCTGCCCTACTCGATATTG\n+CACGTTTGGAAGGCGGTACCATACAGCCAAAGAGACAACCTTATCCGTTGCATGATTTGCTCAGTGATCT\n+TGAGTTGCAGTTTAAATCGATCGCTGCTCAGCGAAATATCTCACTGAAAGTCCACGATGTGTCTTTCTGG\n+ATCGATACCGACCCGCAGTGGATTCGTCGTATTATTCAGAACTTTGTCAGTAATGCTTTGCGTTATACCG\n+CTAAAGGTCGAGTGGTGGTAGGTGTACTCCGCTCTGCGCAGCAGTCTGGACATATTCGAATTGGGGTTTG\n+GGATACTGGACCTGGTATTGCCGAAGAACAACGGATTAAGCTATTCCAAGAGTTTGAGCGCTGTGGGCAT\n+TTATCACCTTGGGGTGAACAAGGTTTAGGGCTAGGACTTGCCATCGTACAACGTATGACAGGTTTGCTAA\n+ATTACCCTGTTCATGTTTACTCAGAGTTGGGCAAAGGCTCATGCTTTATGATTGAAGTACCTATTGTCGA\n+GCCACCAAAAGTTGCAACACCAGCTGTACAAGCCGTACCTTTAAAAACTAAAGCCTACCGTATTTTGTGC\n+CTAGACAATGATGAAACTATTCTTGAAGGAATGAGTAGTTTATTAGGACGATGGGGTTATCAAGTTTTCA\n+AAGCGACTGAACCTGAACAGGCGCTAGAAATTATTCAAAAAGAGAATATTCAGGTTTGGCTCATTGACCA\n+GCACTTAAACCACAATCAACTTGGCGTTGATTTTATTACTCAAAATCGTCAAGAAGATGTTCCTGTTGCC\n+TTAATTACAGCGGACTCGCACCCTGAATTACCGCAGCAATTAAAAGAACTGAATATTGTTTTACTCAAAA\n+AACCGTTAAAACCTGCTTCATTAAGAGCATGGTTATCTGGGCTTAAAATTGCCAGCACGACAGACTAA\n+>NZ_CP043953.1_174 # 199276 # 199608 # 1 # ID=1_174;partial=00;start_type=ATG;rbs_motif=AGGAG;rbs_spacer=5-10bp;gc_cont=0.390\n+ATGGATCAAAGCCAAGTAGAACAGATTCTACGTAATCCAAAGTTTCAAAAAATGGTCAAGAAAAAAAGTG\n+CATTAAGCTGGACGCTCACAATCATCATGTTAGTGCTTTATGTGGGCTTTATGCTACTTGTGGGCTACAA\n+CAAAGAATTTTTGATGAGTTCCTTTAGTGGTGGTGTAACGACATGGGGGATCCCGCTAGGTTTAGGAATT\n+ATTGTTTTATCTTTCCTACTTTGTGGTGTGTATTCCTATATCGCAAATAATACCCTTGACCAATTGAGTG\n+AAGAAGCGTTGAAGGAAGTTGAAGCCATCACGCATGAGAAAGGACTACACTAA\n+>NZ_CP043953.1_175 # 199610 # 199918 # 1 # ID=1_175;partial=01;start_type=ATG;rbs_motif=AGGA;rbs_spacer=5-10bp;gc_cont=0.447\n+ATGAAATGGAATTCATTCAAAGCGAAAGCCTTATTGGCAGCAGCATCGCTATATTCAACTGTTGCTATGG\n+CAAGCCCGGACTTAGGTGAAGCAGAACAGCAAGCCACCAACTGGCATGCCATTATCATGTTTATCATCTT\n+TGTTGGCTTTACCTTGTTTATTACCAAATGGGCGGCTAAACAAACTCAATCGGCGCAAGACTTCTATACT\n+GCTGGTGGTGGGATCAGTGGTTTCCAAAACGGTTTGGCGATTGCGGGTGACTATATGTCAGCAGCGTCAT\n+TTCTTGGTATTTCTGCAATGGTGTTTAGC\n' |
| b |
| diff -r 000000000000 -r 91791b6ecd38 test-data/output_tt.start --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_tt.start Thu Mar 14 16:49:04 2024 +0000 |
| b |
