Convert formats - TSI
Version 1

Workflow Type: Galaxy

This is part of a series of workflows to annotate a genome, tagged with TSI-annotation. These workflows are based on command-line code by Luke Silver, converted into Galaxy Australia workflows.

The workflows can be run in this order:

  • Repeat masking
  • RNAseq QC and read trimming
  • Find transcripts
  • Combine transcripts
  • Extract transcripts
  • Convert formats
  • Fgenesh annotation

About this workflow:

  • Inputs: transdecoder-peptides.fasta, transdecoder-nucleotides.fasta
  • Runs many steps to convert outputs into the formats required for Fgenesh - .pro, .dat and .cdna

Inputs

ID Name Description Type
transdecoder-nucleotides.fasta transdecoder-nucleotides.fasta n/a
  • File
transdecoder-peptides.fasta transdecoder-peptides.fasta n/a
  • File

Steps

ID Name Description
2 STEP 1 Get IDs for complete, pos transcripts: Grep for lines starting with > toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy0
3 grep for lines with complete toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy0
4 Remove > from start of lines toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy0
5 Keep lines that end in (+) toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy0
6 STEP 2 toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy0
7 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy0
8 Sort toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy0
9 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy0
10 Cut Cut1
11 STEP 3. seqtk subseq toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.4+galaxy0
12 Text transformation toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy0
13 FASTA-to-Tabular toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1
14 STEP 4. cut col 1, delimit by pipe Cut1
15 Sort toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy0
16 seqtk_subseq toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.4+galaxy0
17 Tabular-to-FASTA toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1
18 FASTA-to-Tabular toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1
19 Text transformation toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy0
20 Sort toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy0
21 STEP 6 Grep headers toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy0
22 STEP 9B. grep for > toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy0
23 STEP 9A. grep for > toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy0
24 Tabular-to-FASTA toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1
25 Sed to remove parentheses toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy0
26 Cut Cut1
27 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy0
28 STEP 5 get seq lengths toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.3
29 STEP 10A. seqtk seq toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_seq/1.4+galaxy0
30 awk to extract last field in line toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy0
31 Text transformation toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy0
32 Text transformation toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy0
33 Cut Cut1
34 FASTA-to-Tabular toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1
35 Cut Cut1
36 Cut Cut1
37 STEP 7. create chroms file with na lines toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy0
38 STEP 8. create comments.txt toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy0
39 paste starts and stops Paste1
40 STEP 9C. paste transcripts and chroms Paste1
41 paste comments and transcript-lengths Paste1
42 STEP 10B. paste starts stops and chroms Paste1
43 Paste Paste1
44 Paste Paste1
45 Paste Paste1
46 Paste Paste1
47 Cut Cut1
48 Tabular-to-FASTA toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1

Outputs

ID Name Description Type
output output n/a
  • File

Version History

Version 1 (earliest) Created 8th May 2024 at 08:23 by Anna Syme

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Frozen Version-1 caf683f
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Citation
Silver, L., & Syme, A. (2024). Convert formats - TSI. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.880.1
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Views: 918   Downloads: 89

Created: 8th May 2024 at 08:23

Last updated: 9th May 2024 at 05:09

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