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Format conversion using a galaxy tool

Initial Format (EMBL flat file) 
ID   INE1    standard; DNA; INV; 611 BP.
XX
AC   U66884;
XX
DR   FLYBASE; FBte0000312; Dmel\INE-1.
XX
SY   synonym: mini-me
SY   synonym: DINE
SY   synonym: narep1
SY   synonym: Dr. D
XX
FT   source          U66884:4880..15490
XX
CC   This is presumably a dead element.
CC   Derived from U66884 (e1371475) (Rel. 52, Last updated, Version 6).
CC   Michael Ashburner, 28-Sep-2001.
CC   Any changes to original sequence record are annotated in an FT line.
XX
SQ   Sequence 611 BP; 193 A; 123 C; 93 G; 202 T; 0 other;
     TATACCCGTT ACTAGATTCG TTGAAATGAA TGTAACAGGC AGAAGGAAGC GTCTTAGACC        60
     ATATATAGTA TATACATACA TGTATATTCT TGATCAGGAT CAATAGCCGA GTCGATCTTG       120
     CCATATCCGT CTGTCCGTAT GAACGTCGAG ATCTCAGGAA CTATAAAAGC TAGAAGGTTT       180
     AGATTCAGCA TACAGAGACA AAGACGCAAG TAGCCATGCC CACTCTAACG TCCACAAACA       240
     GCGCAAAACT ATCACGCCCA CACTTTTGAA AAATGTGTTG TTCTTTTCAC ATTCTGATTA       300
     GTCTTTTACA TTTCTATCGA TTTCCAAAAA AAAACTTTTT GCCAACGCCC TAAAACCGCC       360
     CAAAACTCCG ACACCCACAT TTGTAAAAAA TTGTTGGGAA TTTTTTTCAT AAATTTATTA       420
     GTTTATTATT TATTATAAAT TTAAGTTTAT ATCGATTTGC CGACAACATA TTTTAATTTT       480
     TTTTCTCATT TTATCTTTTA TCTATCGATA TCCCAGAAAA ATTGTGCAAT TTCGCATTCA       540
     CACTAGCTGA GTAACGGGTA TCTGATAGTC GGGAAACTCG ACTATAGCAT TCTCTCTTTT       600
     TGAAATTGCG G                                                            611
//
Target Format (fasta) 
>INE1
TATACCCGTTACTAGATTCGTTGAAATGAATGTAACAGGCAGAAGGAAGCGTCTTAGACC
ATATATAGTATATACATACATGTATATTCTTGATCAGGATCAATAGCCGAGTCGATCTTG
CCATATCCGTCTGTCCGTATGAACGTCGAGATCTCAGGAACTATAAAAGCTAGAAGGTTT
AGATTCAGCATACAGAGACAAAGACGCAAGTAGCCATGCCCACTCTAACGTCCACAAACA
GCGCAAAACTATCACGCCCACACTTTTGAAAAATGTGTTGTTCTTTTCACATTCTGATTA
GTCTTTTACATTTCTATCGATTTCCAAAAAAAAACTTTTTGCCAACGCCCTAAAACCGCC
CAAAACTCCGACACCCACATTTGTAAAAAATTGTTGGGAATTTTTTTCATAAATTTATTA
GTTTATTATTTATTATAAATTTAAGTTTATATCGATTTGCCGACAACATATTTTAATTTT
TTTTCTCATTTTATCTTTTATCTATCGATATCCCAGAAAAATTGTGCAATTTCGCATTCA
CACTAGCTGAGTAACGGGTATCTGATAGTCGGGAAACTCGACTATAGCATTCTCTCTTTT
TGAAATTGCGG

Import the dataset

  • In galaxy, create a new history and name it "EMBL to Fasta conversion"
  • Copy the url of the flat EMBL file: 
    https://raw.githubusercontent.com/bergmanlab/drosophila-transposons/9b28cdbe9d2b3ef895df37f8495b33104677e516/releases/transposon_sequence_set_v9.5.embl.txt
  • In Galaxy, click the Upload Data button

upload

  • Then click the Paste/Fetch data button, Paste the copied file url in the central field and click Start

Paste/Fetch

Reformat the file using the tool embl2fa:

  • Go to the Admin → Install and Uninstall panel.
  • In the search repository box, type embl2fa
  • The search should likely return the tool at the bottom of the page 
    embl2fa                                       artbio  1   today
Converts EMBL flat format to fasta format
  • Click on the embl2fa, then on the install button.
  • Choose AG 2023 for the Target Section:, then click the OK button
  • The tool installation should only take a few seconds (the button Install turns to a red Uninstall)
  • You can now go back to the analysis interface by clicking the home icon.
  • in the Galaxy search toolbar box, search for embl and select the tool Convert embl flat file to fasta.
  • Select the imported dataset transposon_sequence_set_v9.5.embl.txt (should likely be the dataset #1) and click ▶Run Tool

Inspect the new dataset.

Inspect the new fasta file dataset by clicking the small rounded i icon that shows up when you deploy the dataset.

In particular, you can deploy the Command line box in the datasheet and verify the code executed by the tool.

Check the conversion

  • Download the file reference for the conversion (ie, a file that we know is correctly converted...) 
    https://raw.githubusercontent.com/ARTbio/AnalyseGenome/main/Exercises/transposon_sequence_set_v9.5.fa
  • Use the tool Differences between two files to compare the dataset fasta file and the dataset transposon_sequence_set_v9.5.fa

The resulting dataset should be empty, meaning that the dataset fasta file and the dataset transposon_sequence_set_v9.5.fa are identical.