I would like to compare columns from file one to two. Where column 2 of file1 should un-match from column 1 or 2 from file2 and print output from file 1.
file1.
cat test.head20.R2.fastq.tab
@0_1_2367_1112_211 ENSG00000165837 GAAATTAAGTTATAATTTTCATGGGACATTTTCATCACTGTTGACACAGTTTCAAGCATTCCATCATGTTATTTTGACTCTTTTTCTTTTTTTTTTCTTT + @6@CDCFFEDEIJIIJJJFBFHIIJJJJJGC?CDDDDDDFEDGBFFFFHEDFFBBBDDDDDDDDBDDD@@@@CDDDDDEHHJJJGJIIIGIJJJIIIFCH
@10000000_0_0_0_0 rupesh TCCCTACTCACGTGGTGGACGCACAACCTAAGGTCAAGCTTATAGGTAAACACGCAGTGAAATATCCAGAAACGAAGCTATCACCCGGGTAGTGTCTTGG + =FGIIIFDCCDDDCAA5BBBBGIJIIGJIJJJJJJIIGGHHIIIJIJIIJJIEE8?DDECGGIEDDDDDDHHJJJJJJIGIIIJED?CB5@CFFHHHCFF
@10000001_0_3150_2465_134 ENSG00000137860 GCCTCTCAAGTAGCTGGGATTACAGGCACCTGCCACCACGCCCAGCCAATTTTTGTATTTTTAGTAGAGACAATTTCACTATGTTGGCCAGGCTGGTCTT + DEDDB>HJIGHFJJJIGFFFHJJJJJJJJIIGHHFFDDCCCIIJJJJJJJJJJJJJIGIJJJHJIFHHGJJIIHEEEDDDDDC>?@DDDEEEDFFFFFFC
@10000002_0_2947_952_158 ENSG00000028203 CCCCCAGGACCAGCTGCTGTTTTGTGATGACTGCGATCGGGGTTACCACATGTACTGCCTGAGTCCCCCCATGGCGGAGCCCCCGGAAGGGAGCTGGAGC + JFHHEDDB;;63JJJIJJJHHFIIJIHGHHHHGHHHJJIIIEEEIJJHHHJJHHFFJIJJJJJJJJJJJJJJHDDDDDDFGBB?8BDDDEDDDDDDDDCC
@10000003_0_8902_3193_186 ENSG00000177051 CAAGGCCAGAGAGACAAATAATGCCTCATGTCCCACTGCTTTAAAATTACATTAATTTATAAAATGGCCACTATGGGCTCTTTTTGACTGTTTCTCGGAG + HGEDDDDDDDDDDDCDDB@<DDDD<>CDDDDB@>DDDEIJJJIGJJIIIIGIJHHHGEEIJJJJJJJJIHJJJJJJIIJIIIJJIJJJJIIIIHEDDDCC
@5000345_0_3_0_0 ENSG00000178057 TCCCTACTCACGTGGTGGACGCACAACCTAAGGTCAAGCTTATAGGTAAACACGCAGTGAAATATCCAGAAACGAAGCTATCACCCGGGTAGTGTCTTGG + =FGIIIFDCCDDDCAA5BBBBGIJIIGJIJJJJJJIIGGHHIIIJIJIIJJIEE8?
file2
cat fusions.head16.R2.fastq.tab
ENSG00000137860 ENSG00000165837 1431 1598 0:0:0 0:0:0 0/2 CAGGTCATCTGCTCCTATCTCCTAAGGCCCATGGTTTTCATGATGGGTGTAGAGTGGACAGACTGTCCAATGGTGGCTGAGATGGTGGGAATCAAGTTCT + IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
ENSG00000177051 ENSG00000134905 277 433 0:0:0 0:0:0 451/2 CTTCACTGCACAGCCAGGGTGAGCCTCGCTGGGAAGGTGCAGGTGACTCGTGCCTGTCGGGGAGCCCGTCCTGTCCGTACAAAACATGTGCCAGGCAAGG + IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
ENSG00000137860 ENSG00000165837 2761 2951 0:0:0 0:0:0 2/2 AAACAATCTTACGGATTAAGAGGAGACGTGAAGCTCAAAAGTTAACAGAGATGACCAGTTTCACATTTCATTTAATGAGCAAACCAACACCTGAGAAGCC + IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
ENSG00000028203 ENSG00000157766 183 411 0:0:0 0:0:0 101/2 TTCTTTGTCACCAAAAACAGAAAAATGCACAACAGAGGGACAACAAAAGCCTCCTACAAGAGTCCTACCAAAATACCTGGGATATAGTAATCACTCAATG + IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
desired output:
@10000000_0_0_0_0 rupesh TCCCTACTCACGTGGTGGACGCACAACCTAAGGTCAAGCTTATAGGTAAACACGCAGTGAAATATCCAGAAACGAAGCTATCACCCGGGTAGTGTCTTGG + =FGIIIFDCCDDDCAA5BBBBGIJIIGJIJJJJJJIIGGHHIIIJIJIIJJIEE8?DDECGGIEDDDDDDHHJJJJJJIGIIIJED?CB5@CFFHHHCFF
@5000345_0_3_0_0 ENSG00000178057 TCCCTACTCACGTGGTGGACGCACAACCTAAGGTCAAGCTTATAGGTAAACACGCAGTGAAATATCCAGAAACGAAGCTATCACCCGGGTAGTGTCTTGG + =FGIIIFDCCDDDCAA5BBBBGIJIIGJIJJJJJJIIGGHHIIIJIJIIJJIEE8?
Tried so far to print unmatched entry from second file but don't know how to print from file1 ?
awk '{k=$2} NR==FNR{a[k]; next} !(k in a)' test.head20.R2.fastq.tab fusions.head16.R2.fastq.tab
output from above code that i don't want:
ENSG00000177051 ENSG00000134905 277 433 0:0:0 0:0:0 451/2 CTTCACTGCACAGCCAGGGTGAGCCTCGCTGGGAAGGTGCAGGTGACTCGTGCCTGTCGGGGAGCCCGTCCTGTCCGTACAAAACATGTGCCAGGCAAGG + IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
ENSG00000028203 ENSG00000157766 183 411 0:0:0 0:0:0 101/2 TTCTTTGTCACCAAAAACAGAAAAATGCACAACAGAGGGACAACAAAAGCCTCCTACAAGAGTCCTACCAAAATACCTGGGATATAGTAATCACTCAATG + IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
file2
, but your "desired output" includes the entriesENSG00000028203
andENSG00000177051
, which are found in the first column, on the 4th and 2nd rows respectively.