# Concatenating sequence length to another file **URL:** \ **Category:** UNIX for Beginners Q & A\ **Created:** [March 5, 2019, 1:38pm UTC](https://community.unix.com/t/concatenating-sequence-length-to-another-file/375047 "2019-03-05T13:38:02Z")\ **Posts on this page:** 7\ **Page:** 1
**Author:** ![Ibk](https://community.unix.com/letter_avatar/ibk/32/5_5575768a8748004e209b776fc1b2916d.png) [@Ibk](https://community.unix.com/u/Ibk)\ **Post date:** [March 5, 2019, 1:38pm UTC](https://community.unix.com/t/concatenating-sequence-length-to-another-file/375047/1 "2019-03-05T13:38:02Z")
I want to add the sequence length of File\_1.fa and File \_2.fa to form the form the fifth column in File\_1\_pos.txt and File\_2\_poa.txt respectively using awk and bash. Can anyone help me? Thanks Get sequence length of each file ```nohighlight File_1.fa File_2.fa ``` Add the sequence length to be the third column of File 3 File\_1\_pos.txt ```nohighlight File_1_pos 253 164 File_1_pos 738 827 ``` File\_2\_pos.txt ```nohighlight File_2_pos 1494 1583 File_2_pos 1785 1874 ``` Expected Output File\_1\_pos.txt ```nohighlight 1 File_1_pos 253 164 8126 2 File_1_pos 738 827 8126 ``` File\_2\_poa.txt ```nohighlight 1 File_2_pos 1494 1583 9655 2 File_2_pos 1785 1874 9655 ``` I tried this but I dint get my expected output ```nohighlight for file in *.fa; do a=`awk '/^>/ {if (seqlen){print seqlen};next; } { seqlen += length($0)}END{print seqlen}' $file` | awk -F, '{$1=++i OFS"\t" $1;}1' ${file%.*}pos.txt | awk 'BEGIN{OFS="\t"}{print $1,$2,$3,$4,a}'; done ``` ---
**Author:** ![RudiC](https://community.unix.com/letter_avatar/rudic/32/5_5575768a8748004e209b776fc1b2916d.png) [@RudiC](https://community.unix.com/u/RudiC)\ **Post date:** [March 5, 2019, 2:20pm UTC](https://community.unix.com/t/concatenating-sequence-length-to-another-file/375047/2 "2019-03-05T14:20:24Z")
Please post input file samples. How do you calculate the "sequence length"? Is there one or more of them per file? ---
**Author:** ![Ibk](https://community.unix.com/letter_avatar/ibk/32/5_5575768a8748004e209b776fc1b2916d.png) [@Ibk](https://community.unix.com/u/Ibk)\ **Post date:** [March 5, 2019, 2:42pm UTC](https://community.unix.com/t/concatenating-sequence-length-to-another-file/375047/3 "2019-03-05T14:42:30Z")
These are examples of the input sequence. Just one long sequence per file. thanks \>File\_1.fa ```nohighlight TTGAAAGGGGGCCCGGGGGATCTCCCCCGCGGTAACTGGTCACAGTTGCCGCGGACGGAGATCATCCCCC GGTTACCCCCTTTCGACGCGGGTACTGCGATAGTGCCACCCCAGTCCTTCCTACTCCCGACTCCCGACCC CAACCCAGGTTCCTTGGAACAGGAACACCAATTTATTCATCCCTTGGATGCTGACTAATCAGAGGAACGT CAGCATTTTCCGGCCCAGGCTAAGAGAAGTAGATAAGTTAGAATCTAAATTATTTATCATCCCCTTGACG AATTCGCGTTGGAAAAGCACCTCTCACTTGCCGCTCTTCACACCCATCATTCTAATTCGGCCCCTGTGTT ``` \>File\_2.fa ```nohighlight GAGCCCCTTGTTGAAGTGTTTCCCTCCATCGCGACGTGGTTGGAGATCTAAGTTAACCGACTCCGACGAA ACTACCATCATGCCTCCCCGATTATGTGATGCTTTCTGCCCTGCTGGGTGGAGCATCCTCGGGTTGAGAA ATCTTTCTTCCTTTTACCTTGGACTCCGGTCCCCCGGTCTAAGCCGCTTGGAATAAGACAGGGTTATCTT CACTCCTCTTCTTTTCTACTTCACAGTGTTCTATGCTGTGAAAGGGTATGTGTCGCCCCTTCCTTCTTCG ``` ---
