Workflow: LSU-from-tablehits.cwl

Fetched 2021-09-21 15:07:02 GMT
children parents
Workflow as SVG
  • Selected
  • Default Values
  • Nested Workflows
  • Tools
  • Inputs/Outputs

Inputs

ID Type Title Doc
table_hits File output of infernal's cmsearch

Steps

ID Runs Label Doc
grep
pull-LSUs.cwl (CommandLineTool)
extract_lsu_coords
extract-coords-from-cmsearch.cwl (CommandLineTool)

The awk script takes the output of Infernal's cmsearch so-called fmt=1 mode and makes it suitable for use by esl-sfetch, a sequence selector

Reading the user's guide for Infernal, Version 1.1.2; July 2016 http://eddylab.org/infernal/Userguide.pdf#page=60 we see that the relevant fields in the cmsearch output are: (column number: explanation) 1: The name of the target sequence or profile 3: The name of the query sequence or profile 8: The start of the alignment of this hit with respect to the sequence, numbered 1..L for a sequence of L residues. 9: The end of the alignment of this hit with respect to the sequence, numbered 1..L for a sequence of L residues

Likewise the format esl-sfetch wants is: <newname> <from> <to> <source seqname>

Putting it all together we see that the newname (which esl-sfetch with output using) is a concatenation of the original name, the sequence number, and the coordinates.

Outputs

ID Type Label Doc
LSU_coordinates File
Permalink: https://w3id.org/cwl/view/git/930a2cf6fff820c2461b42dd79d71d9379343013/tools/LSU-from-tablehits.cwl