how to sort the rows of a file as a matrix?

I would like to know how I can sort the rows of a file in the following way:

My file is file.txt (tab delimited):

g1: 00A98_01563 00554_01552 CCUG38_01373    
d2: 00554_01444
g3_3: 00A98_04566 CCUG38_05322

I want to get this (tab delimited):

 00A98 00554 CCUG38
g1 1 1 1
d2 0 1 0
g3_3 1 0 1

How can I do it with the command line?

All the best, Regards

linux

• 1,979 views • link

updated 2.8 years ago by Ram

• written 5.1 years ago by BATMAN •

I think this will be quite cumbersome on the commandline alone I think. This is a task for python or R really.

• 0 views • link

written 5.1 years ago by Joe

2 answers

awk  '{for(i=2;i<=NF;i++) print $1"\t"$i;}' input.tsv |  datamash crosstab 1,2  --filler=0
    strainA_Nbr strainB_Nbr strainC_Nbr
g1  1   1   1
g2  0   1   0
g3  1   0   1

• 0 views • link

written 5.1 years ago by Pierre Lindenbaum

Thanks a lot bro for the help! i am dealing with the query_pan_genome output of roary. I updated the query example, I apologize and if your help returned. Seeing your answer, I should convert to this the table and then your command?

Initial:

g1: 00A98_01563 00554_01552 CCUG38_01373    
d2: 00554_01444
g3_3: 00A98_04566 CCUG38_05322

Delete what follows after the "_"

g1: 00A98 00554 CCUG38  
d2: 00554
g3_3: 00A98 CCUG38

Your command:

00A98 00554 CCUG38
g1 1 1 1
d2 0 1 0
g3_3 1 0 1

How can I do?

• 0 views • link

written 5.1 years ago by BATMAN •

You just need to update the awk code :

awk '{gsub(":","",$1);for(i=2;i<=NF;i++) {split($i,a,"_"); print $1"\t"a[1];}}' input.tsv | datamash crosstab 1,2 --filler=0

• 0 views • link

written 5.1 years ago by Sam

Convoluted to use Python, but this seems to give the desired output:

#!/usr/bin/env python

import sys
import io

rows_str = '''g1: 00A98_01563 00554_01552 CCUG38_01373    
d2: 00554_01444
g3_3: 00A98_04566 CCUG38_05322'''

# read in records
rows_fh = io.StringIO(rows_str)
records = {}
keys = set()
for row in rows_fh:
    elems = row.split()
    value = elems[0].replace(':', '')
    if value not in records: records[value] = set()
    ks = [x.split('_')[0] for x in elems[1:]]
    for k in ks:
        records[value].add(k)
        keys.add(k)

# output matrix
o = [''] + [k for k in keys]
ol = '\t'.join(o) + '\n'
sys.stdout.write(ol)
for rk, rv in records.items():
    o = [rk]
    for k in keys:
        v = '1' if k in rv else '0'
        o.append(v)
    ol = '\t'.join(o)  + '\n'
    sys.stdout.write(ol)

Output:

% ./so9478485.py
    CCUG38  00A98   00554
g1  1   1   1
d2  0   0   1
g3_3    1   1   0

• 0 views • link

written 5.1 years ago by Alex Reynolds