Subject: Looking for a good output format to use a value extracted from a file in new script/process in Nextflow
I can't seem to figure this one out:
I am writing some processes in Nextflow in which I'm extracting a value from a txt.file (PROCESS1) and I want to use it in a second process (PROCESS2). The extraction of the value is no problem but finding the suitable output format is. The problem is that when I save the stdout (OPTION1) to a channel there seems to be some kind of "/n" attached which gives problems in my second script.
Alternatively because this was not working I wanted to save the output of PROCESS1 as a file (OPTION2). Also this is no problem but I can't find the correct way to read the content of the file in PROCESS2. I suspect it has something to do with "getText()" but I tried several things and they all failed.
Finally I wanted to try to save the output as a variable (OPTION3) but I don't know how to do this.
PROCESS1
process txid {
publishDir "$wanteddir", mode:'copy', overwrite: true
input:
file(report) from report4txid
output:
stdout into txid4assembly //OPTION 1
file(txid.txt) into txid4assembly //OPTION 2
val(txid) into txid4assembly //OPTION 3: doesn't work
shell:
'''
column -s, -t < !{report}| awk '$4 == "S"'| head -n 1 | cut -f5 //OPTION1
column -s, -t < !{report}| awk '$4 == "S"'| head -n 1 | cut -f5 > txid.txt //OPTION2
column -s, -t < !{report}| awk '$4 == "S"'| head -n 1 | cut -f5 > txid //OPTION3
'''
}
PROCESS2
process accessions {
publishDir "$wanteddir", mode:'copy', overwrite: true
input:
val(txid) from txid4assembly //OPTION1 & OPTION3
file(txid) from txid4assembly //OPTION2
output:
file("${txid}accessions.txt") into accessionlist
script:
"""
esearch -db assembly -query '${txid}[txid] AND "complete genome"[filter] AND "latest refseq"[filter]' \
| esummary | xtract -pattern DocumentSummary -element AssemblyAccession > ${txid}accessions.txt
"""
}
RESULTING SCRIPT OF PROCESS2 AFTER OPTION 1 (remark: output = 573, lay-out unchanged)
esearch -db assembly -query '573
[txid] AND "complete genome"[filter] AND "latest refseq"[filter]' | esummary | xtract -pattern DocumentSummary -element AssemblyAccession > 573
accessions.txt
Thank you for your help!
As you've discovered, your command-line writes a trailing newline character. You could try removing it somehow, perhaps by piping to another command, or (better) by refactoring to properly parse your report files. Below is an example using awk to print the fifth column without a trailing newline character. This might work fine for a simple CSV report file, but the CSV parsing capabilities of AWK are limited. So if your reports could contain quoted fields etc, consider using a language that offers CSV parsing in it's standard library (e.g. Python and the csv libary, or Perl and the Text::CSV module). Nextflow makes it easy to use your favourite scripting language.
process txid {
publishDir "$wanteddir", mode:'copy', overwrite: true
input:
file(report) from report4txid
output:
stdout into txid4assembly
shell:
'''
awk -F, '$4 == "S" { printf("%s", $5); exit }' "!{report}"
'''
In the case where your file contains an "S" in the forth column and the fifth column has some value with string length >= 1, this will give you a value that you can use in your 'accessions' process. But please be aware that this won't handle the case where the forth column in your file is never equal to "S". Nor will it handle the case where your fifth column could be an empty value (string length == 0). In these cases 'stdout' will be empty, so you'll get an empty value in your output channel. You may want to add some code to make sure that these edge cases are handled somehow.
