I've got two CSV files. The first file contains organism family names and connection weight information but I need to change the format of the file to load it into different programs like Gephi. I have created a second file where each family has an ID value. I haven't found a good example on this site on how to change the family names in the first file to the ids from the second file. Example of my files:
$ cat edge_file.csv
Source,Target,Weight,Type,From,To
Argasidae,Alcaligenaceae,0.040968439,undirected,A_Argasidae,B_Alcaligenaceae
Argasidae,Burkholderiaceae,0.796351574,undirected,A_Argasidae,B_Burkholderiaceae
Argasidae,Methylophilaceae,0.276912259,undirected,A_Argasidae,B_Methylophilaceae
Argasidae,Oxalobacteraceae,0.460508445,undirected,A_Argasidae,B_Oxalobacteraceae
Argasidae,Rhodocyclaceae,0.764558003,undirected,A_Argasidae,B_Rhodocyclaceae
Argasidae,Sphingomonadaceae,0.70198002,undirected,A_Argasidae,B_Sphingomonadaceae
Argasidae,Zoogloeaceae,0.034648156,undirected,A_Argasidae,B_Zoogloeaceae
Argasidae,Agaricaceae,0.190482976,undirected,A_Argasidae,F_Agaricaceae
Argasidae,Bulleribasidiaceae,0.841600859,undirected,A_Argasidae,F_Bulleribasidiaceae
Argasidae,Camptobasidiaceae,0.841600859,undirected,A_Argasidae,F_Camptobasidiaceae
Argasidae,Chrysozymaceae,0.190482976,undirected,A_Argasidae,F_Chrysozymaceae
Argasidae,Cryptococcaceae,0.055650172,undirected,A_Argasidae,F_Cryptococcaceae
$ cat id_file.csv
Id,Family
1,Argasidae
2,Buthidae
3,Alcaligenaceae
4,Burkholderiaceae
5,Methylophilaceae
6,Oxalobacteraceae
7,Rhodocyclaceae
8,Oppiidae
9,Sphingomonadaceae
10,Zoogloeaceae
11,Agaricaceae
12,Bulleribasidiaceae
13,Camptobasidiaceae
14,Chrysozymaceae
15,Cryptococcaceae
I basically want the edge_file.csv output to turn into the output below, where Source and Target have changed from family names to ids instead.
Source,Target,Weight,Type,From,To
1,3,0.040968439,undirected,A_Argasidae,B_Alcaligenaceae
1,4,0.796351574,undirected,A_Argasidae,B_Burkholderiaceae
1,5,0.276912259,undirected,A_Argasidae,B_Methylophilaceae
1,6,0.460508445,undirected,A_Argasidae,B_Oxalobacteraceae
1,7,0.764558003,undirected,A_Argasidae,B_Rhodocyclaceae
1,9,0.70198002,undirected,A_Argasidae,B_Sphingomonadaceae
1,10,0.034648156,undirected,A_Argasidae,B_Zoogloeaceae
1,11,0.190482976,undirected,A_Argasidae,F_Agaricaceae
1,12,0.841600859,undirected,A_Argasidae,F_Bulleribasidiaceae
1,13,0.841600859,undirected,A_Argasidae,F_Camptobasidiaceae
1,14,0.190482976,undirected,A_Argasidae,F_Chrysozymaceae
1,15,0.055650172,undirected,A_Argasidae,F_Cryptococcaceae
I haven't been able to figure it out with awk since I'm new to it, but I tried some variations from other examples here such as (just testing it out for the "Source" column):
awk 'NR==FNR{a[$1]=$1;next}{$1=a[$1];}1' edge_file.csv id_file.csv
Everything just prints out blank. My understanding is that I should create an array for the Source and Target columns in the edge_file.csv, and then replace it with the first column from the id_file.csv, which is the Id column. Can't get the syntax to work even for just one column.
You're close. This oneliner should help:
awk -F, -v OFS=',' 'NR==FNR{a[$2]=$1;next}{$1=a[$1];$2=a[$2]}1' id_file.csv edge_file.csv
I want to replace strings in a target file (target.txt) by strings in a lookup table (lookup.tab), which looks as follows.