| b'@@ -0,0 +1,10981 @@\n+# Sequence Data: seqnum=1;seqlen=199920;seqhdr="NZ_CP043953.1 Acinetobacter baumannii strain K09-14 chromosome, complete genome"\n+# Run Data: version=Prodigal.v2.6.3;run_type=Single;model="Ab initio";gc_cont=40.29;transl_table=4;uses_sd=1\n+\n+Beg\tEnd\tStd\tTotal\tCodPot\tStrtSc\tCodon\tRBSMot\tSpacer\tRBSScr\tUpsScr\tTypeScr\tGCCont\n+\n+138\t590\t-\t4.87\t4.89\t-0.03\tATG\tNone\tNone\t-6.78\t2.88\t3.87\t0.397\n+\n+129\t242\t+\t-73.17\t-30.64\t-42.53\tTTG\tNone\tNone\t-15.27\t-1.81\t-24.95\t0.412\n+\n+257\t388\t+\t-60.73\t-33.08\t-27.65\tGTG\tNone\tNone\t-13.14\t-5.55\t-8.47\t0.402\n+\n+428\t583\t-\t-47.52\t-18.19\t-29.33\tTTG\tNone\tNone\t-11.08\t0.35\t-18.10\t0.423\n+428\t634\t-\t-33.54\t-27.08\t-6.46\tATG\tNone\tNone\t-8.31\t-0.80\t3.16\t0.396\n+\n+548\t652\t+\t-83.71\t-30.08\t-53.64\tTTG\tNone\tNone\t-16.62\t-9.37\t-27.15\t0.390\n+554\t652\t+\t-40.86\t-29.50\t-11.36\tATG\tAGxAG\t5-10bp\t-7.50\t-4.85\t1.48\t0.394\n+\n+659\t754\t-\t-11.95\t-15.36\t3.41\tATG\tGGA/GAG/AGG\t5-10bp\t1.94\t0.54\t1.44\t0.302\n+\n+669\t758\t+\t-72.34\t-37.14\t-35.20\tTTG\tGGA/GAG/AGG\t11-12bp\t-0.06\t-2.81\t-31.83\t0.322\n+\n+698\t793\t+\t-31.82\t-14.37\t-17.45\tATG\tNone\tNone\t-18.23\t-0.17\t1.44\t0.281\n+\n+872\t985\t+\t-49.98\t-19.75\t-30.23\tGTG\tNone\tNone\t-15.27\t-4.62\t-9.84\t0.386\n+875\t985\t+\t-68.48\t-19.34\t-49.14\tTTG\t3Base/5BMM\t13-15bp\t-5.14\t-17.86\t-25.64\t0.378\n+890\t985\t+\t-70.47\t-13.48\t-56.98\tTTG\tNone\tNone\t-18.23\t-8.48\t-29.78\t0.375\n+\n+995\t1084\t+\t-66.25\t-31.92\t-34.33\tGTG\tNone\tNone\t-19.48\t-1.80\t-12.55\t0.433\n+\n+1115\t1213\t-\t-51.26\t-8.86\t-42.40\tGTG\tNone\tNone\t-17.66\t-12.87\t-11.38\t0.414\n+1115\t1351\t-\t-41.84\t-20.87\t-20.96\tTTG\tNone\tNone\t-7.24\t-1.39\t-11.83\t0.456\n+1115\t1414\t-\t-29.59\t-22.50\t-7.09\tATG\tNone\tNone\t-6.78\t-3.68\t3.87\t0.410\n+\n+1\t1398\t+\t210.07\t206.85\t3.22\tEdge\tNone\tNone\t0.00\t3.22\t0.00\t0.399\n+28\t1398\t+\t181.37\t205.16\t-23.79\tTTG\tNone\tNone\t-6.78\t-5.93\t-11.08\t0.398\n+61\t1398\t+\t186.20\t198.33\t-12.12\tATG\tNone\tNone\t-6.78\t-9.21\t3.87\t0.395\n+175\t1398\t+\t138.43\t153.70\t-15.26\tTTG\tGGA/GAG/AGG\t11-12bp\t-0.02\t-4.16\t-11.08\t0.397\n+187\t1398\t+\t128.12\t149.11\t-20.99\tTTG\tNone\tNone\t-6.78\t-3.13\t-11.08\t0.397\n+202\t1398\t+\t133.71\t147.04\t-13.33\tGTG\tAGxAG\t5-10bp\t-2.88\t-6.08\t-4.37\t0.394\n+220\t1398\t+\t123.02\t137.63\t-14.61\tTTG\tGGA/GAG/AGG\t5-10bp\t5.20\t-8.73\t-11.08\t0.393\n+247\t1398\t+\t101.14\t125.57\t-24.43\tTTG\tNone\tNone\t-6.78\t-6.57\t-11.08\t0.392\n+436\t1398\t+\t81.23