**Author:** ![RudiC](https://community.unix.com/letter_avatar/rudic/32/5_5575768a8748004e209b776fc1b2916d.png) [@RudiC](https://community.unix.com/u/RudiC)\ **Post date:** [March 5, 2019, 4:59pm UTC](https://community.unix.com/t/concatenating-sequence-length-to-another-file/375047/4 "2019-03-05T16:59:34Z")
Try ```nohighlight $ wc -cl *.fa | awk ' FILENAME == "-" {sub (".fa", "", $3) T[$3] = $2 - $1 next } FNR == 1 {IX = FILENAME sub (/_[^_]*\..*$/, "", IX) } {print FNR, $0, T[IX] > (FILENAME ".new") } ' - OFS="\t" fil*pos.txt $ cf *.new ---------- file_1_pos.txt.new: ---------- 1 File_1_pos 253 164 350 2 File_1_pos 738 827 350 ---------- file_2_pos.txt.new: ---------- 1 File_2_pos 1494 1583 280 2 File_2_pos 1785 1874 280 ``` Copy exactly as given; then `mv` the ".new" files over the old ".txt" files EDIT: Given there are any number of `.fa` files, and each has a corresponding `_pos.txt` file, you could try ```nohighlight $ wc -cl *.fa | awk ' FILENAME == "-" {if ($3 == "total") next sub (".fa", "", $3) T[$3] = $2 - $1 ARGV[ARGC++] = $3 "_pos.txt" next } FNR == 1 {IX = FILENAME sub (/_[^_]*\..*$/, "", IX) } {print FNR, $0, T[IX] > (FILENAME ".new") } ' - OFS="\t" ``` ---
**Author:** ![Ibk](https://community.unix.com/letter_avatar/ibk/32/5_5575768a8748004e209b776fc1b2916d.png) [@Ibk](https://community.unix.com/u/Ibk)\ **Post date:** [March 7, 2019, 8:37am UTC](https://community.unix.com/t/concatenating-sequence-length-to-another-file/375047/5 "2019-03-07T08:37:31Z")
Thank you Rudic, I have tried the code but did not give me the required output. The input files are separate files as well as the expected output. ---
**Author:** ![rdrtx1](https://community.unix.com/user_avatar/community.unix.com/rdrtx1/32/2721_2.png) [@rdrtx1](https://community.unix.com/u/rdrtx1)\ **Post date:** [March 7, 2019, 3:14pm UTC](https://community.unix.com/t/concatenating-sequence-length-to-another-file/375047/6 "2019-03-07T15:14:42Z")
```nohighlight for file in *.fa; do awk ' NR==FNR { if ($0 ~ /^>/ && why_print_seqlen_for_this_line) {if (seqlen) print seqlen; next;} # is there a record separator /^>/ in the *.fa files not mentioned in samples? seqlen += length($0); next; } {print FNR, $0, seqlen} ' OFS="\t" $file ${file%.*}_pos.txt > t_$$ mv -f t_$$ ${file%.*}_pos.txt done ``` ---
**Author:** ![RudiC](https://community.unix.com/letter_avatar/rudic/32/5_5575768a8748004e209b776fc1b2916d.png) [@RudiC](https://community.unix.com/u/RudiC)\ **Post date:** [March 7, 2019, 4:22pm UTC](https://community.unix.com/t/concatenating-sequence-length-to-another-file/375047/7 "2019-03-07T16:22:23Z")
> [@ibk](#): > > ... The input files are separate files as well as the expected output. So - which files exist, and by what feature are the files connected / related?