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Count and search by sequence in multiple fasta file

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# 1  
Old 03-10-2014
[Solved] Count and search by sequence in multiple fasta file
Hello,

I have 10 fasta files with sequenced reads information with read sizes from 15 - 35 . I have combined the reads and collapsed in to unique reads and filtered for sizes 18 - 26 bp long unique reads. Now i wanted to count each unique read appearance in all the fasta files and make a table with sample names as columns and reads as rows. I tried to use "grep -w "sequence name" file name " to count the tags but this seems to take long time. does anyone know how to do this faster?
# 2  
Old 03-10-2014
Post example input and example output of what you want.
# 3  
Old 03-11-2014
Sorry for the confusion. Here are the input files and required output

This is the input file where it contains unique sequences. i have more than million such unique sequences.
Query:
Code:
>tag1
TCGGA
>tag2
TCTCA
>tag3
TCTCGC

These are multiple files. for example i am showing with 3 files. i have more than 20 such files. each file contains more than 10 million sequences each
File1:
Code:
>file1_id1
TCGGA
>file1_id1
TCGGAT
>file1_id2
TCTCA
>file1_id3
TCTCA

File2:
Code:
>file2_id1
TCTCA
>file2_id2
TCTCA
>file2_id3
TCTCACTA
>file2_id4
TCTCGC
>file2_id5
TCTCGCCTAT
>file2_id6
TCTCGC

File3:
Code:
>file1_id1
TCGGA
>file1_id1
TCGGAT
>file2_id4
TCTCGC
>file2_id5
TCTCGCCTAT
>file2_id6
TCTCGC

I need the following output. Search has to be exact for the count.
output:
Code:
		sequence	file1	file2	file3
tag1	TCGGA		1		0		1
tag2	TCTCA		2		2		0		
tag3	TCTCGC		0		2		2

Moderator's Comments:
Mod Comment Please use CODE tags to mark sample code, sample input, and sample output; not your entire message.
Last edited by Don Cragun; 03-11-2014 at 04:17 AM.. Reason: Fix CODE tags.
# 4  
Old 03-11-2014
Without seeing your code, it is impossible to guess at whether or not something else is faster. You could try something like:
Code:
awk '
FNR == NR {
	if($1 ~ /^>/)
		t[++tn] = substr($1, 2)
	else {	s[$1] = tn
		seq[tn] = $1
	}
	next
}
FNR == 1 {
	fn++
}
$1 in s {
	tc[s[$1], fn]++
}
END {	# Print header:
	printf("\t\tsequence")
	for(i = 1; i <= fn; i++)
		printf("\tfile%d", i)
	printf("\n")
	# Print tag data:
	for(i = 1; i <= tn; i++) {
		printf("%s\t%s", t[i], seq[i])
		for(j = 1; j <= fn; j++)
			printf("\t\t%d", tc[i, j])
		printf("\n")
	}
}' Query File1 File2 File3

which with your sample input files produces:
Code:
		sequence	file1	file2	file3
tag1	TCGGA		1		0		1
tag2	TCTCA		2		2		0
tag3	TCTCGC		0		2		2

# 5  
Old 03-11-2014
a bash approach
Code:
#!/bin/bash

query=query.txt
file_list=(*.txt)
declare -A pattern

printf "%-10s\t%-10s\t" "" "Sequence"
for file in ${file_list[@]}
do
  printf "%-10s\t" $file
  while read line
  do
    [[ "$line" =~ ">" ]] && continue
    ((pattern[$file,$line]+=1))
  done < $file
done
echo

while read line
do
  [[ "$line" =~ ">" ]] && printf "%-10s\t" ${line/>/} && continue
  printf "%-10s\t" $line
  for file in ${file_list[@]}
  do
    printf "%-10s\t" ${pattern[$file,$line]:-0}
  done
  echo
done < $query

# 6  
Old 03-13-2014
Thank you , Don. This works really well. easy to run and easy to understand as well.

---------- Post updated at 04:17 PM ---------- Previous update was at 04:16 PM ----------

ahamed, thank you for your response but don's version was faster and finished my query in less time. Smilie
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