I eventually fixed it by adding the following code, which only gets the numbers from my output
... | tr -dc '0-9'
I have one file like this:
head allGenes.txt
ENSG00000128274
ENSG00000094914
ENSG00000081760
ENSG00000158122
ENSG00000103591
...
and I have a multiple files named like this *.v7.egenes.txt in the current directory. For example one file looks like this:
head Stomach.v7.egenes.txt
ENSG00000238009 RP11-34P13.7 1 89295 129223 - 2073 1.03557 343.245
ENSG00000237683 AL627309.1 1 134901 139379 - 2123 1.02105 359.907
ENSG00000235146 RP5-857K21.2 1 523009 530148 + 4098 1.03503 592.973
ENSG00000231709 RP5-857K21.1 1 521369 523833 - 4101 1.07053 559.642
ENSG00000223659 RP5-857K21.5 1 562757 564390 - 4236 1.05527 595.015
ENSG00000237973 hsa-mir-6723 1 566454 567996 + 4247 1.05299 592.876
I would like to get lines from all *.v7.egenes.txt files that match any entry in allGenes.txt
I tried using:
grep -w -f allGenes.txt *.v7.egenes.txt > output.txt
but this takes forever to complete. Is there is any way to do this in awk or?
Without knowing the size of the files, but assuming the host has enough memory to hold allGenes.txt in memory, one awk solution comes to mind:
awk 'NR==FNR { gene[$1] ; next } ( $1 in gene )' allGenes.txt *.v7.egenes.txt > output.txt
Where:
NR==FNR - this test only matches the first file to be processed (allGenes.txt)
gene[$1] - store each gene as an index in an associative array
next stop processing and go to next line in the file
$1 in gene - applies to all lines in all other files; if the first field is found to be an index in our associative array then we print the current line
I wouldn't expect this to run any/much faster than the grep solution the OP is currently using (especially with shelter's suggestion to use -F instead of -w), but it should be relatively quick to test and see ....
GNU Parallel has a whole section dedicated to grepping n lines for m regular expressions:
https://www.gnu.org/software/parallel/man.html#EXAMPLE:-Grepping-n-lines-for-m-regular-expressions
You could try with a while read loop :
#!/bin/bash
while read -r line; do
grep -rnw Stomach.v7.egenes.txt -e "$line" >> output.txt
done < allGenes.txt
So here tell the while loop to read all the lines from the allGenes.txt, and for each line, check whether there are matching lines in the egenes file. Would that do the trick?
EDIT :
New version :
#!/bin/bash
for name in $(cat allGenes.txt); do
grep -rnw *v7.egenes.txt* -e $name >> output.txt
done
The intent of this question is to provide a canonical answer.
Given a CSV as might be generated by Excel or other tools with embedded newlines and/or double quotes and/or commas in fields, and empty fields like:
$ cat file.csv
"rec1, fld1",,"rec1"",""fld3.1
"",
fld3.2","rec1
fld4"
"rec2, fld1.1
fld1.2","rec2 fld2.1""fld2.2""fld2.3","",rec2 fld4
"""""","""rec3,fld2""",
What's the most robust way efficiently using awk to identify the separate records and fields:
Record 1:
$1=<rec1, fld1>
$2=<>
$3=<rec1","fld3.1
",
fld3.2>
$4=<rec1
fld4>
----
Record 2:
$1=<rec2, fld1.1
fld1.2>
$2=<rec2 fld2.1"fld2.2"fld2.3>
$3=<>
$4=<rec2 fld4>
----
Record 3:
$1=<"">
$2=<"rec3,fld2">
$3=<>
----
so it can be used as those records and fields internally by the rest of the awk script.
A valid CSV would be one that conforms to RFC 4180 or can be generated by MS-Excel.
The solution must tolerate the end of record just being LF (\n) as is typical for UNIX files rather than CRLF (\r\n) as that standard requires and Excel or other Windows tools would generate. It will also tolerate unquoted fields mixed with quoted fields. It will specifically not need to tolerate escaping "s with a preceding backslash (i.e. \" instead of "") as some other CSV formats allow - if you have that then adding a gsub(/\\"/,"\"\"") up front would handle it and trying to handle both escaping mechanisms automatically in one script would make the script unnecessarily fragile and complicated.