Seq_1 Name_one
Seq_2 Name_two
Seq_3 Name_three
...
Seq_10 Name_ten
Seq_11 Name_eleven
Seq_12 Name_twelve
The target.txt file is a large file with a tree structure (Nexus format). It is not arranged in columns.
Therefore I use the following command:
awk 'FNR==NR { array[$1]=$2; next } { for (i in array) gsub(i, array[i]) }1' "lookup.tab" "target.txt"
Unfortunately, this command does not take the full length of the elements from the first column, so that Seq_1, Seq_10, Seq_11, Seq_12 end up as Name_one, Name_one0, Name_one1, Name_one2 etc...
How can the awk command be made more specific to correctly substitute the strings?
Try this please, see if it meets your need:
awk 'FNR==NR { le=length($1); a[le][$1]=$2; if (maxL<le) maxL=le; next } { for(le=maxL;le>0;le--) if(length(a[le])) for (i in a[le]) gsub(i, a[le][i]) }1' "lookup.tab" "target.txt"
It's based on your own trying, but instead of randomly replace using the hashes in the array, replace using those longer keys first.
By this way, and based on your examples, I think it's enough to avoid wrongly substitudes.
I am using orgmode on Emacs and want to automatically update parts of an orgmode file using cron scheduling.
I know how to get the cron job to run at the times I choose but now I am faced with the issue of selecting certain parts of the file to change.
I would like to increment numbers at a certain locations in a file everyday (like every day at 3am or something).
So say I have the file fruit.org:
* Apple
age: 2
* Bananas
age: 1
A really bad fruit
* Cranberry
* Death
* Easter
A cool day
I want to select all the numerical values after age and then increment them every day. How would I do this selection and replacing. I believe it would involve regexp and some tool (maybe awk) but I am relatively clueless from there on.
In awk, you could say:
awk '/age:/ { $2++ } { print }' foo.org
If you have a recent version of GNU awk, you can edit the file in-place using the option -i inplace. Otherwise, just do the usual, i.e. redirect to a temporary file and then replace the original:
awk '/age:/ { $2++ } { print }' foo.org > foo.org.tmp && mv foo.org{.tmp,}
That's basically what the inplace option of awk or sed does behind the scenes anyway.
I've looked at the similar question about removing lines with more than a certain number of characters and my problem is similar but a bit trickier. I have a file that is generated after analyzing some data and each line is supposed to contain 29 numbers. For example:
53.0399 0.203827 7.28285 0.0139936 129.537 0.313907 11.3814 0.0137903 355.008 \
0.160464 12.2717 0.120802 55.7404 0.0875189 11.3311 0.0841887 536.66 0.256761 \
19.4495 0.197625 46.4401 2.38957 15.8914 17.1149 240.192 0.270649 19.348 0.230\
402 23001028 23800855
53.4843 0.198886 7.31329 0.0135975 129.215 0.335697 11.3673 0.014766 355.091 0\
.155786 11.9938 0.118147 55.567 0.368255 11.449 0.0842612 536.91 0.251735 18.9\
639 0.184361 47.2451 0.119655 18.6589 0.592563 240.477 0.298805 20.7409 0.2548\
56 23001585
50.7302 0.226066 7.12251 0.0158698 237.335 1.83226 15.4057 0.059467 -164.075 5\
.14639 146.619 1.37761 55.6474 0.289037 11.4864 0.0857042 536.34 0.252356 19.3\
91 0.198221 46.7011 0.139855 20.1464 0.668163 240.664 0.284125 20.3799 0.24696\
23002153
But every once in a while, a line like the first one appears that has an extra 8 digit number at the end from analyzing an empty file (so it just returns the file ID number but not on a new line like it should). So I just want to find lines that have this extra 30th number and remove just that 30th entry. I figure I could do this with awk but since I have little experience with it I'm not sure how. So if anyone can help I'd appreciate it.
Thanks
Summary: Want to find lines in a text file with an extra entry in a row and remove the last extra entry so all rows have same number of entries.
