view rename.py @ 7:9027a4b529c3 draft default tip

planemo upload commit a5a68ac1b3d4be4b923912f497ba81c6305e18f1

"""
Call rename to rename scaffolds in target genome so that the sequence names are less than 31 characters. Rename all scaffolds to scaffold_1, scaffold_2, ..., scaffold_N and provide a name mapping file
Call truncate to truncate the scaffold names that are more than 31 characters. Replace each invalid character (non-ASCII, '\t', '\n', '\x0b', '\x0c', '\r') with '_'
"""
import sys
import csv
import codecs
import string

def rename(inputfile, outputfile, writer):
    with open(outputfile, 'w') as out:
        with codecs.open(inputfile, 'r', encoding='utf-8') as rf:
            lines = rf.readlines()
            i = 1
            for line in lines:
                if ">" in line:
                    oldname = line[1:].rstrip()
                    newname = "scaffold_" + str(i)
                    line = ">" + newname + "\n"
                    i = i+1
                    writer.writerow([oldname.encode('utf-8'), newname])
                out.write(line)

def truncate(inputFile, outputFile, valid_characters, writer):
    names = []
    with open(outputFile, 'w') as out:
        with codecs.open(inputFile, 'r', encoding='utf-8') as rf:
            lines = rf.readlines()
            for l in lines:
                if ">" in l:
                    print l.encode('utf-8')
                    oldname = l[1:].rstrip()
                    name = substituteNonAscii(oldname, valid_characters)
                    if len(name) > 31:
                        name = name[:31]
                        print "\tTruncate the scaffold name to less than 31 characters: %s" % name
                    if name in names:
                        sys.exit("Name conflict! Name " + name + " already exist.")
                    writer.writerow([oldname.encode('utf-8'), name])
                    names.append(name)
                    l = ">" + name + "\n"
                    print "======================\n"
                out.write(l)

def substituteNonAscii(str, valid_charaters):
    l = []
    for c in str:
        if c not in valid_charaters:
            print "\tSubstitute invalid character %s with _" % c.encode('utf-8')
            c = '_'
        l.append(c)
    return "".join(l)

def main():
    inputfile = str(sys.argv[1])
    manipulate = str(sys.argv[2])
    outputfile = str(sys.argv[3])
    indexfile = str(sys.argv[4])
    csvfile = open(indexfile, 'w')
    writer = csv.writer(csvfile)
    if manipulate == "rename":
        rename(inputfile, outputfile, writer)
    elif manipulate == "truncate":
        valid_characters = string.letters + string.punctuation + string.digits + ' '
        truncate(inputfile, outputfile, valid_characters, writer)

if __name__ == "__main__":
    main()