I have a file seq.txt which consists of multiple aligned sequences:
B_phora_cucurbitarum -----------------------------------------------------MSHIKRD
E_aceosorus_bombacis RAQAPPGSHNDQPPLLDPLSGILSPLGLGGLTPRSDSLPEHLEMQRRHILERLNERDEDV
A_nfragosa_RCEF_1005 ---------------------------------------------------MKYSILHLA
X_crodochium_bolleyi -------------------------------------------MRLSNIAGQLAVGAACL
R_cillium_camemberti --------------------------------------MRILTTGLLLWLLSLINLVSAF
[Bin ]
B_phora_cucurbitarum LSRISGGIGGFLSSIANNIYVFSWDFSLFLLNLVAFKRKVGKVTLEGNPGFGGKWPEYIP
E_aceosorus_bombacis RAQAPPGSHNDQPPL--------QLAVGAACLEHLEM------------LERLNERDEDV
A_nfragosa_RCEF_1005 ---------MTENALSAEDLAKRG---LDKREVSYTGRITTTFDAAAQLVSNTGVHAFQA
X_crodochium_bolleyi NDQPPLLDPLSGILSPLGLGGLTP------------------MRL-SNIAGQLAVGAACL
R_cillium_camemberti -------------------------MS------DIPVHQHSDGRCPVTGISGSNPHPFCP
[Bin ]
I want to combine them in a single line according to their names like this:
>B_phora_cucurbitarum -----------------------------------------------------MSHIKRDLSRISGGIGGFLSSIANNIYVFSWDFSLFLLNLVAFKRKVGKVTLEGNPGFGGKWPEYIP
>E_aceosorus_bombacis RAQAPPGSHNDQPPLLDPLSGILSPLGLGGLTPRSDSLPEHLEMQRRHILERLNERDEDVRAQAPPGSHNDQPPL--------QLAVGAACLEHLEM------------LERLNERDEDV
>A_nfragosa_RCEF_1005 ---------------------------------------------------MKYSILHLA---------MTENALSAEDLAKRG---LDKREVSYTGRITTTFDAAAQLVSNTGVHAFQA
>X_crodochium_bolleyi -------------------------------------------MRLSNIAGQLAVGAACLNDQPPLLDPLSGILSPLGLGGLTP------------------MRL-SNIAGQLAVGAACL
>R_cillium_camemberti --------------------------------------MRILTTGLLLWLLSLINLVSAF-------------------------MS------DIPVHQHSDGRCPVTGISGSNPHPFCP
Awk or sed commands are preferred, any help would be appreciated. Thanks!
4 answers
As I'm a goat in awk, I let you a python solution
###Create a dictionnary containing your seq_merge.txt
merged_dict={}
###Open your seq table
with open("seq_merge.txt", 'r') as f:
for line in f:
###Do a key/value dictionnary
id_seq = line.rstrip().split("\t")[0]
seq = line.rstrip().split("\t")[1]
###Check if the key exists in the dictionnary
if id_seq not in merged_dict:
merged_dict[id_seq] = seq
else:
merged_dict[id_seq] += seq
###Write in new file
with open("new_seq_merge.txt", "a") as new_seq_merge:
for key, value in merged_dict.iteritems():
new_seq_merge.write(">"+key+"\t"+value+"\n")
What is your delimiter in this line : B_phora_cucurbitarum -----------------------------------------------------MSHIKRD ? Tabulation ? 4 spaces ?
It's hard to investigate without your file.
Try to print line.split("\t") before id_seq = line.rstrip().split("\t")[0]
Does these lines really exist in your file ?
[Bin ]
I was thinking about the animal
Nah, expression from my country to say that i'm very bad at awk writing
mkdir whatever
cp inputfile whatever
cd whatever
awk 'BEGIN{FS="\t";ORS=""}{print $2 >> $1}' inputfile
rm inputfile
for f in *; do awk -v N="$f" 'BEGIN{OFS="\t"}{print N,$0}' $f; done > newFile
I ignored the [Bin lines here. You can delete that file before the for loop
$ sed -n '/^$/d;/Bin/!p' test.txt| sed -e 's/\s\+/\t/g' | sort -s -k 1,1 | datamash -g1 collapse 2 | sed 's/,//g'| awk '{print ">"$1"\n"$2}'
>A_nfragosa_RCEF_1005
---------------------------------------------------MKYSILHLA---------MTENALSAEDLAKRG---LDKREVSYTGRITTTFDAAAQLVSNTGVHAFQA
>B_phora_cucurbitarum
-----------------------------------------------------MSHIKRDLSRISGGIGGFLSSIANNIYVFSWDFSLFLLNLVAFKRKVGKVTLEGNPGFGGKWPEYIP
>E_aceosorus_bombacis
RAQAPPGSHNDQPPLLDPLSGILSPLGLGGLTPRSDSLPEHLEMQRRHILERLNERDEDVRAQAPPGSHNDQPPL--------QLAVGAACLEHLEM------------LERLNERDEDV
>R_cillium_camemberti
--------------------------------------MRILTTGLLLWLLSLINLVSAF-------------------------MS------DIPVHQHSDGRCPVTGISGSNPHPFCP
>X_crodochium_bolleyi
-------------------------------------------MRLSNIAGQLAVGAACLNDQPPLLDPLSGILSPLGLGGLTP------------------MRL-SNIAGQLAVGAACL
Install datamash either from here or from distro repos (for debian based; sudo apt install datamash -y; for conda, conda install datamash -y).
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Did you try something yourself with some forums examples close to your question ?
https://stackoverflow.com/questions/18092469/combining-columns-within-a-single-file-using-awk
https://unix.stackexchange.com/questions/224135/merging-columns-in-a-file-using-awk
https://www.unix.com/shell-programming-and-scripting/267681-merge-columns-two-files-using-awk.html
https://stackoverflow.com/questions/7068314/awk-combining-multiple-lines-conditionally
https://www.unix.com/shell-programming-and-scripting/208027-merge-multiple-lines-same-file-common-key-using-awk.html
Yes, I tried but they don't make my case.