With awk, you tell it how many fields there are per record. The extras are ignored
awk '{NF = 29; print}' filename
If you want to save that back to the file, you have to do a little extra work
awk '{NF = 29; print}' filename > filename.new && mv filename.new filename
I have a text file in the below format.The first column represents a timestamp with a very high resolution.The second number represents the sequence number.I want to plot a graph between these two values.i.e Sequence number Over time.For this purpose I want to scale the sequence number and the timestamp.Time stamp can be scaled by subtracting the first time stamp from the remaining time stamps.Sequence number also should be scaled the same way.However when scaled the sequence number can have negative values.How do I write a bash script using awk to achieve this.This file name is print_1010171.txt.Please not that I do have a number of files of the same format.so I want the script to get generic.
5698771509078629376 1133254688
5698771509371165696 1150031904
5698771510035551232 1150031904
5698771510036082688 4170258464
5698771510036715520 2895583264
5698771510037202176 1620908064
5698771510037665280 346232864
5698771510038193664 3366459424
5698771510332259072 2091784224
5698771510332816128 817109024
5698771510333344512 3837335584
5698771510339882240 2562660384
5698771510340411392 1287985184
5698771510340939776 13309984
5698771510348048896 3033536544
5698771510348577280 1758861344
5698771510349228800 484186144
5698771510632804864 3504412704
5698771510633441792 2229737504
5698771510634390272 955062304
5698771510638858496 3975288864
5698771510639347712 2700613664
5698771510642663168 1425938464
5698771510643387136 134486304
5698771510643808768 3154712864
5698771510648858368 1880037664
5698771510649410560 605362464
5698771510655600384 3625589024
5698771510656128768 2350913824
5698771510656657408 1076238624
Very similar to Dennis Williamson's solution -- This should be more efficient (but probably not something you'd ever notice) and it will also silently ignore blank lines (the other solution will give very large negative numbers for blank lines).
#script coolscript.gp
if(!exists("DATAFILE")) DATAFILE='test.dat'
EXT_INDEX=strstr(DATAFILE,'.txt') #assume data has a .txt extension.
set term post enh color
set output DATAFILE[:EXT_INDEX] . '.ps' #gnuplot string slicing and concatenation
plot "< awk 'BEGIN{getline; header_col1=$1; header_col2=$2 }{if(NF){print $1-header_col1,$2-header_col2}}' ".DATAFILE using 1:2
You can definitely do this using an all-gnuplot solution. (See #andyras's nice solution and my answer that he linked to). This (alternate) solution works by reading the first line in awk and assigning the variables header_col1 and header_col2 with the data in column 1 and column 2. It then subtracts those from the future columes (as expected) as long as the line isn't empty.
Note that this solution can be called from the commandline using:
gnuplot -e "DATAFILE='mydatafile.txt'" coolscript.gp
Unfortunately, the quotes are necessary since gnuplot needs them, meaning that if you're using this in a shell loop, you should definitely use the double quotes on the outside as I show.
for FILE in *.dat; do
gnuplot -e "DATAFILE='${FILE}'" coolscript.gp
done
awk 'NR == 1 {basets = $1; baseseq = $2} {print $1 - basets, $2 - baseseq}' inputfile
or, if you don't want to output the initial pair of zeros:
awk 'NR == 1 {basets = $1; baseseq = $2; next} {print $1 - basets, $2 - baseseq}' inputfile
Here is a bash wrapper script which should do what you want:
#!/bin/bash
gnuplot << EOF
set terminal png truecolor size 800,600
set output 'plot_$1.png'
firstx=0
offsetx=0
funcx(x)=(offsetx=(firstx==0)?x:offsetx,firstx=1,x-offsetx)
firsty=0
offsety=0
funcy(x)=(offsety=(firsty==0)?x:offsety,firsty=1,x-offsety)
plot '$1' u (funcx(\$1)):(funcy(\$2))
EOF
To use the script, give it the name of the file you want to plot as an argument:
$ myscript.sh print_1010171.txt
I modified the answer given here to accommodate two variables. See that answer also if you want to subtract the lowest value from all data rather than the first.