Mercurial > repos > greg > gene_family_classifier
changeset 58:0f52ca3dfa9c draft
Uploaded
| author | greg |
|---|---|
| date | Thu, 09 Feb 2017 10:28:49 -0500 |
| parents | c0a85e845050 |
| children | 46ed7233db21 |
| files | gene_family_classifier.xml |
| diffstat | 1 files changed, 20 insertions(+), 17 deletions(-) [+] |
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--- a/gene_family_classifier.xml Thu Feb 09 10:13:29 2017 -0500 +++ b/gene_family_classifier.xml Thu Feb 09 10:28:49 2017 -0500 @@ -14,6 +14,7 @@ <command> <![CDATA[ #import os + #import time #set scaffold_path = $scaffold.fields.path #set scaffold_dir = $os.path.split($scaffold_path)[0] #set scaffold_selection = $os.path.split($scaffold_path)[1] @@ -104,27 +105,29 @@ #end if #end if - && echo $create_ortho_sequences - && echo $orthogroups_fasta_src_dir - && echo $os.path.exists($orthogroups_fasta_src_dir) - && echo $create_corresponding_coding_sequences - && echo $orthogroups_fasta_dest_dir - && echo $single_copy_orthogroup - && echo $single_copy_fasta_src_dir - - #if $create_ortho_sequences and $os.path.exists($orthogroups_fasta_src_dir) and len($os.listdir($orthogroups_fasta_src_dir)) > 0: - #if $create_corresponding_coding_sequences: - && ls -l $orthogroups_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' > $output_ptcgfcs - #else: - && ls -l $orthogroups_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' > $output_ptcgf + #if $create_ortho_sequences: + #while not $os.path.exists($orthogroups_fasta_src_dir): + $time.spleep(5) + #end while + #if len($os.listdir($orthogroups_fasta_src_dir)) > 0: + #if $create_corresponding_coding_sequences: + && ls -l $orthogroups_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' > $output_ptcgfcs + #else: + && ls -l $orthogroups_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' > $output_ptcgf + #end if + && mv $orthogroups_fasta_src_dir/* $orthogroups_fasta_dest_dir #end if - && mv $orthogroups_fasta_src_dir/* $orthogroups_fasta_dest_dir #end if #if $single_copy_orthogroup: - #if $create_ortho_sequences and $os.path.exists($single_copy_fasta_src_dir) and len($os.listdir($single_copy_fasta_src_dir)) > 0: - && ls -l $single_copy_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' > $output_ptsco - && mv $single_copy_fasta_src_dir/* $single_copy_fasta_dest_dir + #if $create_ortho_sequences: + #while not $os.path.exists($single_copy_fasta_src_dir): + $time.sleep(5) + #end while + #if len($os.listdir($single_copy_fasta_src_dir)) > 0: + && ls -l $single_copy_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' > $output_ptsco + && mv $single_copy_fasta_src_dir/* $single_copy_fasta_dest_dir + #end if #else: && mv geneFamilyClassification_dir/*.singleCopy $output_single_copy #end if