Mercurial > repos > miller-lab > genome_diversity
changeset 37:884ccb07885b
Fixed output_id
| author | Richard Burhans <burhans@bx.psu.edu> |
|---|---|
| date | Wed, 20 Nov 2013 16:43:43 -0500 |
| parents | 51cd0307fb70 |
| children | 9d0b1fa77047 |
| files | make_phylip.py make_phylip.xml |
| diffstat | 2 files changed, 3 insertions(+), 1 deletions(-) [+] |
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--- a/make_phylip.py Wed Nov 20 16:32:01 2013 -0500 +++ b/make_phylip.py Wed Nov 20 16:43:43 2013 -0500 @@ -402,6 +402,7 @@ parser.add_argument('--refClmn',metavar='int',type=int,help='the column with the reference nucleotide.',required=True) parser.add_argument('--altrClmn',metavar='int',type=int,help='the column with the derived nucleotide.',required=True) parser.add_argument('--output',metavar='output',type=str,help='the output',required=True) + parser.add_argument('--output_id',metavar='int',type=int,help='the output id',required=True) parser.add_argument('--gd_indivs',metavar='input gd_indivs file',type=str,help='the input reference species columns in the input file.',required=True) #~ parser.add_argument('--inputCover',metavar='input gd_snp cover file',type=str,help='the input file with the table in gd_snp/gd_genotype cover format.',required=False,default=False) @@ -431,6 +432,7 @@ inSNPf = args.input inSNPf_type = args.input_type outfile = args.output + outfile_id = args.output_id gd_indivs = args.gd_indivs pxchrx = args.chrClmn pxpos = args.posClmn
--- a/make_phylip.xml Wed Nov 20 16:32:01 2013 -0500 +++ b/make_phylip.xml Wed Nov 20 16:43:43 2013 -0500 @@ -7,7 +7,7 @@ #set $gen_posClmn = int($input.metadata.rPos) - $zero_based #set $gen_refClmn = int($input.metadata.pos) - $zero_based + 1 #set $gen_altrClmn = int($input.metadata.pos) - $zero_based + 2 - make_phylip.py '--altrClmn=$gen_altrClmn' '--chrClmn=$gen_chrClmn' '--gd_indivs=$indivs_input' '--input=$input' '--input_type=$input.ext' '--output=$output1' '--posClmn=$gen_posClmn' '--refClmn=$gen_refClmn' + make_phylip.py '--altrClmn=$gen_altrClmn' '--chrClmn=$gen_chrClmn' '--gd_indivs=$indivs_input' '--input=$input' '--input_type=$input.ext' '--output=$output1' '--output_id=$output1.id' '--posClmn=$gen_posClmn' '--refClmn=$gen_refClmn' #if $input_type.choice == '0' #set $cov_chrClmn = int($input_type.coverage_input.metadata.ref) - $zero_based #set $cov_posClmn = int($input_type.coverage_input.metadata.rPos) - $zero_based