DataScience Workbook
/
03: Introduction to Command Line
/ 3.
Useful text manipulation programs
/ 3.5. DIFF, COMM, CMP – comparing and collating two files with Unix
Comparing and Collating Two Files with Unix
The diff, comm, and cmp commands are powerful utilities in Unix systems for comparing and analyzing differences between multiple files. diff highlights discrepancies line by line, making it ideal for pinpointing changes between two text files. It provides a detailed output, showing added, removed, and modified lines. Conversely, comm is perfect for comparing sorted files, displaying lines unique to each file and those common to both. Its structured output simplifies identifying differences and similarities between files, particularly in sorted datasets. Meanwhile, cmp offers a byte-level comparison, efficiently highlighting differences in binary files. It displays the first differing bytes and their offsets, making it invaluable for verifying the integrity of binary data or identifying discrepancies in large files. These commands collectively provide versatile solutions for comparing files, catering to various use cases from text to binary comparisons in Unix environments.
The two input files used to demonstrate the tutorial Note: they are tab separated!
Sample files to demonstrate the usefullness of the commands in this tutorial.
File1.txt
##gff-version 3
##sequence-region Chromosome_4 10612335 10618026
Chromosome_4 gffcl gene 10612335 10618026 . - . ID=gene1;Alias=RLOC_00010436
Chromosome_4 Mikado_loci mRNA 10612335 10618026 19 - . ID=mRNA1;Parent=gene1;Alias=mikado.Scaffold_4G3148.1
Chromosome_4 Mikado_loci CDS 10612335 10612436 . - 0 Parent=mRNA1
Chromosome_4 Mikado_loci exon 10612335 10612436 . - . Parent=mRNA1
Chromosome_4 . intron 10612437 10616129 . - . Parent=mRNA1
Chromosome_4 Mikado_loci CDS 10616130 10616190 . - 1 Parent=mRNA1
Chromosome_4 Mikado_loci exon 10616130 10616190 . - . Parent=mRNA1
Chromosome_4 . intron 10616191 10616666 . - . Parent=mRNA1
Chromosome_4 Mikado_loci CDS 10616667 10616725 . - 0 Parent=mRNA1
Chromosome_4 Mikado_loci exon 10616667 10616725 . - . Parent=mRNA1
Chromosome_4 . intron 10616726 10616766 . - . Parent=mRNA1
Chromosome_4 Mikado_loci CDS 10616767 10616850 . - 0 Parent=mRNA1
Chromosome_4 Mikado_loci exon 10616767 10616850 . - . Parent=mRNA1
Chromosome_4 . intron 10616851 10617972 . - . Parent=mRNA1
Chromosome_4 Mikado_loci exon 10617973 10618026 . - . Parent=mRNA1
Chromosome_4 Mikado_loci CDS 10617973 10618026 . - 0 Parent=mRNA1
###
##sequence-region Chromosome_2 6725589 6726696
Chromosome_2 gffcl gene 6725589 6726696 . + . ID=gene2;Alias=RLOC_00001404
Chromosome_2 Mikado_loci mRNA 6725589 6726696 21 + . ID=mRNA2;Parent=gene2;Alias=mikado.Scaffold_1G2094.1
Chromosome_2 Mikado_loci exon 6725589 6725716 . + . Parent=mRNA2
Chromosome_2 Mikado_loci CDS 6725629 6725716 . + 0 Parent=mRNA2
Chromosome_2 . intron 6725717 6725773 . + . Parent=mRNA2
Chromosome_2 Mikado_loci CDS 6725774 6725941 . + 2 Parent=mRNA2
Chromosome_2 Mikado_loci exon 6725774 6725941 . + . Parent=mRNA2
Chromosome_2 . intron 6725942 6725986 . + . Parent=mRNA2
Chromosome_2 Mikado_loci exon 6725987 6726307 . + . Parent=mRNA2
Chromosome_2 Mikado_loci CDS 6725987 6726307 . + 2 Parent=mRNA2
Chromosome_2 . intron 6726308 6726382 . + . Parent=mRNA2
Chromosome_2 Mikado_loci CDS 6726383 6726606 . + 2 Parent=mRNA2
Chromosome_2 Mikado_loci exon 6726383 6726696 . + . Parent=mRNA2
###
File2.txt
##gff-version 3
##sequence-region Chromosome_4 10612335 10618026
Chromosome_4 gffcl gene 10612335 10618026 . - . ID=gene1;Alias=RLOC_00010436
Chromosome_4 Mikado_loci mRNA 10612335 10618026 19 - . ID=mRNA1;Parent=gene1;Alias=mikado.Scaffold_4G3148.1
Chromosome_4 Mikado_loci CDS 10612335 10612436 . - 0 Parent=mRNA1
Chromosome_4 Mikado_loci exon 10612335 10612436 . - . Parent=mRNA1
Chromosome_4 . intron 10612437 10616129 . - . Parent=mRNA1
Chromosome_4 Mikado_loci CDS 10616130 10616190 . - 1 Parent=mRNA1
Chromosome_4 Mikado_loci exon 10616130 10616190 . - . Parent=mRNA1
Chromosome_4 . intron 10616191 10616666 . - . Parent=mRNA1
Chromosome_9 Mikado_loci exon 10818058 10818082 . - . Parent=Hetgly20664.t1
Chromosome_9 Mikado_loci CDS 10818058 10818082 . - 0 Parent=Hetgly20664.t1
Chromosome_9 gffcl gene 10818169 10823373 . + . ID=Hetgly20665;Alias=RLOC_00024670
Chromosome_9 Mikado_loci mRNA 10818169 10823373 19 + . ID=Hetgly20665.t1;Parent=Hetgly20665;Alias=mikado.Scaffold_9G3402.1
Chromosome_9 Mikado_loci exon 10818169 10818212 . + . Parent=Hetgly20665.t1
Chromosome_9 Mikado_loci CDS 10818169 10818212 . + 0 Parent=Hetgly20665.t1
Chromosome_9 Mikado_loci CDS 10818855 10818906 . + 1 Parent=Hetgly20665.t1
Chromosome_9 Mikado_loci exon 10818855 10818906 . + . Parent=Hetgly20665.t1
Chromosome_9 Mikado_loci CDS 10819113 10819217 . + 0 Parent=Hetgly20665.t1
Chromosome_9 Mikado_loci exon 10819113 10819217 . + . Parent=Hetgly20665.t1
Chromosome_9 Mikado_loci CDS 10819271 10819295 . + 0 Parent=Hetgly20665.t1
