Mercurial > repos > greg > phylogenomics_analysis

comparison phylogenomics_analysis.xml @ 12:16861f56079f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author greg
date Thu, 05 Jan 2017 15:13:37 -0500
parents cac8a85418c2
children b37db5a8ed13
comparison
equal deleted inserted replaced
11:cac8a85418c2 12:16861f56079f
18 #if not $os.path.exists($orthogroup_faa.extra_files_path): 18 #if not $os.path.exists($orthogroup_faa.extra_files_path):
19 print > $sys.stderr($invalid_input) 19 print > $sys.stderr($invalid_input)
20 $sys.exit(1) 20 $sys.exit(1)
21 #end if 21 #end if
22 #set src_dir = $os.path.join('phylogenomicsAnalysis_dir', 'orthogroups_fasta') 22 #set src_dir = $os.path.join('phylogenomicsAnalysis_dir', 'orthogroups_fasta')
23 #set num_orthogroup_faa = len([f for f in $os.listdir($src_dir) if f.endswith('.faa')]) 23 #set num_orthogroup_faa = 0
24 #for f in $os.listdir($src_dir):
25 #if $f.endswith('.faa')])
26 set num_orthogroup_faa = $num_orthogroup_faa + 1
27 #end if
28 #end for
24 #if $num_orthogroup_faa == 0: 29 #if $num_orthogroup_faa == 0:
25 print > $sys.stderr($invalid_input) 30 print > $sys.stderr($invalid_input)
26 $sys.exit(1) 31 $sys.exit(1)
27 #end if 32 #end if
28 #set num_orthogroup_fna = len([f for f in $os.listdir($src_dir) if f.endswith('.fna')]) 33 #set num_orthogroup_fna = 0
34 #for f in $os.listdir($src_dir):
35 #if $f.endswith('.fna')])
36 set num_orthogroup_fna = $num_orthogroup_fna + 1
37 #end if
38 #end for
29 #set dest_dir = $output.extra_files_path 39 #set dest_dir = $output.extra_files_path
30 mkdir -p $dest_dir && 40 mkdir -p $dest_dir &&
31 PhylogenomicsAnalysis 41 PhylogenomicsAnalysis
32 --orthogroup_faa "$orthogroup_faa.extra_files_path" 42 --orthogroup_faa "$orthogroup_faa.extra_files_path"
33 --scaffold "$scaffold" 43 --scaffold "$scaffold"