comparison make_phylip.py @ 36:51cd0307fb70

Phylip's extra ouputs are now stored in the job working directory

35:ea52b23f1141

#       along with this program; if not, write to the Free Software
#       Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
#       MA 02110-1301, USA.

import argparse
import errno
import os
import shutil
from Population import Population

def mkdir_p(path):
    try:
        os.makedirs(path)
    except OSError, e:
        if e.errno <> errno.EEXIST:
            raise

def revseq(seq):
    seq=list(seq)
    seq.reverse()
    seq=''.join(seq)

        #~ formtd='\n'.join([hader,seq])
        dPopsFormPhy[eachPop]=formtd
    #~ 
    return dPopsFormPhy,len(seq)

def wrapSeqsFasta(dENSEMBLTPopsFasta,outFastaFold,sPopsIntrst):
    """
    """
    ENSEMBLTKaKs=[]
    nonHeader=True
    cnt=0

        seqPMLformat=['%s %s'%(len(dPopsFormPhy),lenseq)]#generate new PHYML sequence
        #~ seqPMLformat=[]#generate new PHYML sequence
        for namex in sorted(sPopsIntrst):
            seqPMLformat.append(dPopsFormPhy[namex])
        #~ 
        mkdir_p(outFastaFold)
        outFastaf=os.path.join(outFastaFold,'%s.phy'%ENSEMBLT)
        outFastaf=open(outFastaf,'w')
        outFastaf.write('\n'.join(seqPMLformat))
        outFastaf.close()
        #~ 
    return 0

    parser.add_argument('--chrClmn',metavar='int',type=int,help='the column with the chromosome.',required=True)
    parser.add_argument('--posClmn',metavar='int',type=int,help='the column with the SNPs position.',required=True)
    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('--output_dir',metavar='output folder sequences',type=str,help='the output folder with the sequences.',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)
    parser.add_argument('--inputCover_type',metavar='input cover type',type=str,help='the cover input file type (gd_snp or gd_genotype)',required=False,default=False)
    parser.add_argument('--gd_indivs_cover',metavar='input gd_indivs file',type=str,help='the input reference species columns in the input cover file.',required=False,default=False)

    args = parser.parse_args()

    inSNPf = args.input
    inSNPf_type = args.input_type
    outfile = args.output
    outfile_id = args.output_id
    outFastaFold = './out'
    files_dir = args.output_dir
    gd_indivs = args.gd_indivs    
    pxchrx = args.chrClmn
    pxpos = args.posClmn
    pxntA = args.refClmn
    pxntB = args.altrClmn

    #~ 
    dENSEMBLTChrPosdAlls,dChrPosdPopsAllls=rtrnFxdChrPosinCodReg(dChrdStrtEndENSEMBLT,dChrdPosdPopsAlllsInit)#~ print '3. Getting fixed alleles in exons...'
    #~ 
    dENSEMBLTPopsFasta,lchrStartexEndposAll=rtrnSeqVars(dENSEMBLTseqChrStEnEx,dENSEMBLTChrPosdAlls)#~ print '4. Getting fasta sequences of populations...'
    #~ 
    wrapSeqsFasta(dENSEMBLTPopsFasta,outFastaFold,sPopsIntrst)
    #~ 

    ## get a list of output files
    files = []
    for dirpath, dirnames, filenames in os.walk(outFastaFold):
        for file in filenames:
            if file.endswith('.phy'):
                files.append( os.path.join(dirpath, file) )
        del dirnames[:]

    if len(files) == 0:
        with open(outfile, 'w') as ofh:
            print >> ofh, 'No output.'
    else:
        ## the first file becomes the output
        file = files.pop(0)
        shutil.move(file, outfile)

        ## rename/move the rest of the files
        for file in files:
            name = os.path.basename(file)[:-4]
            name = name.replace('_', '-')
            new_filename = 'primary_{0}_{1}_visible_txt_?'.format(outfile_id, name)
            new_pathname = os.path.join(files_dir, new_filename)
            shutil.move(file, new_pathname)

    return 0

if __name__ == '__main__':
    main()

36:51cd0307fb70

#       along with this program; if not, write to the Free Software
#       Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
#       MA 02110-1301, USA.

import argparse
import glob
import os
import shutil
from Population import Population

def revseq(seq):
    seq=list(seq)
    seq.reverse()
    seq=''.join(seq)

        #~ formtd='\n'.join([hader,seq])
        dPopsFormPhy[eachPop]=formtd
    #~ 
    return dPopsFormPhy,len(seq)

def wrapSeqsFasta(dENSEMBLTPopsFasta,sPopsIntrst):
    """
    """
    ENSEMBLTKaKs=[]
    nonHeader=True
    cnt=0

        seqPMLformat=['%s %s'%(len(dPopsFormPhy),lenseq)]#generate new PHYML sequence
        #~ seqPMLformat=[]#generate new PHYML sequence
        for namex in sorted(sPopsIntrst):
            seqPMLformat.append(dPopsFormPhy[namex])
        #~ 
        outFastaf=open('%s.phy'%ENSEMBLT,'w')
        outFastaf.write('\n'.join(seqPMLformat))
        outFastaf.close()
        #~ 
    return 0

    parser.add_argument('--chrClmn',metavar='int',type=int,help='the column with the chromosome.',required=True)
    parser.add_argument('--posClmn',metavar='int',type=int,help='the column with the SNPs position.',required=True)
    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('--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)
    parser.add_argument('--inputCover_type',metavar='input cover type',type=str,help='the cover input file type (gd_snp or gd_genotype)',required=False,default=False)
    parser.add_argument('--gd_indivs_cover',metavar='input gd_indivs file',type=str,help='the input reference species columns in the input cover file.',required=False,default=False)

    args = parser.parse_args()

    inSNPf = args.input
    inSNPf_type = args.input_type
    outfile = args.output
    gd_indivs = args.gd_indivs    
    pxchrx = args.chrClmn
    pxpos = args.posClmn
    pxntA = args.refClmn
    pxntB = args.altrClmn

    #~ 
    dENSEMBLTChrPosdAlls,dChrPosdPopsAllls=rtrnFxdChrPosinCodReg(dChrdStrtEndENSEMBLT,dChrdPosdPopsAlllsInit)#~ print '3. Getting fixed alleles in exons...'
    #~ 
    dENSEMBLTPopsFasta,lchrStartexEndposAll=rtrnSeqVars(dENSEMBLTseqChrStEnEx,dENSEMBLTChrPosdAlls)#~ print '4. Getting fasta sequences of populations...'
    #~ 
    wrapSeqsFasta(dENSEMBLTPopsFasta,sPopsIntrst)
    #~ 

    ## get a list of output files
    files = glob.glob('*.phy')

    if len(files) == 0:
        with open(outfile, 'w') as ofh:
            print >> ofh, 'No output.'
    else:
        ## the first file becomes the output
        file = files.pop(0)
        shutil.move(file, outfile)

        ## rename the rest of the files
        for file in files:
            name = file[:-4]
            name = name.replace('_', '-')
            new_filename = 'primary_{0}_{1}_visible_txt_?'.format(outfile_id, name)
            os.rename(file, new_filename)

    return 0

if __name__ == '__main__':
    main()