Chromosome_9 Mikado_loci exon 10819271 10819295 . + . Parent=Hetgly20665.t1
Chromosome_9 Mikado_loci exon 10819541 10819617 . + . Parent=Hetgly20665.t1
Chromosome_9 Mikado_loci CDS 10819541 10819617 . + 2 Parent=Hetgly20665.t1
Chromosome_9 Mikado_loci exon 10819664 10819732 . + . Parent=Hetgly20665.t1
Chromosome_9 Mikado_loci CDS 10819664 10819732 . + 0 Parent=Hetgly20665.t1
Chromosome_9 Mikado_loci exon 10819815 10819904 . + . Parent=Hetgly20665.t1
Chromosome_9 Mikado_loci CDS 10819815 10819904 . + 0 Parent=Hetgly20665.t1
Chromosome_9 Mikado_loci CDS 10820027 10820149 . + 0 Parent=Hetgly20665.t1
Chromosome_9 Mikado_loci exon 10820027 10820149 . + . Parent=Hetgly20665.t1
Chromosome_9 Mikado_loci CDS 10820510 10820594 . + 0 Parent=Hetgly20665.t1
Chromosome_9 Mikado_loci exon 10820510 10820594 . + . Parent=Hetgly20665.t1
Chromosome_9 Mikado_loci exon 10820645 10820714 . + . Parent=Hetgly20665.t1
Chromosome_9 Mikado_loci CDS 10820645 10820714 . + 2 Parent=Hetgly20665.t1
Chromosome_9 Mikado_loci CDS 10822063 10822254 . + 1 Parent=Hetgly20665.t1
Chromosome_9 Mikado_loci exon 10822063 10822254 . + . Parent=Hetgly20665.t1
Chromosome_9 Mikado_loci exon 10822759 10822892 . + . Parent=Hetgly20665.t1
Chromosome_9 Mikado_loci CDS 10822759 10822892 . + 1 Parent=Hetgly20665.t1
Chromosome_9 Mikado_loci exon 10823285 10823373 . + . Parent=Hetgly20665.t1
Chromosome_9 Mikado_loci CDS 10823285 10823373 . + 2 Parent=Hetgly20665.t1
Chromosome_9 gffcl gene 10824580 10826264 . + . ID=Hetgly20666;Alias=RLOC_00024671
Chromosome_9 Mikado_loci mRNA 10824580 10826264 19 + . ID=Hetgly20666.t1;Parent=Hetgly20666;Alias=mikado.Scaffold_9G3403.1
Chromosome_9 Mikado_loci CDS 10824580 10824850 . + 0 Parent=Hetgly20666.t1
Chromosome_9 Mikado_loci exon 10824580 10824850 . + . Parent=Hetgly20666.t1
Chromosome_9 Mikado_loci exon 10825921 10826126 . + . Parent=Hetgly20666.t1
Chromosome_9 Mikado_loci CDS 10825921 10826126 . + 2 Parent=Hetgly20666.t1
Chromosome_9 Mikado_loci exon 10826178 10826264 . + . Parent=Hetgly20666.t1
Chromosome_9 Mikado_loci CDS 10826178 10826264 . + 0 Parent=Hetgly20666.t1
Chromosome_9 gffcl gene 10844215 10844802 . + . ID=Hetgly20667;Alias=RLOC_00024672
Chromosome_9 Mikado_loci mRNA 10844215 10844805 22 + . ID=Hetgly20667.t1;Parent=Hetgly20667;Alias=mikado.Scaffold_9G3409.1
Chromosome_9 Mikado_loci exon 10844215 10844242 . + . Parent=Hetgly20667.t1
Chromosome_9 Mikado_loci exon 10844287 10844521 . + . Parent=Hetgly20667.t1
Chromosome_9 Mikado_loci exon 10844574 10844805 . + . Parent=Hetgly20667.t1
Chromosome_9 Mikado_loci CDS 10844574 10844801 . + 0 Parent=Hetgly20667.t1
Chromosome_9 Mikado_loci mRNA 10846322 10846912 22 - . ID=Hetgly20668.t1;Parent=Hetgly20668;Alias=mikado.Scaffold_9G3413.1
Chromosome_9 Mikado_loci exon 10846322 10846553 . - . Parent=Hetgly20668.t1
Chromosome_9 gffcl gene 10846325 10846912 . - . ID=Hetgly20668;Alias=RLOC_00024673
Chromosome_9 Mikado_loci CDS 10846326 10846553 . - 0 Parent=Hetgly20668.t1
Chromosome_9 Mikado_loci exon 10846606 10846840 . - . Parent=Hetgly20668.t1
Chromosome_9 Mikado_loci exon 10846885 10846912 . - . Parent=Hetgly20668.t1
The diff command
diff is a command that will immediately tell you the differences and commonalities in each line between two sorted files.
diff File1.txt File2.txt
Using process substitutions we can sort them in place if needed
diff <(sort File1.txt) <(sort File2.txt)
Output
< Chromosome_4 Mikado_loci CDS 10616667 10616725 . - 0 Parent=mRNA1 < Chromosome_4 Mikado_loci exon 10616667 10616725 . - . Parent=mRNA1 < Chromosome_4 . intron 10616726 10616766 . - . Parent=mRNA1 < Chromosome_4 Mikado_loci CDS 10616767 10616850 . - 0 Parent=mRNA1 < Chromosome_4 Mikado_loci exon 10616767 10616850 . - . Parent=mRNA1 < Chromosome_4 . intron 10616851 10617972 . - . Parent=mRNA1 < Chromosome_4 Mikado_loci exon 10617973 10618026 . - . Parent=mRNA1 < Chromosome_4 Mikado_loci CDS 10617973 10618026 . - 0 Parent=mRNA1 < ### < ##sequence-region Chromosome_2 6725589 6726696 < Chromosome_2 gffcl gene 6725589 6726696 . + . ID=gene2;Alias=RLOC_00001404 < Chromosome_2 Mikado_loci mRNA 6725589 6726696 21 + . ID=mRNA2;Parent=gene2;Alias=mikado.Scaffold_1G2094.1 < Chromosome_2 Mikado_loci exon 6725589 6725716 . + . Parent=mRNA2 < Chromosome_2 Mikado_loci CDS 6725629 6725716 . + 0 Parent=mRNA2 < Chromosome_2 . intron 6725717 6725773 . + . Parent=mRNA2 < Chromosome_2 Mikado_loci CDS 6725774 6725941 . + 2 Parent=mRNA2 < Chromosome_2 Mikado_loci exon 6725774 6725941 . + . Parent=mRNA2 < Chromosome_2 . intron 6725942 6725986 . + . Parent=mRNA2 < Chromosome_2 Mikado_loci exon 6725987 6726307 . + . Parent=mRNA2 < Chromosome_2 Mikado_loci CDS 6725987 6726307 . + 2 Parent=mRNA2 < Chromosome_2 . intron 6726308 6726382 . + . Parent=mRNA2 < Chromosome_2 Mikado_loci CDS 6726383 6726606 . + 2 Parent=mRNA2 < Chromosome_2 Mikado_loci exon 6726383 6726696 . + . Parent=mRNA2 < ### --- > Chromosome_9 Mikado_loci exon 10818058 10818082 . - . Parent=Hetgly20664.t1 > Chromosome_9 Mikado_loci CDS 10818058 10818082 . - 0 Parent=Hetgly20664.t1 > Chromosome_9 gffcl gene 10818169 10823373 . + . ID=Hetgly20665;Alias=RLOC_00024670 > Chromosome_9 Mikado_loci mRNA 10818169 10823373 19 + . ID=Hetgly20665.t1;Parent=Hetgly20665;Alias=mikado.Scaffold_9G3402.1 > Chromosome_9 Mikado_loci exon 10818169 10818212 . + . Parent=Hetgly20665.t1 > Chromosome_9 Mikado_loci CDS 10818169 10818212 . + 0 Parent=Hetgly20665.t1 > Chromosome_9 Mikado_loci CDS 10818855 10818906 . + 1 Parent=Hetgly20665.t1 > Chromosome_9 Mikado_loci exon 10818855 10818906 . + . Parent=Hetgly20665.t1 > Chromosome_9 Mikado_loci CDS 10819113 10819217 . + 0 Parent=Hetgly20665.t1 > Chromosome_9 Mikado_loci exon 10819113 10819217 . + . Parent=Hetgly20665.t1 > Chromosome_9 Mikado_loci CDS 10819271 10819295 . + 0 Parent=Hetgly20665.t1 > Chromosome_9 Mikado_loci exon 10819271 10819295 . + . Parent=Hetgly20665.t1 > Chromosome_9 Mikado_loci exon 10819541 10819617 . + . Parent=Hetgly20665.t1 > Chromosome_9 Mikado_loci CDS 10819541 10819617 . + 2 Parent=Hetgly20665.t1 > Chromosome_9 Mikado_loci exon 10819664 10819732 . + . Parent=Hetgly20665.t1 > Chromosome_9 Mikado_loci CDS 10819664 10819732 . + 0 Parent=Hetgly20665.t1 > Chromosome_9 Mikado_loci exon 10819815 10819904 . + . Parent=Hetgly20665.t1 > Chromosome_9 Mikado_loci CDS 10819815 10819904 . + 0 Parent=Hetgly20665.t1 > Chromosome_9 Mikado_loci CDS 10820027 10820149 . + 0 Parent=Hetgly20665.t1 > Chromosome_9 Mikado_loci exon 10820027 10820149 . + . Parent=Hetgly20665.t1 > Chromosome_9 Mikado_loci CDS 10820510 10820594 . + 0 Parent=Hetgly20665.t1 > Chromosome_9 Mikado_loci exon 10820510 10820594 . + . Parent=Hetgly20665.t1 > Chromosome_9 Mikado_loci exon 10820645 10820714 . + . Parent=Hetgly20665.t1 > Chromosome_9 Mikado_loci CDS 10820645 10820714 . + 2 Parent=Hetgly20665.t1 > Chromosome_9 Mikado_loci CDS 10822063 10822254 . + 1 Parent=Hetgly20665.t1 > Chromosome_9 Mikado_loci exon 10822063 10822254 . + . Parent=Hetgly20665.t1 > Chromosome_9 Mikado_loci exon 10822759 10822892 . + . Parent=Hetgly20665.t1 > Chromosome_9 Mikado_loci CDS 10822759 10822892 . + 1 Parent=Hetgly20665.t1 > Chromosome_9 Mikado_loci exon 10823285 10823373 . + . Parent=Hetgly20665.t1 > Chromosome_9 Mikado_loci CDS 10823285 10823373 . + 2 Parent=Hetgly20665.t1 > Chromosome_9 gffcl gene 10824580 10826264 . + . ID=Hetgly20666;Alias=RLOC_00024671 > Chromosome_9 Mikado_loci mRNA 10824580 10826264 19 + . ID=Hetgly20666.t1;Parent=Hetgly20666;Alias=mikado.Scaffold_9G3403.1 > Chromosome_9 Mikado_loci CDS 10824580 10824850 . + 0 Parent=Hetgly20666.t1 > Chromosome_9 Mikado_loci exon 10824580 10824850 . + . Parent=Hetgly20666.t1 > Chromosome_9 Mikado_loci exon 10825921 10826126 . + . Parent=Hetgly20666.t1 > Chromosome_9 Mikado_loci CDS 10825921 10826126 . + 2 Parent=Hetgly20666.t1 > Chromosome_9 Mikado_loci exon 10826178 10826264 . + . Parent=Hetgly20666.t1 > Chromosome_9 Mikado_loci CDS 10826178 10826264 . + 0 Parent=Hetgly20666.t1 > Chromosome_9 gffcl gene 10844215 10844802 . + . ID=Hetgly20667;Alias=RLOC_00024672 > Chromosome_9 Mikado_loci mRNA 10844215 10844805 22 + . ID=Hetgly20667.t1;Parent=Hetgly20667;Alias=mikado.Scaffold_9G3409.1 > Chromosome_9 Mikado_loci exon 10844215 10844242 . + . Parent=Hetgly20667.t1 > Chromosome_9 Mikado_loci exon 10844287 10844521 . + . Parent=Hetgly20667.t1 > Chromosome_9 Mikado_loci exon 10844574 10844805 . + . Parent=Hetgly20667.t1 > Chromosome_9 Mikado_loci CDS 10844574 10844801 . + 0 Parent=Hetgly20667.t1 > Chromosome_9 Mikado_loci mRNA 10846322 10846912 22 - . ID=Hetgly20668.t1;Parent=Hetgly20668;Alias=mikado.Scaffold_9G3413.1 > Chromosome_9 Mikado_loci exon 10846322 10846553 . - . Parent=Hetgly20668.t1 > Chromosome_9 gffcl gene 10846325 10846912 . - . ID=Hetgly20668;Alias=RLOC_00024673 > Chromosome_9 Mikado_loci CDS 10846326 10846553 . - 0 Parent=Hetgly20668.t1 > Chromosome_9 Mikado_loci exon 10846606 10846840 . - . Parent=Hetgly20668.t1 > Chromosome_9 Mikado_loci exon 10846885 10846912 . - . Parent=Hetgly20668.t1
The comm command
Print only lines that are common between the two files
comm -1 -2 <(sort File1.txt) <(sort File2.txt) | less
Using process substitutions we can sort them in place if needed
comm <(sort File1.txt) <(sort File2.txt)
Output
Chromosome_4 gffcl gene 10612335 10618026 . - . ID=gene1;Alias=RLOC_00010436 Chromosome_4 . intron 10612437 10616129 . - . Parent=mRNA1 Chromosome_4 . intron 10616191 10616666 . - . Parent=mRNA1 Chromosome_4 Mikado_loci CDS 10612335 10612436 . - 0 Parent=mRNA1 Chromosome_4 Mikado_loci CDS 10616130 10616190 . - 1 Parent=mRNA1 Chromosome_4 Mikado_loci exon 10612335 10612436 . - . Parent=mRNA1 Chromosome_4 Mikado_loci exon 10616130 10616190 . - . Parent=mRNA1 Chromosome_4 Mikado_loci mRNA 10612335 10618026 19 - . ID=mRNA1;Parent=gene1;Alias=mikado.Scaffold_4G3148.1 ##gff-version 3 ##sequence-region Chromosome_4 10612335 10618026
The cmp command
What is the first difference between two files? The cmp will print which byte and which line contains this first difference.
