http://ocan.com.mx/?chydesa=ponteceso-minutos-dating&f62=f1 Quick fix of command line typo
^typo^correct
This will replace the word ‘typo’ with ‘correct’ from the previous command line.
http://lifehacker.com/5698494/quickly-fix-command-line-mistakes-with-the–symbol
Find duplicates in MySQL
SELECT col1, col2, count(col3) FROM t1 GROUP BY col1, col2 HAVING count(col3) > 1
Adapted from
http://support.microsoft.com/default.aspx?scid=kb;en-us;139444
Rewrapping in Vim
gq
or
gw
to stay at the word where the cursor was.
It will re-wrap the text depending on the textwidth or windowmargin value.
Another way of adjusting the spacing after line with stretched table
Use bookends package and \toprule, \midrule, and \bottomrule instead of \hline.
In premeble
\usepackage{booktabs}
In context
{table}[h]
\begin{tabular*}{\linewidth}{@{\extracolsep{\fill}} ccr}
\toprule
Site pattern & supported $T_i$ & count \\
\midrule
xxx & $T_0$ & 4 \\
xxy & $T_1$ & 3 \\
\bottomrule
\end{tabular*}
\caption{Table1}
\end{table}
Adjusting spacing after \hline in tabular environment
in preamble
\newcommand\tstrut{\rule{0pt}{2.4ex}}
\newcommand\bstrut{\rule[-1.0ex]{0pt}{0pt}}
in content
\begin{tabular}{ccc}
\hline\hline
Head 1 & Head 2 & Head 3 \tstrut \bstrut \\
\hline
a1 & a2 & a3 \tstrut \\
b1 & b2 & b3 \\
c1 & c2 & c3 \\
d1 & d2 & d3 \bstrut \\
\hline\hline
\end{tabular}
https://www.msu.edu/~harris41/latex_tablespacing.html
http://stackoverflow.com/questions/696157/latex-hline-spacing
To find out what method is attached to an object in BioPerl during debugging, use ref commend.
>x ref($seq)
It’ll show the class where the object belongs to and search for the class.
Not so funny… Any other way?
NB. As it was said, the commend working during the debugging session; perl -d
Simple code example to retrieve annotations
1 #!/usr/bin/perl -w
2
3 use strict;
4 use Carp;
5 use Bio::SeqIO;
6
7 my $embl_file = shift;
8 my $informat = "embl";
9
10 my $seq_in = Bio::SeqIO -> new(-file => "<$embl_file",
11 -format => $informat)
12 or croak("File Open Error: $embl_file\n");
13
14 while (my $seq = $seq_in->next_seq) {
15
16
17 # ID
18 $seq->primary_seq->display_id();
19 # AC
20 $seq->primary_seq->accession_number();
21
22 # DE
23 $seq->primary_seq->desc();
24
25 # CC
26 my $annotation = $seq->annotation();
27 my @comments = $annotation->get_Annotations('comment');
28 foreach my $comment (@comments){
29 print $comment->as_text;
30 }
31
32
33 print "\n";
34 }
35
36 $seq_in->close() or croak("Close error: $embl_file\n");
Recursively cat all the txt files.
find . -name “*.txt” -print0 |xargs -0 cat
Got a clue here.
gff3 file format
Make sure the fields are separated by TAB.
The format consists of 9 columns, separated by tabs (NOT spaces).
Change the output directory of pdflatex in TeXworks.
Go to Preferences -> Typesetting. Then select the tool you want to change in the Processing tools section. Click Edit and add the directory where the output goes by pressing + button.
NB. There is no aux directory option in pdflatex unlike latex. So the final pdf file as well as aux and log files will be in the output directory.
NB. The output directory option should be before the $fullname.
-output-directory=$directory/temp