\t84.80\t-3.56\tATG\t3Base/5BMM\t13-15bp\t-2.22\t-5.21\t3.87\t0.395\n+496\t1398\t+\t44.02\t67.78\t-23.75\tTTG\tNone\tNone\t-6.78\t-5.89\t-11.08\t0.394\n+538\t1398\t+\t49.48\t56.09\t-6.60\tATG\t3Base/5BMM\t13-15bp\t-2.22\t-8.25\t3.87\t0.395\n+589\t1398\t+\t36.59\t47.36\t-10.78\tATG\tNone\tNone\t-6.78\t-7.86\t3.87\t0.388\n+595\t1398\t+\t47.00\t45.46\t1.54\tATG\tGGA/GAG/AGG\t5-10bp\t5.20\t-7.54\t3.87\t0.389\n+625\t1398\t+\t21.02\t37.86\t-16.84\tGTG\tNone\tNone\t-6.78\t-5.69\t-4.37\t0.394\n+685\t1398\t+\t8.33\t29.00\t-20.66\tTTG\tNone\tNone\t-6.78\t-2.81\t-11.08\t0.398\n+712\t1398\t+\t0.79\t18.33\t-17.54\tTTG\t3Base/5BMM\t13-15bp\t-2.22\t-4.25\t-11.08\t0.405\n+838\t1398\t+\t-51.42\t-26.86\t-24.55\tTTG\tNone\tNone\t-6.78\t-6.20\t-11.08\t0.422\n+961\t1398\t+\t-84.29\t-61.72\t-22.56\tTTG\tNone\tNone\t-6.78\t-4.20\t-11.08\t0.427\n+1141\t1398\t+\t-143.09\t-126.34\t-16.76\tGTG\tNone\tNone\t-6.78\t-5.11\t-4.37\t0.430\n+1219\t1398\t+\t-186.01\t-148.55\t-37.47\tTTG\tNone\tNone\t-9.58\t-11.74\t-15.65\t0.422\n+1225\t1398\t+\t-169.99\t-149.77\t-20.21\tATG\tNone\tNone\t-9.91\t-12.45\t2.65\t0.414\n+1273\t1398\t+\t-201.20\t-173.01\t-28.19\tATG\tNone\tNone\t-13.78\t-15.82\t1.90\t0.389\n+1303\t1398\t+\t-234.16\t-178.42\t-55.74\tGTG\tNone\tNone\t-18.23\t-25.27\t-11.74\t0.354\n+1306\t1398\t+\t-228.77\t-178.97\t-49.81\tATG\tNone\tNone\t-18.83\t-31.86\t1.39\t0.344\n+\n+1426\t1530\t-\t-60.63\t-4.46\t-56.17\tTTG\tNone\tNone\t-16.62\t-11.90\t-27.15\t0.362\n+1426\t1596\t-\t-39.00\t-15.45\t-23.55\tTTG\t3Base/5BMM\t13-15bp\t-3.30\t-3.27\t-16.48\t0.380\n+1426\t1623\t-\t-31.29\t-24.58\t-6.71\tGTG\tGGA/GAG/AGG\t5-10bp\t4.06\t-4.66\t-5.60\t0.389\n+1426\t1665\t-\t-54.11\t-29.25\t-24.86\tGTG\tNone\tNone\t-7.15\t-12.60\t-4.61\t0.408\n+\n+1268\t1444\t+\t-55.08\t-28.10\t-26.98\tTTG\t3Base/5BMM\t13-15bp\t-3.19\t-7.37\t-15.92\t0.379\n+1280\t1444\t+\t-43.42\t-28.73\t-14.69\tTTG\tGGA/GAG/AGG\t5-10bp\t3.37\t-0.47\t-17.09\t0.376\n+1283\t1444\t+\t-34.65\t-28.26\t-6.39\tGTG\tGGA/GAG/AGG\t5-10bp\t3.31\t-2.33\t-6.87\t0.377\n+1289\t1444\t+\t-55.21\t-31.71\t-23.49\tGTG\tNone\tNone\t-11.08\t-4.78\t-7.14\t0.359\n+1310\t1444\t+\t-42'..b'e\tNone\t-16.14\t-5.38\t-10.40\t0.361\n+199257\t199370\t-\t-48.13\t-24.34\t-23.79\tATG\tNone\tNone\t-15.27\t-9.74\t1.72\t0.360\n+199257\t199373\t-\t-39.49\t-23.68\t-15.80\tATG\tNone\tNone\t-14.87