cd-hit has given me an output that looks just like the example below.
>Cluster 0
0 496aa, >SRR5892231.2396932... *
>Cluster 1
0 496aa, >SRR5892231.3763255... *
1 390aa, >SRR5892231.1558909... at 91.03%
>Cluster 2
0 496aa, >SRR5892231.1710795... *
>Cluster 3
0 496aa, >SRR5892231.2083014... *
1 464aa, >SRR5892231.14158... at 91.59%
2 423aa, >SRR5892231.1116524... at 94.56%
3 314aa, >SRR5892231.1717279... at 95.86%
4 268aa, >SRR5892231.2309241... at 99.63%
5 371aa, >SRR5892231.480233... at 99.46%
>Cluster 4
0 496aa, >SRR5892231.3954388... *
1 319aa, >SRR5892231.1752373... at 99.69%
>Cluster 5
0 496aa, >SRR5892231.14746... *
>Cluster 6
0 496aa, >SRR5892231.2340653... *
1 407aa, >SRR5892231.2608197... at 100.00%
2 340aa, >SRR5892231.1216749... at 100.00%
3 345aa, >SRR5892231.3205930... at 92.46%
Each line that starts with a > shows the cluster label. The next line that ends with a ... * shows the representative sequence for the particular cluster.
How do I create a csv file containing the cluster label and its representative sequence?
(note: a cluster that appeared once in this file can re-appear somewhere in the middle of the file even though it is not shown in this case)
Thank you in advance for the help.
2 answers
I created my own answer for this question.
# this program takes in cltr file and create a mapping file
#cluster,representative sequence name
import re
# Using readlines()
file1 = open('sub_SRR5892231_90.clstr', 'r')
file2 = open('map.sub_SRR5892231_90.clstr.csv', 'w')
Lines = file1.readlines()
# since I am using a while loop I need the following index
LineIndex = 0
while LineIndex < len(Lines):
# check if >Cluster lines are there
FF = re.search(r'^(>Cluster.*)', Lines[LineIndex])
# if the lines re found, then prep it for first column
if FF != None:
#print(FF.group())
firstcol = FF.group().replace('>','')
file2.write(firstcol+',')
print(firstcol, end =",")
LineIndex = LineIndex + 1
while LineIndex < len(Lines):
KK = re.search(r'^(.*\*)', Lines[LineIndex])
if KK != None:
seccol = KK.group()
seccol = re.sub(r'.*>','',seccol)
seccol = re.sub(r'\.\.\. \*','',seccol)
print(seccol)
file2.write(seccol+'\n')
break
LineIndex = LineIndex + 1
LineIndex = LineIndex + 1
file1.close()
file2.close()
There is a set of tools by Joe that may help you here.
https://github.com/jrjhealey/bioinfo-tools
Look for ParseCDHIT.py. It doesn't do exactly what you want, but close enough. You should be able to modify the script with minimal Python knowledge.
Log in to answer this question.
You can try using scripts provided by CD-HIT devs:
https://github.com/weizhongli/cdhit/blob/master/clstr2txt.plandhttps://github.com/weizhongli/cdhit/blob/master/clstr_select_rep.pl.Thanks for this solution. This solution works if the representative sequence is exactly the next line after line starting with >Cluster. I noticed that some lines may be present as the third or fifth etc line. Therefore, it is better if we capture the line ending with *. I created my own solution (posted here) which does this using python.
If you can modify your solution using awk, that would be great.