If your CSV cannot contain newlines then all you need is (with GNU awk for FPAT):
$ echo 'foo,"field,""with"",commas",bar' |
awk -v FPAT='[^,]*|("([^"]|"")*")' '{for (i=1; i<=NF;i++) print i " <" $i ">"}'
1 <foo>
2 <"field,""with"",commas">
3 <bar>
or the equivalent using any awk:
$ echo 'foo,"field,""with"",commas",bar' |
awk -v fpat='[^,]*|("([^"]|"")*")' -v OFS=',' '{
rec = $0
$0 = ""
i = 0
while ( (rec!="") && match(rec,fpat) ) {
$(++i) = substr(rec,RSTART,RLENGTH)
rec = substr(rec,RSTART+RLENGTH+1)
}
for (i=1; i<=NF;i++) print i " <" $i ">"
}'
1 <foo>
2 <"field,""with"",commas">
3 <bar>
See https://www.gnu.org/software/gawk/manual/gawk.html#More-CSV for info on the specific FPAT setting I use above.
If all you actually want to do is convert your CSV to individual lines by, say, replacing newlines with blanks and commas with semi-colons inside quoted fields then all you need is this, again using GNU awk for multi-char RS and RT:
$ awk -v RS='"([^"]|"")*"' -v ORS= '{gsub(/\n/," ",RT); gsub(/,/,";",RT); print $0 RT}' file.csv
"rec1; fld1",,"rec1"";""fld3.1 ""; fld3.2","rec1 fld4"
"rec2; fld1.1 fld1.2","rec2 fld2.1""fld2.2""fld2.3","",rec2 fld4
"""""","""rec3;fld2""",
Otherwise, though, the general, robust, portable solution to identify the fields that will work with any modern awk* is:
$ cat decsv.awk
function buildRec( fpat,fldNr,fldStr,done) {
CurrRec = CurrRec $0
if ( gsub(/"/,"&",CurrRec) % 2 ) {
# The string built so far in CurrRec has an odd number
# of "s and so is not yet a complete record.
CurrRec = CurrRec RS
done = 0
}
else {
# If CurrRec ended with a null field we would exit the
# loop below before handling it so ensure that cannot happen.
# We use a regexp comparison using a bracket expression here
# and in fpat so it will work even if FS is a regexp metachar
# or a multi-char string like "\\\\" for \-separated fields.
CurrRec = CurrRec ( CurrRec ~ ("[" FS "]$") ? "\"\"" : "" )
$0 = ""
fpat = "([^" FS "]*)|(\"([^\"]|\"\")+\")"
while ( (CurrRec != "") && match(CurrRec,fpat) ) {
fldStr = substr(CurrRec,RSTART,RLENGTH)
# Convert <"foo"> to <foo> and <"foo""bar"> to <foo"bar>
if ( gsub(/^"|"$/,"",fldStr) ) {
gsub(/""/, "\"", fldStr)
}
$(++fldNr) = fldStr
CurrRec = substr(CurrRec,RSTART+RLENGTH+1)
}
CurrRec = ""
done = 1
}
return done
}
# If your input has \-separated fields, use FS="\\\\"; OFS="\\"
BEGIN { FS=OFS="," }
!buildRec() { next }
{
printf "Record %d:\n", ++recNr
for (i=1;i<=NF;i++) {
# To replace newlines with blanks add gsub(/\n/," ",$i) here
printf " $%d=<%s>\n", i, $i
}
print "----"
}
.
$ awk -f decsv.awk file.csv
Record 1:
$1=<rec1, fld1>
$2=<>
$3=<rec1","fld3.1
",
fld3.2>
$4=<rec1
fld4>
----
Record 2:
$1=<rec2, fld1.1
fld1.2>
$2=<rec2 fld2.1"fld2.2"fld2.3>
$3=<>
$4=<rec2 fld4>
----
Record 3:
$1=<"">
$2=<"rec3,fld2">
$3=<>
----
The above assumes UNIX line endings of \n. With Windows \r\n line endings it's much simpler as the "newlines" within each field will actually just be line feeds (i.e. \ns) and so you can set RS="\r\n" (using GNU awk for multi-char RS) and then the \ns within fields will not be treated as line endings.
It works by simply counting how many "s are present so far in the current record whenever it encounters the RS - if it's an odd number then the RS (presumably \n but doesn't have to be) is mid-field and so we keep building the current record but if it's even then it's the end of the current record and so we can continue with the rest of the script processing the now complete record.
