Extract information from txt
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5.1 years ago

Dear All!

I have a txt with this kind of information:

query: NB501791:62:HLKV3AFXY:4:21507:10794:16613 1:N:0:AAGCAGA
match:gi|1548994288|gb|CP034492.1| Eukaryotic synthetic construct chromosome 14 >gi|1549096114|gb|CP034517
match:gi|1351431640|ref|XM_024231364.1| PREDICTED: Pongo abelii spectrin repeat containing nuclear envelop
match:gi|1351431635|ref|XM_024231363.1| PREDICTED: Pongo abelii spectrin repeat containing nuclear envelop
match:gi|1351431627|ref|XM_024231362.1| PREDICTED: Pongo abelii spectrin repeat containing nuclear envelop
match:gi|1351431621|ref|XM_024231361.1| PREDICTED: Pongo abelii spectrin repeat containing nuclear envelop
query: NB501791:62:HLKV3AFXY:4:21603:8250:2021 1:N:0:AGGCAGT
match:gi|301129233|ref|NG_023414.1| Homo sapiens tetratricopeptide repeat domain 37 (TTC37), RefSeqGene (L
match:gi|21263230|gb|AC090071.3| Homo sapiens chromosome 5 clone CTD-2538A21, complete sequence
match:gi|262527239|ref|NG_015800.1| Homo sapiens 5'-nucleotidase, cytosolic IIIA (NT5C3A), RefSeqGene on c
match:gi|11465072|gb|AC083863.2|AC083863 Homo sapiens chromosome 7 clone RP11-162O1, complete sequence
match:gi|9558609|gb|AC074338.1|AC074338 Human Chromosome 7 clone RP11-81O10, complete sequence

I need to extract every read, where the the first match isn't homo sapiens/human. Someone have an idea how should I start?

python blast sequence archeogenetics • 858 views
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Check usage of grep -vE with human and Homo Sapiens as query.

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Thank you, it worked perfectly! I would have an another question. Can I make a list of sequences with grep? For example:

    Pasteurella multocida 
query: NB501791:62:HLKV3AFXY:3:11601:15774:10353 1:N:0:AAGCAGA
query: NB501791:62:HLKV3AFXY:3:11601:15774:10353 1:N:0:AAGCAGA
query: NB501791:62:HLKV3AFXY:3:11601:15774:10353 1:N:0:AAGCAGA


    Mus musculus
query: NB501791:62:HLKV3AFXY:3:11601:15774:10353 1:N:0:AAGCAGA
query: NB501791:62:HLKV3AFXY:3:11601:15774:10353 1:N:0:AAGCAGA
query: NB501791:62:HLKV3AFXY:3:11601:15774:10353 1:N:0:AAGCAGA

(I know, same queries, jut for the example)

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