allpy
changeset 760:92d83d437d66
utils/make_homologies.py can read a file of markup format
| author | Andrei <aba@belozersky.msu.ru> |
|---|---|
| date | Tue, 12 Jul 2011 16:05:21 +0400 |
| parents | ad576e4acdf1 |
| children | 5f0c15a3cbca |
| files | utils/make_homologies.py |
| diffstat | 1 files changed, 3 insertions(+), 1 deletions(-) [+] |
line diff
1.1 --- a/utils/make_homologies.py Tue Jul 12 16:05:07 2011 +0400 1.2 +++ b/utils/make_homologies.py Tue Jul 12 16:05:21 2011 +0400 1.3 @@ -21,6 +21,8 @@ 1.4 parser.add_option("-d", "--base_in", help="Name of directory with alignment files (default=\"\")", dest="base_in", default="") 1.5 parser.add_option("-s", "--suffix", help="Suffix for out files", dest="suffix", default = "hom") 1.6 parser.add_option("-o", "--base_out", help="Name of directory for outfiles (default=\"\")", dest="base_out", default="") 1.7 +parser.add_option("-f", "--format", help="Format of input file: 'markup' or 'fasta' (default)", dest="format", default = "fasta") 1.8 + 1.9 1.10 # FOR ONE INPUT ALIGNMENT 1.11 #parser.add_option("-i", "--in_file", help="File with an alignment in fasta", dest="in_file") 1.12 @@ -63,7 +65,7 @@ 1.13 in_file_name = base_in + alignment_name 1.14 out_file_name = base_out + alignment_name.partition(".fasta")[0] + ".xls" 1.15 1.16 - classes_number = MonomerHomology.case_homology(in_file_name,out_file_name, case) 1.17 + classes_number = MonomerHomology.case_homology(in_file_name,out_file_name, case, format) 1.18 print ("File %s: %s monomer homology classes stored" % (out_file_name,classes_number)) 1.19 1.20 print("...Done")