Mercurial > repos > jjohnson > iedb_api
changeset 2:883cdf0ffae5 draft
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
| author | jjohnson |
|---|---|
| date | Wed, 26 Feb 2020 15:02:37 -0500 |
| parents | 4a89ba6cfc63 |
| children | 153d5fa7af53 |
| files | iedb_api.xml static/images/IEDB_Workflow_QueryTabular.png static/images/IEDB_Workflow_TextProcessing.png static/images/IEDB_formatted_alleles.png static/images/TextProcessingConversion.png static/images/seq2HLA_ClassI.HLAgenotype4digits.png |
| diffstat | 6 files changed, 62 insertions(+), 0 deletions(-) [+] |
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--- a/iedb_api.xml Tue Feb 25 17:37:34 2020 -0500 +++ b/iedb_api.xml Wed Feb 26 15:02:37 2020 -0500 @@ -401,6 +401,68 @@ A tabular file containing the results returned from the IEDB web service +**Typical Workflow for Human MHC I Binding Prediction** + +The RNAseq data for the subject would be used for: + + - HLA prediction by seq2HLA_ + - Novel Antigen Prediction by a variety of workflows to generate a Antigen peptide fasta + +.. _seq2HLA: https://toolshed.g2.bx.psu.edu/view/iuc/seq2hla/52bba1cd3823 + +.. image:: $PATH_TO_IMAGES/IEDB_Workflow_QueryTabular.png + :width: 584 + :height: 430 + +.. note:: The seq2HLA ClassI.HLAgenotype4digits output needs to be converted for IEDB alleles. + +The seq2HLA ClassI.HLAgenotype4digits output: + +.. image:: $PATH_TO_IMAGES/seq2HLA_ClassI.HLAgenotype4digits.png + :width: 285 + :height: 77 + +Needs to be converted into IEDB formatted alleles: + +.. image:: $PATH_TO_IMAGES/IEDB_formatted_alleles.png + :width: 74 + :height: 81 + +In the workflow above QueryTabular_ tool converts the alleles: + + - Filter Dataset Input + + * skip leading lines - *skip lines:* 1 + * select columns - *columns:* 2,4 + * regex replace value in column - *column:* 1 *regex pattern:* ^(\\w+[*]\\d\\d:\\d\\d\\d?).*$ *replacement expression:* HLA-\\1 + * regex replace value in column - *column:* 2 *regex pattern:* ^(\\w+[*]\\d\\d:\\d\\d\\d?).*$ *replacement expression:* HLA-\\1 + + - SQL Query to generate tabular output + + * SELECT c1 FROM t1 UNION SELECT c2 FROM t1 + +.. _QueryTabular: https://toolshed.g2.bx.psu.edu/view/iuc/query_tabular/0c95a3f1654f + + +The IEDB formatting can also be performed by TextProcessing_ tools: + +.. _TextProcessing: https://toolshed.g2.bx.psu.edu/view/bgruening/text_processing/0a8c6b61f0f4 + +.. image:: $PATH_TO_IMAGES/TextProcessingConversion.png + :width: 608 + :height: 87 + +The TextProcessing steps to convert the alleles: + + - Remove beginning - removes the header line + - Replace Text - picks Allele 1 and Allele 2 from each line and reformats each on a separate line + + * *Find pattern:* ^.*\\t([a-zA-Z]+[*][0-9]{2}:[0-9]{2,3}).*\\t.*\\t([a-zA-Z]+[*][0-9]{2}:[0-9]{2,3}).*\\t.*$ + * *Replace with:* HLA-\\1\\nHLA-\\2 + + - Unique - remove duplicates + + ]]></help> <citations> <citation type="doi">10.1093/nar/gku938</citation>