\t-2.20\t1.76\t0.359\n+\n+199106\t199264\t+\t-46.46\t-19.70\t-26.76\tGTG\tNone\tNone\t-10.86\t-8.39\t-7.00\t0.327\n+\n+199274\t199366\t-\t-73.47\t-18.03\t-55.44\tTTG\tNone\tNone\t-18.83\t-5.34\t-30.77\t0.355\n+\n+199501\t199590\t-\t-30.95\t-13.17\t-17.79\tATG\tNone\tNone\t-19.48\t0.85\t1.35\t0.411\n+\n+199600\t199716\t-\t-36.23\t-12.64\t-23.59\tGTG\tNone\tNone\t-14.87\t1.35\t-9.58\t0.444\n+199600\t199719\t-\t-54.28\t-12.88\t-41.40\tTTG\tNone\tNone\t-14.49\t-2.75\t-23.67\t0.442\n+199600\t199731\t-\t-25.29\t-14.38\t-10.90\tATG\tNone\tNone\t-13.14\t0.74\t2.00\t0.447\n+199600\t199737\t-\t-27.92\t-16.95\t-10.97\tATG\tNone\tNone\t-12.56\t0.00\t2.09\t0.442\n+199600\t199746\t-\t-22.81\t-20.79\t-2.02\tATG\t3Base/5BMM\t13-15bp\t-3.85\t0.10\t2.23\t0.429\n+199600\t199776\t-\t-62.69\t-30.66\t-32.03\tTTG\tNone\tNone\t-9.74\t-5.87\t-15.92\t0.407\n+\n+199240\t199608\t+\t23.30\t29.47\t-6.17\tGTG\tNone\tNone\t-6.78\t4.98\t-4.37\t0.398\n+199270\t199608\t+\t12.95\t30.96\t-18.02\tTTG\tNone\tNone\t-6.78\t-0.16\t-11.08\t0.389\n+199276\t199608\t+\t46.23\t30.52\t15.70\tATG\tAGGAG\t5-10bp\t13.73\t-1.89\t3.87\t0.390\n+199327\t199608\t+\t7.66\t13.03\t-5.37\tATG\tNone\tNone\t-6.78\t-2.46\t3.87\t0.401\n+199372\t199608\t+\t16.66\t13.90\t2.76\tATG\t3Base/5BMM\t13-15bp\t-2.37\t1.51\t3.62\t0.401\n+199378\t199608\t+\t-2.50\t10.57\t-13.08\tGTG\tNone\tNone\t-7.43\t-0.85\t-4.79\t0.407\n+199387\t199608\t+\t-6.08\t8.29\t-14.37\tGTG\tNone\tNone\t-7.74\t-1.64\t-4.99\t0.410\n+199396\t199608\t+\t-2.90\t4.35\t-7.25\tATG\tNone\tNone\t-8.07\t-2.43\t3.25\t0.404\n+199405\t199608\t+\t-9.69\t3.60\t-13.29\tGTG\tNone\tNone\t-8.43\t0.58\t-5.43\t0.407\n+199426\t199608\t+\t-33.80\t-0.13\t-33.68\tTTG\tNone\tNone\t-9.42\t-8.37\t-15.39\t0.410\n+199429\t199608\t+\t-17.74\t0.40\t-18.15\tATG\tNone\tNone\t-9.58\t-11.31\t2.74\t0.411\n+199513\t199608\t+\t-62.95\t-25.14\t-37.81\tGTG\tNone\tNone\t-18.23\t-7.34\t-11.74\t0.406\n+\n+199691\t199792\t-\t-69.57\t-2.32\t-67.25\tTTG\tNone\tNone\t-17.12\t-21.65\t-27.97\t0.402\n+199691\t199798\t-\t-63.35\t-2.44\t-60.91\tTTG\tNone\tNone\t-16.14\t-17.89\t-26.38\t0.398\n+199691\t199807\t-\t-54.80\t-3.96\t-50.83\tTTG\tAGxAG\t5-10bp\t-6.32\t-19.72\t-24.29\t0.419\n+199691\t199846\t-\t-44.80\t-5.31\t-39.49\tTTG\tNone\tNone\t-11.08\t-9.82\t-18.10\t0.429\n+199691\t199918\t-\t-23.69\t-26.41\t2.72\tEdge\tNone\tNone\t0.00\t0.00\t3.22\t0.443\n+\n+199615\t199788\t+\t-27.87\t-23.57\t-4.30\tATG\t3Base/5BMM\t13-15bp\t-3.25\t-3.20\t2.65\t0.437\n+\n+199785\t199889\t-\t-42.85\t-21.75\t-21.10\tATG\tNone\tNone\t-16.62\t-5.56\t1.58\t0.486\n+199785\t199907\t-\t-42.87\t-20.47\t-22.40\tTTG\tGGA/GAG/AGG\t5-10bp\t2.50\t-1.32\t-23.08\t0.472\n+\n+199487\t199918\t+\t-11.88\t2.80\t-14.68\tTTG\tGGA/GAG/AGG\t5-10bp\t5.20\t-8.81\t-11.08\t0.428\n+199508\t199918\t+\t-7.95\t3.53\t-11.48\tGTG\tNone\tNone\t-6.78\t-0.33\t-4.37\t0.438\n+199511\t199918\t+\t-13.39\t2.99\t-16.37\tGTG\tNone\tNone\t-6.78\t-5.23\t-4.37\t0.436\n+199541\t199918\t+\t-11.56\t9.11\t-20.67\tTTG\tNone\tNone\t-6.78\t-2.81\t-11.08\t0.442\n+199553\t199918\t+\t-0.63\t13.22\t-13.85\tGTG\tNone\tNone\t-6.78\t-2.70\t-4.37\t0.445\n+199574\t199918\t+\t4.94\t24.07\t-19.13\tTTG\tNone\tNone\t-6.78\t-1.27\t-11.08\t0.443\n+199589\t199918\t+\t20.99\t27.52\t-6.53\tATG\tNone\tNone\t-6.78\t-3.61\t3.87\t0.439\n+199610\t199918\t+\t44.71\t30.24\t14.47\tATG\tAGGA\t5-10bp\t11.85\t-1.25\t3.87\t0.447\n+199643\t199918\t+\t9.20\t29.10\t-19.91\tTTG\tNone\tNone\t-6.78\t-2.05\t-11.08\t0.460\n+199676\t199918\t+\t18.90\t26.11\t-7.21\tATG\tNone\tNone\t-6.78\t-4.30\t3.87\t0.461\n+199736\t199918\t+\t0.84\t8.22\t-7.38\tATG\tNone\tNone\t-6.78\t-4.46\t3.87\t0.437\n+199763\t199918\t+\t-9.78\t10.91\t-20.69\tTTG\tNone\tNone\t-6.78\t-2.83\t-11.08\t0.455\n+199853\t199918\t+\t-41.87\t-15.34\t-26.53\tTTG\tNone\tNone\t-6.78\t-4.33\t-11.08\t0.455\n+\n+199695\t199919\t+\t-27.51\t-18.37\t-9.14\tGTG\tGGA/GAG/AGG\t5-10bp\t5.20\t-5.62\t-4.37\t0.449\n+199725\t199919\t+\t-26.13\t-14.57\t-11.56\tATG\tNone\tNone\t-6.78\t-4.29\t3.87\t0.431\n+199749\t199919\t+\t-39.08\t-13.02\t-26.05\tTTG\tNone\tNone\t-6.78\t-3.85\t-11.08\t0.450\n+199752\t199919\t+\t-37.98\t-12.37\t-25.61\tTTG\tNone\tNone\t-6.78\t-3.40\t-11.08\t0.452\n+199824\t199919\t+\t-27.48\t-6.77\t-20.71\tGTG\tNone\tNone\t-6.78\t-5.21\t-4.37\t0.469\n+199827\t199919\t+\t-26.47\t-7.28\t-19.20\tGTG\tNone\tNone\t-6.78\t-3.70\t-4.37\t0.462\n+199836\t199919\t+\t-26.41\t-8.05\t-18.35\tGTG\tNone\tNone\t-6.78\t-2.85\t-4.37\t0.452\n+199860\t199919\t+\t-36.03\t-4.87\t-31.16\tTTG\tNone\tNone\t-6.78\t-8.95\t-11.08\t0.433\n+\n' |
| b |
| diff -r 000000000000 -r 91791b6ecd38 test-data/train_file.trn |
| b |
| Binary file test-data/train_file.trn has changed |