Workflow: SSU-from-tablehits.cwl

Fetched 2019-09-19 10:27:44 GMT
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Inputs

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

Steps

ID Runs Label Doc
grep
pull-SSUs.cwl (CommandLineTool)
extract_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
SSU_coordinates File
Permalink: https://w3id.org/cwl/view/git/6430df56f7345f837d3f9c3f7fb5af5aa9dadc90/tools/SSU-from-tablehits.cwl