如何从文本文件“块”中循环提取行

Question

I have a huge text file and I want to use grep to search if some "blocks" in my text file is existing in another file. So, I need to extract these blocks first.

This is my file:

>gi|60117238|gb|AY897435.1| Wolbachia endosymbiont of Drosophila mojavensis, genomic survey sequence
TCTGTTGCGAGTGTGCTGATAACTACTGAATCTATGATAGTTGATGTACCAAGCAAAGAAAATGCTTCATCTCCTATGGG
TGCAGGAGAAATGAGTGGCATGGGTGGATTCTAAGTAGAATGAAACCGTGGAGCAATTGCTCCACGGTAGTTCCAAAAAA
TCTCACATTTTACTATTCGTTAAAGGTAATACGTTTGGTGCAGAAATGCACTACTGTTTGCATCCGTTTCGCTCCTTTAT
ATTGTGGTTGTCTAATAACAAAAAGGCAGCATAAGAAAACTATAACACCTAGTATATTTATACTATAGCTGACCCAAGCA
ACACGTCATACCGCGATTCATTCCACAACTGTACGAACATTACAATATGGCACATAGTAAACGATGTCATGAAAGTAGCT
GACACTGGAATTCAGAAAAAAGGATTATGTCATTCCAGTGCTTGACACTGGAATCCAGCATTTCCATAATCATCAAAACA
TTGTATTTTAACAAAAAACATGTATTTTTATGCTTGCCAACTTAATAAAATTCCTGGATCCCAGTGTCAAGCACTGGGAT
GACAC
>gi|60117239|gb|AY897436.1| Wolbachia endosymbiont of Drosophila mojavensis, genomic survey sequence
TTTTCATCGCTCATGTCCTTAGTTTACCCCCTGTTTCACCATTACATTAATATCTACAGAACCTCCCACTGGGGAGTAGT
AATCTAGGATAGTTTCTATCACTAAAACGCGTGGTATTCCTTTATTTTTTACCAATTTTAAATAAGACAATACCTTATTA
TCATCATAATGCTGCAGAAAGCGGCAAAAGACACCTAATTCATAATTTGTAGCTGATAATTCTTCTTGAGTTATGAGTTT
AATTTTTAAATCTTCTACTGCCTGCCTAGGCACTTTATGTTCGTTGTAATAATATAAGCCTATAGAACCTTTATTGTGTA
TATCAGAATAAGCAAGAAATAAAGAGTGTACGCCAAATAGCAATATATTTTTAGCACCATCTATATTAACCCTAGAATTA
AACTCTTTAGTGTCAAACCTGGAATATCCTAGCAATGCTTGGTAAAACGCTATTTTCCTGTCTTCTGATGTTTCTTTCTC
CTTAAAAAGAATCAAATGAAAATATTGACTCCTGCCTTAAAATATCCGGCATTTTTAACCAATTCTTTTCAGCGGCAACC
CTTGCCCACATTGCTGCTGCTTTAGGAAAAATGGTATTTCTTTAAACACTTACCTTTTGATGAAAGTTGCCCAAAATCCT
TTGTTCTATCCGAATCCAAAACCCCTATTTCCCAAACGCCCCTTAAAACCTTTTTTAAAATTGGAACAAAAAATATTTAA
TTTTTAAAAAAAAACG
>gi|60117240|gb|AY897437.1| Wolbachia endosymbiont of Drosophila mojavensis, genomic survey sequence
TTGNCCATCAATTGGCCACCAGAAAAGTTGCGTCCGTTTACTTCTACACCATGTATAAATGCACCTAAAATCATGCCTTG
GCAAAATGCAGCACCAAGTGACCCAAAATGAAAGGCATAATCCCATAATCGCCTGTATTTTCCTTCTGCCTTAAAACGAA
ACTCAAAGGATACTCCGCGCACTATAAGGCCAAGCAGCATAATAATGATTGGAATATAAAAAGCAGGCATTAATATTGAA
TATGCAAGAGGAAAAGCAGCAAACAACCCTCCACCACCTAGTACCAACCATGTTTCGTTTCCATCCCAAAATGGTGCAAT
TGAGCTTATCATGTGATCACGGCATTTATCTGACGGTGCAAAAGGAAGTAAAATACCAATACCTAAATCAAACCCATCCA
TTAAAATATACAGTAAAACAGCTATGGCAATTAGTAATCCCCAGATTAGGGGTAAATTAATTAAGGAAGAAAAATCAAAC
ATGATTGTTGTCCTTTCCAGATGTACCAGCATCAATCACTGAAGCTCCAATACCGTGTTTATAAAATTGCTCTTCTTCTT
TAATGACAGGAATTCCTTTGTATATAAGTTTCAGAATATAGTATCTACCTGCTCCAAATATAAGGGTATACATAAACGAT
AAATGCAATCAAAGACCATGCAACCTGAGGACCGGTAATCGCAGATGAAAATGATTCAATTGTGCCGTTAATTCCATATA
CAGTGTAAAGTTGACGGCCAATTTCATAGTAAACCAAACTGCAAGTAACGCTATGGACCCCGACGGCATCTTTGAAATCC
ACAATCCTTTGAAAACACAACTTTGGAATAATTTGCCCCGAAAAATACTGAAAAAAAATTTACTGGACCCATTTTGGATT
ATTAAAATTTCAACTCCAACCATTTATACGGG

Block is starting from > to the letter befor the next >.

