How can I introduce a lower case letter before an underscore in a gff3 file
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I have used the following command to introduce a letter in front of underscores in my gff3 file as requested by the program i am using to generate a genepred file:
sed 's/;_/;x_/g' in.transcripts.gff3 > altered.transcripts.gff3
However, the output file contained an uppercase x instead of the lower case as expected, despite using the lower case in the command.I get the following error messages when I use the altered file to generate a genepred file:
-user defined attributes must start with a lower-case letter:X_AED
How can I change a letter within a file from upper to lower case.
command-line sed
edited Oct 4 at 12:11
jimmij
29.5k867101
asked Oct 4 at 11:53
Yewon
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up vote
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down vote
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I have used the following command to introduce a letter in front of underscores in my gff3 file as requested by the program i am using to generate a genepred file:
sed 's/;_/;x_/g' in.transcripts.gff3 > altered.transcripts.gff3
However, the output file contained an uppercase x instead of the lower case as expected, despite using the lower case in the command.I get the following error messages when I use the altered file to generate a genepred file:
-user defined attributes must start with a lower-case letter:X_AED
How can I change a letter within a file from upper to lower case.
command-line sed
edited Oct 4 at 12:11
jimmij
29.5k867101
asked Oct 4 at 11:53
Yewon
1
New contributor
Yewon is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
Were the uppercase X’s already there? They should not even introduced by your sed command.
– Jeff Schaller
Oct 4 at 12:06
Th upper case X's were not there before, I introduced them because the
– Yewon
Oct 4 at 12:41
The upper case X's were not there before. I introduced them because the gff3togenepred tool (which I was using to convert my gff3 file to a genepred intermediate) required that an attribute tag must start with an alphabetic character which was not the case with my original file where the attributes start with an underscore (_QI, _eAED, _AED). That is why I introduced a lower case x but it appears as an upper case x in the file. However, when I reun the command using the edited gff3 file, i get another message saying that user defined attributes must start with a lower case letter.
– Yewon
Oct 4 at 12:53
add a comment |Â
up vote
0
down vote
favorite
up vote
0
down vote
favorite
I have used the following command to introduce a letter in front of underscores in my gff3 file as requested by the program i am using to generate a genepred file:
sed 's/;_/;x_/g' in.transcripts.gff3 > altered.transcripts.gff3
However, the output file contained an uppercase x instead of the lower case as expected, despite using the lower case in the command.I get the following error messages when I use the altered file to generate a genepred file:
-user defined attributes must start with a lower-case letter:X_AED
How can I change a letter within a file from upper to lower case.
command-line sed
edited Oct 4 at 12:11
jimmij
29.5k867101
asked Oct 4 at 11:53
Yewon
1
New contributor
Yewon is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
I have used the following command to introduce a letter in front of underscores in my gff3 file as requested by the program i am using to generate a genepred file:
sed 's/;_/;x_/g' in.transcripts.gff3 > altered.transcripts.gff3
However, the output file contained an uppercase x instead of the lower case as expected, despite using the lower case in the command.I get the following error messages when I use the altered file to generate a genepred file:
-user defined attributes must start with a lower-case letter:X_AED
How can I change a letter within a file from upper to lower case.
command-line sed
command-line sed
edited Oct 4 at 12:11
jimmij
29.5k867101
asked Oct 4 at 11:53
Yewon
1
New contributor
Yewon is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
edited Oct 4 at 12:11
jimmij
29.5k867101
asked Oct 4 at 11:53
Yewon
1
New contributor
Yewon is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
edited Oct 4 at 12:11
jimmij
29.5k867101
edited Oct 4 at 12:11
jimmij
29.5k867101
edited Oct 4 at 12:11
jimmij
29.5k867101
29.5k867101
asked Oct 4 at 11:53
Yewon
1
New contributor
Yewon is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
asked Oct 4 at 11:53
Yewon
1
asked Oct 4 at 11:53
Yewon
1
1
New contributor
Yewon is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
New contributor
Yewon is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
Yewon is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
Were the uppercase X’s already there? They should not even introduced by your sed command.
– Jeff Schaller
Oct 4 at 12:06
Th upper case X's were not there before, I introduced them because the
– Yewon
Oct 4 at 12:41
The upper case X's were not there before. I introduced them because the gff3togenepred tool (which I was using to convert my gff3 file to a genepred intermediate) required that an attribute tag must start with an alphabetic character which was not the case with my original file where the attributes start with an underscore (_QI, _eAED, _AED). That is why I introduced a lower case x but it appears as an upper case x in the file. However, when I reun the command using the edited gff3 file, i get another message saying that user defined attributes must start with a lower case letter.
– Yewon
Oct 4 at 12:53
add a comment |Â
Were the uppercase X’s already there? They should not even introduced by your sed command.
– Jeff Schaller
Oct 4 at 12:06
Th upper case X's were not there before, I introduced them because the
– Yewon
Oct 4 at 12:41
The upper case X's were not there before. I introduced them because the gff3togenepred tool (which I was using to convert my gff3 file to a genepred intermediate) required that an attribute tag must start with an alphabetic character which was not the case with my original file where the attributes start with an underscore (_QI, _eAED, _AED). That is why I introduced a lower case x but it appears as an upper case x in the file. However, when I reun the command using the edited gff3 file, i get another message saying that user defined attributes must start with a lower case letter.
– Yewon
Oct 4 at 12:53
Were the uppercase X’s already there? They should not even introduced by your sed command.
– Jeff Schaller
Oct 4 at 12:06
Were the uppercase X’s already there? They should not even introduced by your sed command.
– Jeff Schaller
Oct 4 at 12:06
Th upper case X's were not there before, I introduced them because the
– Yewon
Oct 4 at 12:41
Th upper case X's were not there before, I introduced them because the
– Yewon
Oct 4 at 12:41
The upper case X's were not there before. I introduced them because the gff3togenepred tool (which I was using to convert my gff3 file to a genepred intermediate) required that an attribute tag must start with an alphabetic character which was not the case with my original file where the attributes start with an underscore (_QI, _eAED, _AED). That is why I introduced a lower case x but it appears as an upper case x in the file. However, when I reun the command using the edited gff3 file, i get another message saying that user defined attributes must start with a lower case letter.
– Yewon
Oct 4 at 12:53
The upper case X's were not there before. I introduced them because the gff3togenepred tool (which I was using to convert my gff3 file to a genepred intermediate) required that an attribute tag must start with an alphabetic character which was not the case with my original file where the attributes start with an underscore (_QI, _eAED, _AED). That is why I introduced a lower case x but it appears as an upper case x in the file. However, when I reun the command using the edited gff3 file, i get another message saying that user defined attributes must start with a lower case letter.
– Yewon
Oct 4 at 12:53
add a comment |Â
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Were the uppercase X’s already there? They should not even introduced by your sed command.
– Jeff Schaller
Oct 4 at 12:06
Th upper case X's were not there before, I introduced them because the
– Yewon
Oct 4 at 12:41
The upper case X's were not there before. I introduced them because the gff3togenepred tool (which I was using to convert my gff3 file to a genepred intermediate) required that an attribute tag must start with an alphabetic character which was not the case with my original file where the attributes start with an underscore (_QI, _eAED, _AED). That is why I introduced a lower case x but it appears as an upper case x in the file. However, when I reun the command using the edited gff3 file, i get another message saying that user defined attributes must start with a lower case letter.
– Yewon
Oct 4 at 12:53