Extremely useful when verifying the contents of binary or large files.
cmp File1.txt File2.txt
Output
/dev/fd/63 /dev/fd/62 differ: byte 1, line 1
These files are different at the first byte and line.
The join command
The join command in Unix is a versatile tool for combining lines from two different files based on a common field or key. It merges lines with matching field values from both files, producing a unified output that incorporates data from both sources. join is particularly useful for relational operations, such as database-style joins, where you need to merge data sets based on a shared attribute. join is based on whitespace delimiters, which can also be changed.
This command sorts both files based on their ninth field, then performs a join operation on the sorted data using the ninth field as the key.
join -1 9 -2 9 <(sort -k9,9 File1.txt) <(sort -k9,9 File2.txt) | less
Output
### ##gff-version 3 ### ##sequence-region Chromosome_4 10612335 10618026 ### ##gff-version 3 ### ##sequence-region Chromosome_4 10612335 10618026 ##gff-version 3 ##gff-version 3 ##gff-version 3 ##sequence-region Chromosome_4 10612335 10618026 ##sequence-region Chromosome_2 6725589 6726696 ##gff-version 3 ##sequence-region Chromosome_2 6725589 6726696 ##sequence-region Chromosome_4 10612335 10618026 ##sequence-region Chromosome_4 10612335 10618026 ##gff-version 3 ##sequence-region Chromosome_4 10612335 10618026 ##sequence-region Chromosome_4 10612335 10618026 ID=gene1;Alias=RLOC_00010436 Chromosome_4 gffcl gene 10612335 10618026 . - . Chromosome_4 gffcl gene 10612335 10618026 . - . ID=mRNA1;Parent=gene1;Alias=mikado.Scaffold_4G3148.1 Chromosome_4 Mikado_loci mRNA 10612335 10618026 19 - . Chromosome_4 Mikado_loci mRNA 10612335 10618026 19 - . Parent=mRNA1 Chromosome_4 . intron 10612437 10616129 . - . Chromosome_4 . intron 10612437 10616129 . - . Parent=mRNA1 Chromosome_4 . intron 10612437 10616129 . - . Chromosome_4 . intron 10616191 10616666 . - . Parent=mRNA1 Chromosome_4 . intron 10612437 10616129 . - . Chromosome_4 Mikado_loci CDS 10612335 10612436 . - 0 Parent=mRNA1 Chromosome_4 . intron 10612437 10616129 . - . Chromosome_4 Mikado_loci CDS 10616130 10616190 . - 1 Parent=mRNA1 Chromosome_4 . intron 10612437 10616129 . - . Chromosome_4 Mikado_loci exon 10612335 10612436 . - . Parent=mRNA1 Chromosome_4 . intron 10612437 10616129 . - . Chromosome_4 Mikado_loci exon 10616130 10616190 . - . Parent=mRNA1 Chromosome_4 . intron 10616191 10616666 . - . Chromosome_4 . intron 10612437 10616129 . - . Parent=mRNA1 Chromosome_4 . intron 10616191 10616666 . - . Chromosome_4 . intron 10616191 10616666 . - . Parent=mRNA1 Chromosome_4 . intron 10616191 10616666 . - . Chromosome_4 Mikado_loci CDS 10612335 10612436 . - 0 Parent=mRNA1 Chromosome_4 . intron 10616191 10616666 . - . Chromosome_4 Mikado_loci CDS 10616130 10616190 . - 1 Parent=mRNA1 Chromosome_4 . intron 10616191 10616666 . - . Chromosome_4 Mikado_loci exon 10612335 10612436 . - . Parent=mRNA1 Chromosome_4 . intron 10616191 10616666 . - . Chromosome_4 Mikado_loci exon 10616130 10616190 . - . Parent=mRNA1 Chromosome_4 . intron 10616726 10616766 . - . Chromosome_4 . intron 10612437 10616129 . - . Parent=mRNA1 Chromosome_4 . intron 10616726 10616766 . - . Chromosome_4 . intron 10616191 10616666 . - . Parent=mRNA1 Chromosome_4 . intron 10616726 10616766 . - . Chromosome_4 Mikado_loci CDS 10612335 10612436 . - 0 Parent=mRNA1 Chromosome_4 . intron 10616726 10616766 . - . Chromosome_4 Mikado_loci CDS 10616130 10616190 . - 1 Parent=mRNA1 Chromosome_4 . intron 10616726 10616766 . - . Chromosome_4 Mikado_loci exon 10612335 10612436 . - . Parent=mRNA1 Chromosome_4 . intron 10616726 10616766 . - . Chromosome_4 Mikado_loci exon 10616130 10616190 . - . Parent=mRNA1 Chromosome_4 . intron 10616851 10617972 . - . Chromosome_4 . intron 10612437 10616129 . - . Parent=mRNA1 Chromosome_4 . intron 10616851 10617972 . - . Chromosome_4 . intron 10616191 10616666 . - . Parent=mRNA1 Chromosome_4 . intron 10616851 10617972 . - . Chromosome_4 Mikado_loci CDS 10612335 10612436 . - 0 Parent=mRNA1 Chromosome_4 . intron 10616851 10617972 . - . Chromosome_4 Mikado_loci CDS 10616130 10616190 . - 1 Parent=mRNA1 Chromosome_4 . intron 10616851 10617972 . - . Chromosome_4 Mikado_loci exon 10612335 10612436 . - . Parent=mRNA1 Chromosome_4 . intron 10616851 10617972 . - . Chromosome_4 Mikado_loci exon 10616130 10616190 . - . Parent=mRNA1 Chromosome_4 Mikado_loci CDS 10612335 10612436 . - 0 Chromosome_4 . intron 10612437 10616129 . - . Parent=mRNA1 Chromosome_4 Mikado_loci CDS 10612335 10612436 . - 0 Chromosome_4 . intron 10616191 10616666 . - . Parent=mRNA1 Chromosome_4 Mikado_loci CDS 10612335 10612436 . - 0 