So, 1st block is:

TCTGTTGCGAGTGTGCTGATAACTACTGAATCTATGATAGTTGATGTACCAAGCAAAGAAAATGCTTCATCTCCTATGGG
TGCAGGAGAAATGAGTGGCATGGGTGGATTCTAAGTAGAATGAAACCGTGGAGCAATTGCTCCACGGTAGTTCCAAAAAA
TCTCACATTTTACTATTCGTTAAAGGTAATACGTTTGGTGCAGAAATGCACTACTGTTTGCATCCGTTTCGCTCCTTTAT
ATTGTGGTTGTCTAATAACAAAAAGGCAGCATAAGAAAACTATAACACCTAGTATATTTATACTATAGCTGACCCAAGCA
ACACGTCATACCGCGATTCATTCCACAACTGTACGAACATTACAATATGGCACATAGTAAACGATGTCATGAAAGTAGCT
GACACTGGAATTCAGAAAAAAGGATTATGTCATTCCAGTGCTTGACACTGGAATCCAGCATTTCCATAATCATCAAAACA
TTGTATTTTAACAAAAAACATGTATTTTTATGCTTGCCAACTTAATAAAATTCCTGGATCCCAGTGTCAAGCACTGGGAT
GACAC

2nd block is:

TTTTCATCGCTCATGTCCTTAGTTTACCCCCTGTTTCACCATTACATTAATATCTACAGAACCTCCCACTGGGGAGTAGT
AATCTAGGATAGTTTCTATCACTAAAACGCGTGGTATTCCTTTATTTTTTACCAATTTTAAATAAGACAATACCTTATTA
TCATCATAATGCTGCAGAAAGCGGCAAAAGACACCTAATTCATAATTTGTAGCTGATAATTCTTCTTGAGTTATGAGTTT
AATTTTTAAATCTTCTACTGCCTGCCTAGGCACTTTATGTTCGTTGTAATAATATAAGCCTATAGAACCTTTATTGTGTA
TATCAGAATAAGCAAGAAATAAAGAGTGTACGCCAAATAGCAATATATTTTTAGCACCATCTATATTAACCCTAGAATTA
AACTCTTTAGTGTCAAACCTGGAATATCCTAGCAATGCTTGGTAAAACGCTATTTTCCTGTCTTCTGATGTTTCTTTCTC
CTTAAAAAGAATCAAATGAAAATATTGACTCCTGCCTTAAAATATCCGGCATTTTTAACCAATTCTTTTCAGCGGCAACC
CTTGCCCACATTGCTGCTGCTTTAGGAAAAATGGTATTTCTTTAAACACTTACCTTTTGATGAAAGTTGCCCAAAATCCT
TTGTTCTATCCGAATCCAAAACCCCTATTTCCCAAACGCCCCTTAAAACCTTTTTTAAAATTGGAACAAAAAATATTTAA
TTTTTAAAAAAAAACG

Third block:

TTGNCCATCAATTGGCCACCAGAAAAGTTGCGTCCGTTTACTTCTACACCATGTATAAATGCACCTAAAATCATGCCTTG
GCAAAATGCAGCACCAAGTGACCCAAAATGAAAGGCATAATCCCATAATCGCCTGTATTTTCCTTCTGCCTTAAAACGAA
ACTCAAAGGATACTCCGCGCACTATAAGGCCAAGCAGCATAATAATGATTGGAATATAAAAAGCAGGCATTAATATTGAA
TATGCAAGAGGAAAAGCAGCAAACAACCCTCCACCACCTAGTACCAACCATGTTTCGTTTCCATCCCAAAATGGTGCAAT
TGAGCTTATCATGTGATCACGGCATTTATCTGACGGTGCAAAAGGAAGTAAAATACCAATACCTAAATCAAACCCATCCA
TTAAAATATACAGTAAAACAGCTATGGCAATTAGTAATCCCCAGATTAGGGGTAAATTAATTAAGGAAGAAAAATCAAAC
ATGATTGTTGTCCTTTCCAGATGTACCAGCATCAATCACTGAAGCTCCAATACCGTGTTTATAAAATTGCTCTTCTTCTT
TAATGACAGGAATTCCTTTGTATATAAGTTTCAGAATATAGTATCTACCTGCTCCAAATATAAGGGTATACATAAACGAT
AAATGCAATCAAAGACCATGCAACCTGAGGACCGGTAATCGCAGATGAAAATGATTCAATTGTGCCGTTAATTCCATATA
CAGTGTAAAGTTGACGGCCAATTTCATAGTAAACCAAACTGCAAGTAACGCTATGGACCCCGACGGCATCTTTGAAATCC
ACAATCCTTTGAAAACACAACTTTGGAATAATTTGCCCCGAAAAATACTGAAAAAAAATTTACTGGACCCATTTTGGATT
ATTAAAATTTCAACTCCAACCATTTATACGGG

How can I loop my file and extract one block in each iteration? To grep it with the other file?

Edit 1:

For more clarification:

I want to do some operation on each block. First, I perform diff between two files and but the result in a new file. For the new file which contains the blocks, i want to search if each block is included in the first file or in the second file. If it is included in the first file, i want to extract it to another new file. If it is included in the second file, i want to escape and go to next block.

Hope you getting my point.

Thanks,

Answer 1

Do you want to create a separate file for each block? And then you want to do any operation on those files? Or you just want to do some operation(say search/grep) for each block in each loop iteration? Please clarify your requirement.