Awk merge the results of processing two files into a single file

Question

I use awk to extract and calculate information from two different files and I want to merge the results into a single file in columns ( for example, the output of first file in columns 1 and 2 and the output of the second one in 3 and 4 ).

The input files contain:

file1

SRR513804.1218581HWI-ST695_116193610:4:1307:17513:49120 SRR513804.16872HWI ST695_116193610:4:1101:7150:72196    SRR513804.2106179HWI-
ST695_116193610:4:2206:10596:165949 SRR513804.1710546HWI-ST695_116193610:4:2107:13906:128004    SRR513804.544253

file2

>SRR513804.1218581HWI-ST695_116193610:4:1307:17513:49120
TTTTGTTTTTTCTATATTTGAAAAAGAAATATGAAAACTTCATTTATATTTTCCACAAAG
AATGATTCAGCATCCTTCAAAGAAATTCAATATGTATAAAACGGTAATTCTAAATTTTAT
ACATATTGAATTTCTTTGAAGGATGCTGAATCATTCTTTGTGGAAAATATAAATGAAGTT
TTCATATTTCTTTTTCAAAT

To parse the first file I do this:

awk '
{
  s      = NF
  center = $1
}
{
  printf "%s\t %d\n", center, s
}
' file1

To parse the second file I do this:

awk '
/^>/ {
    if (count != "")
      printf "%s\t %d\n", seq_id, count
    count  = 0
    seq_id = $0
    next
}

NF {
  long  = length($0)
  count = count+long
}
END{
  if (count != "")
    printf "%s\t %d\n", seq_id, count
}
' file2

My provisional solution is create one temporal and overwrite in the second step. There is a more "elegant" way to get this output?

Answer 1

I am not fully clear on the requirement and if you can update the question may be we can help improvise the answer. However, from what I have gathered is that you would like to summarize the output from both files. I have made an assumption that content in both files are in sequential order. If that is not the case, then we will have to add additional checks while printing the summary.

Content of script.awk (re-using most of your existing code):

NR==FNR {
    s[NR]      = NF
    center[NR] = $1
    next
}

/^>/ {
    seq_id[++y] = $0
    ++i
    next
}

NF {
    long[i] += length($0)
}
END {
    for(x=1;x<=length(s);x++) {
        printf "%s\t %d\t %d\n", center[x], s[x], long[x]
    }
}

Test:

$ cat file1
SRR513804.1218581HWI-ST695_116193610:4:1307:17513:49120 SRR513804.16872HWI ST695_116193610:4:1101:7150:72196    SRR513804.2106179HWI-
ST695_116193610:4:2206:10596:165949 SRR513804.1710546HWI-ST695_116193610:4:2107:13906:128004    SRR513804.544253

$ cat file2
>SRR513804.1218581HWI-ST695_116193610:4:1307:17513:49120
TTTTGTTTTTTCTATATTTGAAAAAGAAATATGAAAACTTCATTTATATTTTCCACAAAG
AATGATTCAGCATCCTTCAAAGAAATTCAATATGTATAAAACGGTAATTCTAAATTTTAT
ACATATTGAATTTCTTTGAAGGATGCTGAATCATTCTTTGTGGAAAATATAAATGAAGTT
TTCATATTTCTTTTTCAAAT

$ awk -f script.awk file1 file2
SRR513804.1218581HWI-ST695_116193610:4:1307:17513:49120  4   200
ST695_116193610:4:2206:10596:165949  3   0