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run_pfam_scan.sh wants *protein.fa not *proteins.fa #5

Open peterjc opened 6 years ago

peterjc commented 6 years ago

The script run_pfam_scan.sh looks for files ending ...protein.fa, https://github.com/krasileva-group/plant_rgenes/blob/master/bash_scripts/run_pfam_scan.sh#L24

protfiles=$(find $IN_DIR -name '*protein.fa')

The documentation https://github.com/krasileva-group/plant_rgenes/blob/master/README.md says to name files master_dir/species/annotation/species_version_proteins.fa (proteins with a s), which therefore fails.

krasileva commented 6 years ago

Hi Peter,

This is a typo in documentation. Thank you for pointing this out.

Best wishes,

Ksenia

Ksenia Krasileva Group Leader

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From: Peter Cock notifications@github.com Reply-To: krasileva-group/plant_rgenes reply@reply.github.com Date: Thursday, 2 November 2017 at 09:35 To: krasileva-group/plant_rgenes plant_rgenes@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [krasileva-group/plant_rgenes] run_pfam_scan.sh wants protein.fa not proteins.fa (#5)

The script run_pfam_scan.sh looks for files ending ...protein.fa, https://github.com/krasileva-group/plant_rgenes/blob/master/bash_scripts/run_pfam_scan.sh#L24

protfiles=$(find $IN_DIR -name '*protein.fa')

The documentation https://github.com/krasileva-group/plant_rgenes/blob/master/README.md says to name files master_dir/species/annotation/species_version_proteins.fa (proteins with a s), which therefore fails.

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