Mercurial > repos > greg > gene_family_classifier

comparison gene_family_classifier.xml @ 62:ffaedadf9c18 draft

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Uploaded
author greg
date Thu, 09 Feb 2017 10:53:31 -0500
parents 43d6e752f181
children dd22169524ee
comparison
equal deleted inserted replaced
61:43d6e752f181 62:ffaedadf9c18
104 && rm geneFamilyClassification_dir/hmmscan.log 104 && rm geneFamilyClassification_dir/hmmscan.log
105 #end if 105 #end if
106 #end if 106 #end if
107 107
108 #if $create_ortho_sequences: 108 #if $create_ortho_sequences:
109 #if len($os.listdir($orthogroups_fasta_src_dir)) > 0: 109 #if $create_corresponding_coding_sequences:
110 #if $create_corresponding_coding_sequences: 110 && ls -l $orthogroups_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' > $output_ptcgfcs
111 && ls -l $orthogroups_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' > $output_ptcgfcs 111 #else:
112 #else: 112 && ls -l $orthogroups_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' > $output_ptcgf
113 && ls -l $orthogroups_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' > $output_ptcgf 113 #end if
114 #end if 114 && mv $orthogroups_fasta_src_dir/* $orthogroups_fasta_dest_dir
115 && mv $orthogroups_fasta_src_dir/* $orthogroups_fasta_dest_dir
116 #end if
117 #end if 115 #end if
118 116
119 #if $single_copy_orthogroup: 117 #if $single_copy_orthogroup:
120 #if $create_ortho_sequences: 118 #if $create_ortho_sequences:
121 #if len($os.listdir($single_copy_fasta_src_dir)) > 0: 119 && ls -l $single_copy_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' > $output_ptsco
122 && ls -l $single_copy_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' > $output_ptsco 120 && mv $single_copy_fasta_src_dir/* $single_copy_fasta_dest_dir
123 && mv $single_copy_fasta_src_dir/* $single_copy_fasta_dest_dir
124 #end if
125 #else: 121 #else:
126 && mv geneFamilyClassification_dir/*.singleCopy $output_single_copy 122 && mv geneFamilyClassification_dir/*.singleCopy $output_single_copy
127 #end if 123 #end if
128 #end if 124 #end if
129 ]]> 125 ]]>