*I say "modern awk" above because there's apparently extremely old (i.e. circa 2000) versions of tawk and mawk1 still around which have bugs in their gsub() implementation such that gsub(/^"|"$/,"",fldStr) would not remove the start/end "s from fldStr. If you're using one of those then get a new awk, preferably gawk, as there could be other issues with them too but if that's not an option then I expect you can work around that particular bug by changing this:
if ( gsub(/^"|"$/,"",fldStr) ) {
to this:
if ( sub(/^"/,"",fldStr) && sub(/"$/,"",fldStr) ) {
Thanks to the following people for identifying and suggesting solutions to the stated issues with the original version of this answer:
#mosvy for escaped double quotes within fields.
#datatraveller1 for multiple contiguous pairs of escaped quotes in a field and null fields at the end of records.
Related: also see How do I use awk under cygwin to print fields from an excel spreadsheet? for how to generate CSVs from Excel spreadsheets.
An improvement upon #EdMorton's FPAT solution, which should be able to handle double-quotes(") escaped by doubling ("" -- as allowed by the CSV standard).
gawk -v FPAT='[^,]*|("[^"]*")+' ...
This STILL
isn't able to handle newlines inside quoted fields, which are perfectly legit in standard CSV files.
assumes GNU awk (gawk), a standard awk won't do.
Example:
$ echo 'a,,"","y""ck","""x,y,z"," ",12' |
gawk -v OFS='|' -v FPAT='[^,]*|("[^"]*")+' '{$1=$1}1'
a||""|"y""ck"|"""x,y,z"|" "|12
$ echo 'a,,"","y""ck","""x,y,z"," ",12' |
gawk -v FPAT='[^,]*|("[^"]*")+' '{
for(i=1; i<=NF;i++){
if($i~/"/){ $i = substr($i, 2, length($i)-2); gsub(/""/,"\"", $i) }
print "<"$i">"
}
}'
<a>
<>
<>
<y"ck>
<"x,y,z>
< >
<12>
This is exactly what csvquote is for - it makes things simple for awk and other command line data processing tools.
Some things are difficult to express in awk. Instead of running a single awk command and trying to get awk to handle the quoted fields with embedded commas and newlines, the data gets prepared for awk by csvquote, so that awk can always interpret the commas and newlines it finds as field separators and record separators. This makes the awk part of the pipeline simpler. Once awk is done with the data, it goes back through csvquote -u to restore the embedded commas and newlines inside quoted fields.
csvquote file.csv | awk -f my_awk_script | csvquote -u
EDIT:
For a complete description on csvquote, see: How it works. this also explains the `` characters which are shown in places where there was a carriage return.
csvquote file.csv | awk -f decsv.awk | csvquote -u
(for the source of decsv.awk see answer from Ed Morton )
outut:
Record 1:
$1=<rec1 fld1>
$2=<>
$3=<rec1","fld3.1",
fld3.2>
$4=<rec1
fld4>
----
Record 2:
$1=<rec2, fld1.1
fld1.2>
$2=<rec2 fld2.1"fld2.2"fld2.3>
$3=<>
$4=<rec2 fld4>
----
Record 3:
$1=<"">
$2=<"rec3fld2">
$3=<>
----
I have found csvkit a really useful toolkit to handle with csv files in command line.
line='test,t2,t3,"t5,"'
echo $line | csvcut -c 4
"t5,"
echo 'foo,"field,""with"",commas",bar' | csvcut -c 3
bar
It also contains csvstat, csvstack etc. tools which are also very handy.
cat file.csv
"rec1, fld1",,"rec1"",""fld3.1
"",
fld3.2","rec1
fld4"
"rec2, fld1.1
fld1.2","rec2 fld2.1""fld2.2""fld2.3","",rec2 fld4
"""""","""rec3,fld2""",
csvcut -c 1 file.csv
"rec1, fld1"
"rec2, fld1.1
fld1.2"
""""""
csvcut -c 3 file.csv
"rec1"",""fld3.1
"",
fld3.2"
""
""
Awk (gawk) actually provides extensions, one of which being csv processing, which is the most robust way to do so with gawk in my opinion. The extension takes care of many gotchas and parses the csv for you.
Assuming that extension is installed, you can use awk to show all lines where a specific csv field matches 123.
