Recognizing empty line using ""

[demis001]

The following script works when I have changed to ==1 but will not exclude when I changed to ==0. The other problem is that I want to recognize and exclude lines with shorter reads less than 14 character using index(substr($1, 1, 14), " ")==0 but will not work

awk 'index(substr($1, 2, 10), ".")==0||index(substr($1, 1, 15), "AAAAAAAAAAAAAAA")==0||index(substr($1, 1, 15), "GGGGGGGGGGGG")==0||index(substr($1, 1, 15), "TTTTTTTTTTTTT")==0||index(substr($1,1, 15), "CCCCCCCCCCCCC")==0||index(substr($1, 1, 14), " ")==0{print $1}' gcb110_adaptor_removed.txt

Data will looks like this:

AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
TGAGGTAGTAGATTGTATAGTTTCGTATTCCGTTTT
TGAGGTAGTAGATTGTATAGTT
A...................................

CGGATGAGCAAAGAAAGTGGTT
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
ATCGT

TAGCTTATCAGACTGATGTTT
TGAGGTAGTAGATTGTATAGTTA
CAACGGAATACCATAAGCAGCTTTGTATTTCGGTCT
GTCAA

I want to exclude these with shorter, empety line, with A's T's and so on and only print quality sequence

Dereje

 

[PHV]

exclude lines with shorter reads less than 14 character
length($0)<14{next}

Hope This Helps, PH.
FAQ219-2884
FAQ181-2886

 

[demis001]

Is this also exclude empty lines?

 

[PHV]

Yes, just try it !

 

[demis001]

I tested by including the line you have suggested to the above script and didn't work. When I excute separetly as

awk 'length($0)>14{print $1}' input file, it will work.
My intention is to put a statement on the awk line I have spacified:

awk 'index(substr($1, 2, 10), ".")==0||index(substr($1, 1, 15), "AAAAAAAAAAAAAAA")==0||index(substr($1, 1, 15), "GGGGGGGGGGGG")==0||index(substr($1, 1, 15), "TTTTTTTTTTTTT")==0||index(substr($1,1, 15), "CCCCCCCCCCCCC")==0||index(substr($1, 1, 14), " ")==0{print $1}' gcb110_adaptor_removed.txt

Dereje

 

[demis001]

I want to exclude the output from the following statment together with the one I have specified:

awk 'length($0)<14{print $1}'

Derje

 

[PHV]

Could you please explain us which output you want from the data you've posted, ie what are the rules ?

Hope This Helps, PH.
FAQ219-2884
FAQ181-2886

 

[demis001]

From this file:
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
TGAGGTAGTAGATTGTATAGTTTCGTATTCCGTTTT
TGAGGTAGTAGATTGTATAGTT
A...................................

CGGATGAGCAAAGAAAGTGGTT
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
ATCGT
CCCCCCCCCCCCCCCCCCCCCCCCC
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
.AACGGAATACCATAAGCAGCTTTGTATTTCGGTCT

TAGCTTATCAGACTGATGTTT
TGAGGTAGTAGATTGTATAGTTA
CAACGGAATACCATAAGCAGCTTTGTATTTCGGTCT
GTCAA

I want the following lines:
TGAGGTAGTAGATTGTATAGTTTCGTATTCCGTTTT
TGAGGTAGTAGATTGTATAGTT
CGGATGAGCAAAGAAAGTGGTT
.AACGGAATACCATAAGCAGCTTTGTATTTCGGTCT
TAGCTTATCAGACTGATGTTT
TGAGGTAGTAGATTGTATAGTTA
CAACGGAATACCATAAGCAGCTTTGTATTTCGGTCT

 

[demis001]

Litrally, If I am able to exclude the output of this statment. I will achieve what I want:
awk '{gsub(/\r/, ""); print $1}' gcb110_adaptor_removed.txt | awk 'index(substr($1, 2, 10), ".")==1||index(substr($1, 1, 15), "AAAAAAAAAAAAAA")==1||index(substr($1, 1, 15), "GGGGGGGGGGGG")==1||index(substr($1, 1, 15), "TTTTTTTTTTTTT")==1||index(substr($1,1, 15), "CCCCCCCCCCCCC")==1||(length($0)<14)==1'

