comparison filter_fasta.py @ 6:5990c4dbfbaa draft

Uploaded

5:af454e5a9ef5

        output = []
        for line in x:
            line = line.strip()
            temp = line.split('\t')
            output.append(temp)
            print temp
    return output
def getAccessions(infile): # get list of protein accessions from your data
    data = readtab(infile)
    cnt = 0
    header_start = 0

            if temp != []:
                merged = "\n".join(temp)
                if merged!="":
                    seq.append(merged)
    cnt=0
    with open("output.fasta","wt") as x:
        for i in header:
            x.write(i+'\n'+seq[cnt]+'\n')
            print i+'\n'+seq[cnt]+'\n'
            cnt+=1
fasta = sys.argv[1] # fasta file to filter
data = sys.argv[2] # scaffold report #2 -- filename

FilterFastaSeq(fasta,getAccessions(data))

6:5990c4dbfbaa

        output = []
        for line in x:
            line = line.strip()
            temp = line.split('\t')
            output.append(temp)
    return output
def getAccessions(infile): # get list of protein accessions from your data
    data = readtab(infile)
    cnt = 0
    header_start = 0

            if temp != []:
                merged = "\n".join(temp)
                if merged!="":
                    seq.append(merged)
    cnt=0
    with open("output.fasta","w") as x:
        for i in header:
            x.write(i+'\n'+seq[cnt]+'\n')
            cnt+=1
fasta = sys.argv[1] # fasta file to filter
data = sys.argv[2] # scaffold report #2 -- filename

FilterFastaSeq(fasta,getAccessions(data))