Mercurial > repos > yating-l > rename_scaffolds

comparison rename.py @ 6:2d143f0ac727 draft

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planemo upload commit 921e3c4788a88874c4ac7b7097e609d0b1e646c9
author yating-l
date Tue, 31 Jul 2018 14:04:59 -0400
parents 7c8b327f298c
children
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5:7c8b327f298c 6:2d143f0ac727
1 """ 1 """
2 Call rename to rename scaffolds in reference 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 2 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
3 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 '_' 3 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 '_'
4 """ 4 """
5 import sys 5 import sys
6 import csv 6 import csv
7 import codecs 7 import codecs