Assuming test.csv contains the following:
Name,Phone
"Woo, John",425-555-1212
"James T. Kirk",123
The following will print all lines where the Phone (aka the second field) is equal to 123:
gawk -l csv 'csvsplit($0,a) && a[2] == 123 {print a[1]}'
The output is:
James T. Kirk
How does it work?
-l csv asks gawk to load the csv extension by looking for it in $AWKLIBPATH;
csvsplit($0, a) splits the current line, and stores each field into a new array named a
&& a[2] == 123 checks that the second field is 123
if both conditions are true, it { print a[1] }, aka prints first csv field of the line.
If you're using one of the common AWK interpreters (Gawk, onetrueawk, mawk), the other solutions are your best bet. However, if you're able to use a different interpreter, frawk and GoAWK have proper CSV support built-in.
frawk is a very fast AWK implementation written in Rust. Use -i csv to process input in CSV mode. Note that frawk is not quite POSIX compatible (see differences).
GoAWK is a POSIX-compatible AWK implementation written in Go. Also supports -i csv mode, as well as -H (parse header row) with #"named_field" syntax (read more). Disclaimer: I'm the author of GoAWK.
With file.csv as per the question, you can simply use an AWK script with a regular for loop over the fields as follows:
$ cat records.awk
{
printf "Record %d:\n", NR
for (i=1; i<=NF; i++)
printf " $%d=<%s>\n", i, $i
print "----"
}
Then use either frawk -i csv or goawk -i csv to get the expected output. For example:
$ frawk -i csv -f records.awk file.csv
Record 1:
$1=<rec1, fld1>
$2=<>
$3=<rec1","fld3.1
",
fld3.2>
$4=<rec1
fld4>
----
Record 2:
$1=<rec2, fld1.1
fld1.2>
$2=<rec2 fld2.1"fld2.2"fld2.3>
$3=<>
$4=<rec2 fld4>
----
Record 3:
$1=<"">
$2=<"rec3,fld2">
$3=<>
----
$ goawk -i csv -f records.awk file.csv
Record 1:
... same as above ...
----
I have a small script that simply reads each line of a file, retrieves id field, runs utility to get the name and appends the name at the end. The problem is the input file is huge (2GB). Since output is same as input with a 10-30 char name appended, it is of the same order of magnitude. How can I optimize it to read large buffers, process in buffers and then write buffers to the file so the number of file accesses are minimized?
#!/bin/ksh
while read line
do
id=`echo ${line}|cut -d',' -f 3`
NAME=$(id2name ${id} | cut -d':' -f 4)
if [[ $? -ne 0 ]]; then
NAME="ERROR"
echo "Error getting name from id2name for id: ${id}"
fi
echo "${line},\"${NAME}\"" >> ${MYFILE}
done < ${MYFILE}.csv
Thanks
You can speed things up considerably by eliminating the two calls to cut in each iteration of the loop. It also might be faster to move the redirection to your output file to the end of the loop. Since you don't show an example of an input line, or what id2name consists of (it's possible it's a bottleneck) or what its output looks like, I can only offer this approximation:
#!/bin/ksh
while IFS=, read -r field1 field2 id remainder # use appropriate var names
do
line=$field1,$field2,$id,$remainder
# warning - reused variables
IFS=: read -r field1 field2 field3 NAME remainder <<< $(id2name "$id")
if [[ $? -ne 0 ]]; then
NAME="ERROR"
# if you want this message to go to stderr instead of being included in the output file include the >&2 as I've done here
echo "Error getting name from id2name for id: ${id}" >&2
fi
echo "${line},\"${NAME}\""
done < "${MYFILE}.csv" > "${MYFILE}"
The OS will do the buffering for you.
Edit:
If your version of ksh doesn't have <<<, try this:
id2name "$id" | IFS=: read -r field1 field2 field3 NAME remainder
(If you were using Bash, this wouldn't work.)
I currently have a request to build a shell script to get some data from the table using SQL (Oracle). The query which I'm running return a number of rows. Is there a way to use something like result set?
Currently, I'm re-directing it to a file, but I'm not able to reuse the data again for the further processing.