Chromosome_4 Mikado_loci CDS 10612335 10612436 . - 0 Parent=mRNA1 Chromosome_4 Mikado_loci CDS 10612335 10612436 . - 0 Chromosome_4 Mikado_loci CDS 10616130 10616190 . - 1 Parent=mRNA1 Chromosome_4 Mikado_loci CDS 10612335 10612436 . - 0 Chromosome_4 Mikado_loci exon 10612335 10612436 . - . Parent=mRNA1 Chromosome_4 Mikado_loci CDS 10612335 10612436 . - 0 Chromosome_4 Mikado_loci exon 10616130 10616190 . - . Parent=mRNA1 Chromosome_4 Mikado_loci CDS 10616130 10616190 . - 1 Chromosome_4 . intron 10612437 10616129 . - . Parent=mRNA1 Chromosome_4 Mikado_loci CDS 10616130 10616190 . - 1 Chromosome_4 . intron 10616191 10616666 . - . Parent=mRNA1 Chromosome_4 Mikado_loci CDS 10616130 10616190 . - 1 Chromosome_4 Mikado_loci CDS 10612335 10612436 . - 0 Parent=mRNA1 Chromosome_4 Mikado_loci CDS 10616130 10616190 . - 1 Chromosome_4 Mikado_loci CDS 10616130 10616190 . - 1 Parent=mRNA1 Chromosome_4 Mikado_loci CDS 10616130 10616190 . - 1 Chromosome_4 Mikado_loci exon 10612335 10612436 . - . Parent=mRNA1 Chromosome_4 Mikado_loci CDS 10616130 10616190 . - 1 Chromosome_4 Mikado_loci exon 10616130 10616190 . - . Parent=mRNA1 Chromosome_4 Mikado_loci CDS 10616667 10616725 . - 0 Chromosome_4 . intron 10612437 10616129 . - . Parent=mRNA1 Chromosome_4 Mikado_loci CDS 10616667 10616725 . - 0 Chromosome_4 . intron 10616191 10616666 . - . Parent=mRNA1 Chromosome_4 Mikado_loci CDS 10616667 10616725 . - 0 Chromosome_4 Mikado_loci CDS 10612335 10612436 . - 0 Parent=mRNA1 Chromosome_4 Mikado_loci CDS 10616667 10616725 . - 0 Chromosome_4 Mikado_loci CDS 10616130 10616190 . - 1 Parent=mRNA1 Chromosome_4 Mikado_loci CDS 10616667 10616725 . - 0 Chromosome_4 Mikado_loci exon 10612335 10612436 . - . Parent=mRNA1 Chromosome_4 Mikado_loci CDS 10616667 10616725 . - 0 Chromosome_4 Mikado_loci exon 10616130 10616190 . - . Parent=mRNA1 Chromosome_4 Mikado_loci CDS 10616767 10616850 . - 0 Chromosome_4 . intron 10612437 10616129 . - . Parent=mRNA1 Chromosome_4 Mikado_loci CDS 10616767 10616850 . - 0 Chromosome_4 . intron 10616191 10616666 . - . Parent=mRNA1 Chromosome_4 Mikado_loci CDS 10616767 10616850 . - 0 Chromosome_4 Mikado_loci CDS 10612335 10612436 . - 0 Parent=mRNA1 Chromosome_4 Mikado_loci CDS 10616767 10616850 . - 0 Chromosome_4 Mikado_loci CDS 10616130 10616190 . - 1 Parent=mRNA1 Chromosome_4 Mikado_loci CDS 10616767 10616850 . - 0 Chromosome_4 Mikado_loci exon 10612335 10612436 . - . Parent=mRNA1 Chromosome_4 Mikado_loci CDS 10616767 10616850 . - 0 Chromosome_4 Mikado_loci exon 10616130 10616190 . - . Parent=mRNA1 Chromosome_4 Mikado_loci CDS 10617973 10618026 . - 0 Chromosome_4 . intron 10612437 10616129 . - . Parent=mRNA1 Chromosome_4 Mikado_loci CDS 10617973 10618026 . - 0 Chromosome_4 . intron 10616191 10616666 . - . Parent=mRNA1 Chromosome_4 Mikado_loci CDS 10617973 10618026 . - 0 Chromosome_4 Mikado_loci CDS 10612335 10612436 . - 0 Parent=mRNA1 Chromosome_4 Mikado_loci CDS 10617973 10618026 . - 0 Chromosome_4 Mikado_loci CDS 10616130 10616190 . - 1 Parent=mRNA1 Chromosome_4 Mikado_loci CDS 10617973 10618026 . - 0 Chromosome_4 Mikado_loci exon 10612335 10612436 . - . Parent=mRNA1 Chromosome_4 Mikado_loci CDS 10617973 10618026 . - 0 Chromosome_4 Mikado_loci exon 10616130 10616190 . - . Parent=mRNA1 Chromosome_4 Mikado_loci exon 10612335 10612436 . - . Chromosome_4 . intron 10612437 10616129 . - . Parent=mRNA1 Chromosome_4 Mikado_loci exon 10612335 10612436 . - . Chromosome_4 . intron 10616191 10616666 . - . Parent=mRNA1 Chromosome_4 Mikado_loci exon 10612335 10612436 . - . Chromosome_4 Mikado_loci CDS 10612335 10612436 . - 0 Parent=mRNA1 Chromosome_4 Mikado_loci exon 10612335 10612436 . - . Chromosome_4 Mikado_loci CDS 10616130 10616190 . - 1 Parent=mRNA1 Chromosome_4 Mikado_loci exon 10612335 10612436 . - . Chromosome_4 Mikado_loci exon 10612335 10612436 . - . Parent=mRNA1 Chromosome_4 Mikado_loci exon 10612335 10612436 . - . Chromosome_4 Mikado_loci exon 10616130 10616190 . - . Parent=mRNA1 Chromosome_4 Mikado_loci exon 10616130 10616190 . - . Chromosome_4 . intron 10612437 10616129 . - . Parent=mRNA1 Chromosome_4 Mikado_loci exon 10616130 10616190 . - . Chromosome_4 . intron 10616191 10616666 . - . Parent=mRNA1 Chromosome_4 Mikado_loci exon 10616130 10616190 . - . Chromosome_4 Mikado_loci CDS 10612335 10612436 . - 0 Parent=mRNA1 Chromosome_4 Mikado_loci exon 10616130 10616190 . - . Chromosome_4 Mikado_loci CDS 10616130 10616190 . - 1 Parent=mRNA1 Chromosome_4 Mikado_loci exon 10616130 10616190 . - . Chromosome_4 Mikado_loci exon 10612335 10612436 . - . Parent=mRNA1 Chromosome_4 Mikado_loci exon 10616130 10616190 . - . Chromosome_4 Mikado_loci exon 10616130 10616190 . - . Parent=mRNA1 Chromosome_4 Mikado_loci exon 10616667 10616725 . - . Chromosome_4 . intron 10612437 10616129 . - . Parent=mRNA1 Chromosome_4 Mikado_loci exon 10616667 10616725 . - . Chromosome_4 . intron 10616191 10616666 . - . Parent=mRNA1 Chromosome_4 Mikado_loci exon 10616667 10616725 . - . Chromosome_4 Mikado_loci CDS 10612335 10612436 . - 0 Parent=mRNA1 Chromosome_4 Mikado_loci exon 10616667 10616725 . - . Chromosome_4 Mikado_loci CDS 10616130 10616190 . - 1 Parent=mRNA1 Chromosome_4 Mikado_loci exon 10616667 10616725 . - . Chromosome_4 Mikado_loci exon 10612335 10612436 . - . Parent=mRNA1 Chromosome_4 Mikado_loci exon 10616667 10616725 . - . Chromosome_4 Mikado_loci exon 10616130 10616190 . - . Parent=mRNA1 Chromosome_4 Mikado_loci exon 10616767 10616850 . - . Chromosome_4 . intron 10612437 10616129 . - . Parent=mRNA1 Chromosome_4 Mikado_loci exon 10616767 10616850 . - . Chromosome_4 . intron 10616191 10616666 . - . Parent=mRNA1 Chromosome_4 Mikado_loci exon 10616767 10616850 . - . Chromosome_4 Mikado_loci CDS 10612335 10612436 . - 0 Parent=mRNA1 Chromosome_4 Mikado_loci exon 10616767 10616850 . - . Chromosome_4 Mikado_loci CDS 10616130 10616190 . - 1 Parent=mRNA1 Chromosome_4 Mikado_loci exon 10616767 10616850 . - . Chromosome_4 Mikado_loci exon 10612335 10612436 . - . Parent=mRNA1 Chromosome_4 Mikado_loci exon 10616767 10616850 . - . Chromosome_4 Mikado_loci exon 10616130 10616190 . - . Parent=mRNA1 Chromosome_4 Mikado_loci exon 10617973 10618026 . - . Chromosome_4 . intron 10612437 10616129 . - . Parent=mRNA1 Chromosome_4 Mikado_loci exon 10617973 10618026 . - . Chromosome_4 . intron 10616191 10616666 . - .
Using Awk to compare two files
Awk stands out as a robust utility for comparing two files in Unix environments due to its text-processing prowess and simplicity. Its primary strength lies in its ability to handle structured data efficiently. Awk processes input line by line, making it ideal for comparing files containing records or lines with similar structures. By specifying field delimiters and comparison criteria, users can precisely identify differences or similarities between corresponding fields in the two files.
STEP 1
This command compares the combinations of the first and second fields in both files. It outputs lines from File2.txt where these combinations are unique, meaning they do not occur in File1.txt.
awk 'NR==FNR { c[$1$2]++; next} c[$1$2]++ == 0' File1.txt File2.txt
Output
Chromosome_9 Mikado_loci exon 10818058 10818082 . - . Parent=Hetgly20664.t1 Chromosome_9 gffcl gene 10818169 10823373 . + . ID=Hetgly20665;Alias=RLOC_00024670
This command prints the first occurence of a line from file2 if file2’s column1 and 2 match column 1 and 2 from file 1:
STEP 2
This command outputs lines from File2.txt where the value of the ninth field is not present in File1.txt, effectively showing differences or unique values between the two files based on the ninth field.
awk 'FNR==NR{a[$9];next}!($9 in a)' File1.txt File2.txt
Output
Chromosome_9 Mikado_loci exon 10818058 10818082 . - . Parent=Hetgly20664.t1 Chromosome_9 Mikado_loci CDS 10818058 10818082 . - 0 Parent=Hetgly20664.t1 Chromosome_9 gffcl gene 10818169 10823373 . + . ID=Hetgly20665;Alias=RLOC_00024670 Chromosome_9 Mikado_loci mRNA 10818169 10823373 19 + . ID=Hetgly20665.t1;Parent=Hetgly20665;Alias=mikado.Scaffold_9G3402.1 Chromosome_9 Mikado_loci exon 10818169 10818212 . + . Parent=Hetgly20665.t1 Chromosome_9 Mikado_loci CDS 10818169 10818212 . + 0 Parent=Hetgly20665.t1 Chromosome_9 Mikado_loci CDS 10818855 10818906 . + 1 Parent=Hetgly20665.t1 Chromosome_9 Mikado_loci exon 10818855 10818906 . + . Parent=Hetgly20665.t1 Chromosome_9 Mikado_loci CDS 10819113 10819217 . + 0 Parent=Hetgly20665.t1 Chromosome_9 Mikado_loci exon 10819113 10819217 . + . Parent=Hetgly20665.t1 Chromosome_9 Mikado_loci CDS 10819271 10819295 . + 0 Parent=Hetgly20665.t1 Chromosome_9 Mikado_loci exon 10819271 10819295 . + . Parent=Hetgly20665.t1 Chromosome_9 Mikado_loci exon 10819541 10819617 . + . Parent=Hetgly20665.t1 Chromosome_9 Mikado_loci CDS 10819541 10819617 . + 2 Parent=Hetgly20665.t1 Chromosome_9 Mikado_loci exon 10819664 10819732 . + . Parent=Hetgly20665.t1 Chromosome_9 Mikado_loci CDS 10819664 10819732 . + 0 Parent=Hetgly20665.t1 Chromosome_9 Mikado_loci exon 10819815 10819904 . + . Parent=Hetgly20665.t1 Chromosome_9 Mikado_loci CDS 10819815 10819904 . + 0 Parent=Hetgly20665.t1 Chromosome_9 Mikado_loci CDS 10820027 10820149 . + 0 Parent=Hetgly20665.t1 Chromosome_9 Mikado_loci exon 10820027 10820149 . + . Parent=Hetgly20665.t1 Chromosome_9 Mikado_loci CDS 10820510 10820594 . + 0 Parent=Hetgly20665.t1 Chromosome_9 Mikado_loci exon 10820510 10820594 . + . Parent=Hetgly20665.t1 Chromosome_9 Mikado_loci exon 10820645 