Dereje

 

[PHV]

awk '{gsub(/\r/,"")/^.\./||/^A{15}/||/^G{15}/||/^T{15}/||/^C{15}/||length($0)<14{next}1' gcb110_adaptor_removed.txt


Hope This Helps, PH.
FAQ219-2884
FAQ181-2886

 

[demis001]

got error and edited some syntax error.
awk: {gsub(/\r/,"")/^.\./||/^A{15}/||/^G{15}/||/^T{15}/||/^C{15}/||length($0)<14{next}1
awk: ^ syntax error
I edited like this and still got an error:
awk: {gsub(/\r/,"")/^\.\./||/^A{15}/||/^G{15}/||/^T{15}/||/^C{15}/||length($0)<14{next}$1

There is also another problem this doesn't handle, I want to keep if the sequence is like this
.AACGGAATACCATAAGCAGCTTTGTATTTCGGTCT
and delet if it is like AA...AAA

Dereje

 

[PHV]

OOps, sorry for the typo:
awk '{gsub(/\r/,"")}/^.\./||/^A{15}/||/^G{15}/||/^T{15}/||/^C{15}/||length($0)<14{next}1' gcb110_adaptor_removed.txt

Hope This Helps, PH.
FAQ219-2884
FAQ181-2886

 

[demis001]

The following line is not deleted

AAC.................................

But it did most of the job. are you able to include the index(substr,,) for this one. I want to escape the line if it contain single . between character 2-15.

Dereje

 

[PHV]

awk '{gsub(/\r/,"")}substr($0,2,15)~/\./||/^A{15}/||/^G{15}/||/^T{15}/||/^C{15}/||length($0)<14{next}1' gcb110_adaptor_removed.txt

Hope This Helps, PH.
FAQ219-2884
FAQ181-2886

 

[demis001]

Oops Many problem:

Doesn't escape the following line

AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
Dereje

 

[PHV]

It does for me ...
FYI, this is this pattern /^A{15}/

 

[demis001]

It is wierd to see that but it will print these line on the output. I know the pattern is correct. I just coppied and pest your code to command line and pipe the output to file.

Thanks

 

[PHV]

With your posted data I get your posted expected result.

 

[demis001]

I have excuted this line:

awk '{gsub(/\r/,"")}substr($0,2,15)~/\./||/^A{15}/||/^G{15}/||/^T{15}/||/^C{15}/||length($0)<15{next}1' gcb110_adaptor_removed.txt

Part of data printed
AACGGAATCCCAAAAGCAGCTGTTCGTATCCTGTTT
GATTCTCAGGGATGGGTTA
ATCCGGCTCGAAGGACCA
CTGGACTTGGAGTCAGAAGGT
TGAGGTAGTAGATTGTATAGTT
GAAGCGGGTGCTCTTATTT
TGAGGTAGTAGGTTGTATAGTT
TACTATGCGGTGGGGCCTCGGACGCGGTCTTCGGCT
TGAGGTAGTAGATTGTATAGTT
TGAGGTAGTAGTTTGTACAGTT
TGAGGTAGTAGATTGTATAGTT
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
TGAGGTAGCAGATTCTGTATGT
TAGCTTCTCAGACTGATGTTGAC
TCGCACCCTCTGAACACGTTTC
AGAGGGAGTAGATTGTATTTCTTCTTATGCCGTCTT

Dereje

 

[demis001]

I have saved the data I have printed as test1.txt and excuted with the awk line
$ awk 'substr($0,2,15)~/\./||/^A{15}/||/^G{15}/||/^T{15}/||/^C{15}/||length($0)<15{next}1' test1.txt
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
TGAGGTAGTAGATTGTATAGTTTCGTATTCCGTTTT
TGAGGTAGTAGATTGTATAGTT
CGGATGAGCAAAGAAAGTGGTT
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
CCCCCCCCCCCCCCCCCCCCCCCCC
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
.AACGGAATACCATAAGCAGCTTTGTATTTCGGTCT
TAGCTTATCAGACTGATGTTT
TGAGGTAGTAGATTGTATAGTTA
CAACGGAATACCATAAGCAGCTTTGTATTTCGGTCT

I looks like not working except the last regex!! OOPs

Dereje