Edit: Thanks for the reply Gene. The result file looks like:
UNIX_PID 37165
----------
PARTNER_ID prad
--------------------------------------------------------------------------------
XML_FILE
--------------------------------------------------------------------------------
/mnt/publish/gbl/backup/pradeep1/27241-20090722/kumarelec2.xml
pradeep1
/mnt/soar_publish/gbl/backup/pradeep1/11089-20090723/dataonly.xml
UNIX_PID 27654
----------
PARTNER_ID swam
--------------------------------------------------------------------------------
XML_FILE
--------------------------------------------------------------------------------
smariswam2
/mnt/publish/gbl/backup/smariswam2/10235-20090929/swam2.xml
There are multiple rows like this. My requirement is only to use shell script and write this program.
I need to take each of the pid and check if the process is running, which I can take care of.
My question is how do I check for each PID so I can loop and get corresponding partner_id and the xml_file name? Since it is a file, how can I get the exact corresponding values?
Your question is pretty short on specifics (a sample of the file to which you've redirected your query output would be helpful, as well as some idea of what you actually want to do with the data), but as a general approach, once you have your query results in a file, why not use the power of your scripting language of choice (ruby and perl are both good choices) to parse the file and act on each row?
Here is one suggested approach. It wasn't clear from the sample you posted, so I am assuming that this is actually what your sample file looks like:
UNIX_PID 37165 PARTNER_ID prad XML_FILE /mnt/publish/gbl/backup/pradeep1/27241-20090722/kumarelec2.xml pradeep1 /mnt/soar_publish/gbl/backup/pradeep1/11089-20090723/dataonly.xml
UNIX_PID 27654 PARTNER_ID swam XML_FILE smariswam2 /mnt/publish/gbl/backup/smariswam2/10235-20090929/swam2.xml
I am also assuming that:
There is a line-feed at the end of
the last line of your file.
The columns are separated by a single
space.
Here is a suggested bash script (not optimal, I'm sure, but functional):
#! /bin/bash
cat myOutputData.txt |
while read line;
do
myPID=`echo $line | awk '{print $2}'`
isRunning=`ps -p $myPID | grep $myPID`
if [ -n "$isRunning" ]
then
echo "PARTNER_ID `echo $line | awk '{print $4}'`"
echo "XML_FILE `echo $line | awk '{print $6}'`"
fi
done
The script iterates through every line (row) of the input file. It uses awk to extract column 2 (the PID), and then does a check (using ps -p) to see if the process is running. If it is, it uses awk again to pull out and echo two fields from the file (PARTNER ID and XML FILE). You should be able to adapt the script further to suit your needs. Read up on awk if you want to use different column delimiters or do additional text processing.
Things get a little more tricky if the output file contains one row for each data element (as you indicated). A good approach here is to use a simple state mechanism within the script and "remember" whether or not the most recently seen PID is running. If it is, then any data elements that appear before the next PID should be printed out. Here is a commented script to do just that with a file of the format you provided. Note that you must have a line-feed at the end of the last line of input data or the last line will be dropped.
#! /bin/bash
cat myOutputData.txt |
while read line;
do
# Extract the first (myKey) and second (myValue) words from the input line
myKey=`echo $line | awk '{print $1}'`
myValue=`echo $line | awk '{print $2}'`
# Take action based on the type of line this is
case "$myKey" in
"UNIX_PID")
# Determine whether the specified PID is running
isRunning=`ps -p $myValue | grep $myValue`
;;
"PARTNER_ID")
# Print the specified partner ID if the PID is running
if [ -n "$isRunning" ]
then
echo "PARTNER_ID $myValue"
fi
;;
*)
# Check to see if this line represents a file name, and print it
# if the PID is running
inputLineLength=${#line}
if (( $inputLineLength > 0 )) && [ "$line" != "XML_FILE" ] && [ -n "$isRunning" ]
then
isHyphens=`expr "$line" : -`
if [ "$isHyphens" -ne "1" ]
then
echo "XML_FILE $line"
fi
fi
;;
esac
done
I think that we are well into custom software development territory now so I will leave it at that. You should have enough here to customize the script to your liking. Good luck!