10820714 . + . Parent=Hetgly20665.t1 Chromosome_9 Mikado_loci CDS 10820645 10820714 . + 2 Parent=Hetgly20665.t1 Chromosome_9 Mikado_loci CDS 10822063 10822254 . + 1 Parent=Hetgly20665.t1 Chromosome_9 Mikado_loci exon 10822063 10822254 . + . Parent=Hetgly20665.t1 Chromosome_9 Mikado_loci exon 10822759 10822892 . + . Parent=Hetgly20665.t1 Chromosome_9 Mikado_loci CDS 10822759 10822892 . + 1 Parent=Hetgly20665.t1 Chromosome_9 Mikado_loci exon 10823285 10823373 . + . Parent=Hetgly20665.t1 Chromosome_9 Mikado_loci CDS 10823285 10823373 . + 2 Parent=Hetgly20665.t1 Chromosome_9 gffcl gene 10824580 10826264 . + . ID=Hetgly20666;Alias=RLOC_00024671 Chromosome_9 Mikado_loci mRNA 10824580 10826264 19 + . ID=Hetgly20666.t1;Parent=Hetgly20666;Alias=mikado.Scaffold_9G3403.1 Chromosome_9 Mikado_loci CDS 10824580 10824850 . + 0 Parent=Hetgly20666.t1 Chromosome_9 Mikado_loci exon 10824580 10824850 . + . Parent=Hetgly20666.t1 Chromosome_9 Mikado_loci exon 10825921 10826126 . + . Parent=Hetgly20666.t1 Chromosome_9 Mikado_loci CDS 10825921 10826126 . + 2 Parent=Hetgly20666.t1 Chromosome_9 Mikado_loci exon 10826178 10826264 . + . Parent=Hetgly20666.t1 Chromosome_9 Mikado_loci CDS 10826178 10826264 . + 0 Parent=Hetgly20666.t1 Chromosome_9 gffcl gene 10844215 10844802 . + . ID=Hetgly20667;Alias=RLOC_00024672 Chromosome_9 Mikado_loci mRNA 10844215 10844805 22 + . ID=Hetgly20667.t1;Parent=Hetgly20667;Alias=mikado.Scaffold_9G3409.1 Chromosome_9 Mikado_loci exon 10844215 10844242 . + . Parent=Hetgly20667.t1 Chromosome_9 Mikado_loci exon 10844287 10844521 . + . Parent=Hetgly20667.t1 Chromosome_9 Mikado_loci exon 10844574 10844805 . + . Parent=Hetgly20667.t1 Chromosome_9 Mikado_loci CDS 10844574 10844801 . + 0 Parent=Hetgly20667.t1 Chromosome_9 Mikado_loci mRNA 10846322 10846912 22 - . ID=Hetgly20668.t1;Parent=Hetgly20668;Alias=mikado.Scaffold_9G3413.1 Chromosome_9 Mikado_loci exon 10846322 10846553 . - . Parent=Hetgly20668.t1 Chromosome_9 gffcl gene 10846325 10846912 . - . ID=Hetgly20668;Alias=RLOC_00024673 Chromosome_9 Mikado_loci CDS 10846326 10846553 . - 0 Parent=Hetgly20668.t1 Chromosome_9 Mikado_loci exon 10846606 10846840 . - . Parent=Hetgly20668.t1 Chromosome_9 Mikado_loci exon 10846885 10846912 . - . Parent=Hetgly20668.t1
This command added all of column 9 from file 1 to the array (a), and if there is not a column 9 from file2 that matches, print the line
STEP 3
Likewise, we can do the opposite of the above just by removing the “!”. If column 9 from file 1 is found in column 9 from file2, print the line
awk 'FNR==NR{a[$9];next}($9 in a)' File1.txt File2.txt
Output
##gff-version 3 ##sequence-region Chromosome_4 10612335 10618026 Chromosome_4 gffcl gene 10612335 10618026 . - . ID=gene1;Alias=RLOC_00010436 Chromosome_4 Mikado_loci mRNA 10612335 10618026 19 - . ID=mRNA1;Parent=gene1;Alias=mikado.Scaffold_4G3148.1 Chromosome_4 Mikado_loci CDS 10612335 10612436 . - 0 Parent=mRNA1 Chromosome_4 Mikado_loci exon 10612335 10612436 . - . Parent=mRNA1 Chromosome_4 . intron 10612437 10616129 . - . Parent=mRNA1 Chromosome_4 Mikado_loci CDS 10616130 10616190 . - 1 Parent=mRNA1 Chromosome_4 Mikado_loci exon 10616130 10616190 . - . Parent=mRNA1 Chromosome_4 . intron 10616191 10616666 . - . Parent=mRNA1
STEP 4
Attach column1 and 2 to an array and match these with column 1 and 2 from file 2. If there is a difference (true), print line from File2.txt that maches.
awk 'NR==FNR{c[$1$2];next};c[$1$2] > 0' File1.txt File2.txt
Output
##gff-version 3 ##sequence-region Chromosome_4 10612335 10618026 Chromosome_4 gffcl gene 10612335 10618026 . - . ID=gene1;Alias=RLOC_00010436 Chromosome_4 Mikado_loci mRNA 10612335 10618026 19 - . ID=mRNA1;Parent=gene1;Alias=mikado.Scaffold_4G3148.1 Chromosome_4 Mikado_loci CDS 10612335 10612436 . - 0 Parent=mRNA1 Chromosome_4 Mikado_loci exon 10612335 10612436 . - . Parent=mRNA1 Chromosome_4 . intron 10612437 10616129 . - . Parent=mRNA1 Chromosome_4 Mikado_loci CDS 10616130 10616190 . - 1 Parent=mRNA1 Chromosome_4 Mikado_loci exon 10616130 10616190 . - . Parent=mRNA1 Chromosome_4 . intron 10616191 10616666 . - . Parent=mRNA1
STEP 5
If column 9 from file 1 does not match column 9 from file 2, print the line from file 2
awk 'NR==FNR { a[$9]; next } !($9 in a) { print $0 }' File1.txt File2.txt
Output
Chromosome_9 Mikado_loci exon 10818058 10818082 . - . Parent=Hetgly20664.t1 Chromosome_9 Mikado_loci CDS 10818058 10818082 . - 0 Parent=Hetgly20664.t1 Chromosome_9 gffcl gene 10818169 10823373 . + . ID=Hetgly20665;Alias=RLOC_00024670 Chromosome_9 Mikado_loci mRNA 10818169 10823373 19 + . ID=Hetgly20665.t1;Parent=Hetgly20665;Alias=mikado.Scaffold_9G3402.1 Chromosome_9 Mikado_loci exon 10818169 10818212 . + . Parent=Hetgly20665.t1 Chromosome_9 Mikado_loci CDS 10818169 10818212 . + 0 Parent=Hetgly20665.t1 Chromosome_9 Mikado_loci CDS 10818855 10818906 . + 1 Parent=Hetgly20665.t1 Chromosome_9 Mikado_loci exon 10818855 10818906 . + . Parent=Hetgly20665.t1 Chromosome_9 Mikado_loci CDS 10819113 10819217 . + 0 Parent=Hetgly20665.t1 Chromosome_9 Mikado_loci exon 10819113 10819217 . + . Parent=Hetgly20665.t1 Chromosome_9 Mikado_loci CDS 10819271 10819295 . + 0 Parent=Hetgly20665.t1 Chromosome_9 Mikado_loci exon 10819271 10819295 . + . Parent=Hetgly20665.t1 Chromosome_9 Mikado_loci exon 10819541 10819617 . + . Parent=Hetgly20665.t1 Chromosome_9 Mikado_loci CDS 10819541 10819617 . + 2 Parent=Hetgly20665.t1 Chromosome_9 Mikado_loci exon 10819664 10819732 . + . Parent=Hetgly20665.t1 Chromosome_9 Mikado_loci CDS 10819664 10819732 . + 0 Parent=Hetgly20665.t1 Chromosome_9 Mikado_loci exon 10819815 10819904 . + . Parent=Hetgly20665.t1 Chromosome_9 Mikado_loci CDS 10819815 10819904 . + 0 Parent=Hetgly20665.t1 Chromosome_9 Mikado_loci CDS 10820027 10820149 . + 0 Parent=Hetgly20665.t1 Chromosome_9 Mikado_loci exon 10820027 10820149 . + . Parent=Hetgly20665.t1 Chromosome_9 Mikado_loci CDS 10820510 10820594 . + 0 Parent=Hetgly20665.t1 Chromosome_9 Mikado_loci exon 10820510 10820594 . + . Parent=Hetgly20665.t1 Chromosome_9 Mikado_loci exon 10820645 10820714 . + . Parent=Hetgly20665.t1 Chromosome_9 Mikado_loci CDS 10820645 10820714 . + 2 Parent=Hetgly20665.t1 Chromosome_9 Mikado_loci CDS 10822063 10822254 . + 1 Parent=Hetgly20665.t1 Chromosome_9 Mikado_loci exon 10822063 10822254 . + . Parent=Hetgly20665.t1 Chromosome_9 Mikado_loci exon 10822759 10822892 . + . Parent=Hetgly20665.t1 Chromosome_9 Mikado_loci CDS 10822759 10822892 . + 1 Parent=Hetgly20665.t1 Chromosome_9 Mikado_loci exon 10823285 10823373 . + . Parent=Hetgly20665.t1 Chromosome_9 Mikado_loci CDS 10823285 10823373 . + 2 Parent=Hetgly20665.t1 Chromosome_9 gffcl gene 10824580 10826264 . + . ID=Hetgly20666;Alias=RLOC_00024671 Chromosome_9 Mikado_loci mRNA 10824580 10826264 19 + . ID=Hetgly20666.t1;Parent=Hetgly20666;Alias=mikado.Scaffold_9G3403.1 Chromosome_9 Mikado_loci CDS 10824580 10824850 . + 0 Parent=Hetgly20666.t1 Chromosome_9 Mikado_loci exon 10824580 10824850 . + . Parent=Hetgly20666.t1 Chromosome_9 Mikado_loci exon 10825921 10826126 . + . Parent=Hetgly20666.t1 Chromosome_9 Mikado_loci CDS 10825921 10826126 . + 2 Parent=Hetgly20666.t1 Chromosome_9 Mikado_loci exon 10826178 10826264 . + . Parent=Hetgly20666.t1 Chromosome_9 Mikado_loci CDS 10826178 10826264 . + 0 Parent=Hetgly20666.t1 Chromosome_9 gffcl gene 10844215 10844802 . + . ID=Hetgly20667;Alias=RLOC_00024672 Chromosome_9 Mikado_loci mRNA 10844215 10844805 22 + . ID=Hetgly20667.t1;Parent=Hetgly20667;Alias=mikado.Scaffold_9G3409.1 Chromosome_9 Mikado_loci exon 10844215 10844242 . + . Parent=Hetgly20667.t1 Chromosome_9 Mikado_loci exon 10844287 10844521 . + . Parent=Hetgly20667.t1 Chromosome_9 Mikado_loci exon 10844574 10844805 . + . Parent=Hetgly20667.t1 Chromosome_9 Mikado_loci CDS 10844574 10844801 . + 0 Parent=Hetgly20667.t1 Chromosome_9 Mikado_loci mRNA 10846322 10846912 22 - . ID=Hetgly20668.t1;Parent=Hetgly20668;Alias=mikado.Scaffold_9G3413.1 Chromosome_9 Mikado_loci exon 10846322 10846553 . - . Parent=Hetgly20668.t1 Chromosome_9 gffcl gene 10846325 10846912 . - . ID=Hetgly20668;Alias=RLOC_00024673 Chromosome_9 Mikado_loci CDS 10846326 10846553 . - 0 Parent=Hetgly20668.t1 Chromosome_9 Mikado_loci exon 10846606 10846840 . - . Parent=Hetgly20668.t1 Chromosome_9 Mikado_loci exon 10846885 10846912 . - . Parent=Hetgly20668.t1
STEP 6
Like the above example, if column 9 from file 1 does match column 9 from file2, print the column 9 from file 1 and the matching line from file 2. Note that this time I am naming the array’s key $9 and making the key value $9 as well.
awk 'NR==FNR { a[$9]=$9; next } ($9 in a) { print a[$9],$0 }' File1.txt File2.txt
Output
##gff-version 3 ##sequence-region Chromosome_4 10612335 10618026 ID=gene1;Alias=RLOC_00010436 Chromosome_4 gffcl gene 10612335 10618026 . - . ID=gene1;Alias=RLOC_00010436 ID=mRNA1;Parent=gene1;Alias=mikado.Scaffold_4G3148.1 Chromosome_4 Mikado_loci mRNA 10612335 10618026 19 - . ID=mRNA1;Parent=gene1;Alias=mikado.Scaffold_4G3148.1 Parent=mRNA1 Chromosome_4 Mikado_loci CDS 10612335 10612436 . - 0 Parent=mRNA1 Parent=mRNA1 Chromosome_4 Mikado_loci exon 10612335 10612436 . - . Parent=mRNA1 Parent=mRNA1 Chromosome_4 . intron 10612437 10616129 . - . Parent=mRNA1 Parent=mRNA1 Chromosome_4 Mikado_loci CDS 10616130 10616190 . - 1 Parent=mRNA1 Parent=mRNA1 Chromosome_4 Mikado_loci exon 10616130 10616190 . - . Parent=mRNA1 Parent=mRNA1 Chromosome_4 . intron 10616191 10616666 . - . Parent=mRNA1