I have a dataset with 3 columns and '#' occupying the empty lines.
Danio_rerio tmem129 transmembrane_protein_129,_E3_ubiquitin_protein_ligase
Danio_rerio si:zfos-2326c3.2 si:zfos-2326c3.2
Danio_rerio il1rapl2 interleukin_1_receptor_accessory_protein-like_2
Danio_rerio fam199x family_with_sequence_similarity_199,_X-linked
Danio_rerio commd5 COMM_domain_containing_5
Danio_rerio cysltr1 cysteinyl_leukotriene_receptor_1
Danio_rerio lpar4 lysophosphatidic_acid_receptor_4
Danio_rerio p2ry10 P2Y_receptor_family_member_10
Danio_rerio LOC101883727 uncharacterized_protein_K02A2.6-like
Danio_rerio gpr174 G_protein-coupled_receptor_174
Danio_rerio si:dkey-92i17.2 si:dkey-92i17.2
#
#
#
Danio_rerio cysltr1 cysteinyl_leukotriene_receptor_1
Danio_rerio lpar4 lysophosphatidic_acid_receptor_4
Danio_rerio p2ry10 P2Y_receptor_family_member_10
Danio_rerio LOC101883727 uncharacterized_protein_K02A2.6-like
Danio_rerio gpr174 G_protein-coupled_receptor_174
Danio_rerio si:dkey-92i17.2 si:dkey-92i17.2
#
#
#
#
#
#
#
Etheostoma_spectabile LOC116696506 integral_membrane_protein_2A-like
Etheostoma_spectabile gpr174 G_protein-coupled_receptor_174
Etheostoma_spectabile p2ry10 P2Y_receptor_family_member_10
Etheostoma_spectabile lpar4 lysophosphatidic_acid_receptor_4
Etheostoma_spectabile LOC116696505 uncharacterized_LOC116696505
Etheostoma_spectabile cysltr1 cysteinyl_leukotriene_receptor_1
Etheostoma_spectabile LOC116697110 endothelin_receptor_type_B-like
Etheostoma_spectabile polr1d RNA_polymerase_I_and_III_subunit_D
Etheostoma_spectabile sybl1 synaptobrevin-like_1
Etheostoma_spectabile mtus1a microtubule_associated_tumor_suppressor_1a
Etheostoma_spectabile pdgfrl platelet-derived_growth_factor_receptor-like
#
#
#
#
#
#
#
#
#
Pimephales_promelas sulf1 sulfatase_1
Pimephales_promelas LOC120475969 solute_carrier_organic_anion_transporter_family_member_5A1
Pimephales_promelas si:ch211-51h4.2 uncharacterized_si:ch211-51h4.2
Pimephales_promelas tbl1xr1a TBL1X/Y_related_1a
Pimephales_promelas zgc:113516 uncharacterized_LOC120475971
Pimephales_promelas cysltr1 cysteinyl_leukotriene_receptor_1
Pimephales_promelas lpar4 lysophosphatidic_acid_receptor_4
Pimephales_promelas p2ry10 P2Y_receptor_family_member_10
Pimephales_promelas LOC120475975 probable_G-protein_coupled_receptor_174
Pimephales_promelas mettl15 methyltransferase_like_15
Pimephales_promelas kif18a kinesin_family_member_18A
The first column should be printed first followed by the second column arranged horizontally. In the next line the first column should be printed followed by the third column arranged horizontally. After that there must be an empty line separating the two lines for a particular paragraph and then the columns must be aligned to each other for easy visualisation.
I used the following command:
cat input | sed 's/# #/ /g' | sed 's/^ *$//' | awk -v RS= '{str=$1; for (i=2; i<=NF; i =2) str=str OFS $i; print str}' | column -t | awk -v ORS='\n\n' '1' > output
which gave me the following output:
Danio_rerio tmem129 si:zfos-2326c3.2 il1rapl2 fam199x commd5 cysltr1 lpar4 p2ry10 LOC101883727 gpr174 si:dkey-92i17.2
Danio_rerio cysltr1 lpar4 p2ry10 LOC101883727 gpr174 si:dkey-92i17.2
Etheostoma_spectabile LOC116696506 gpr174 p2ry10 lpar4 LOC116696505 cysltr1 LOC116697110 polr1d sybl1 mtus1a pdgfrl
Pimephales_promelas sulf1 LOC120475969 si:ch211-51h4.2 tbl1xr1a zgc:113516 cysltr1 lpar4 p2ry10 LOC120475975 mettl15 kif18a
Also I tried:
cat input | sed 's/# #/ /g' | sed 's/^ *$//' | awk -v RS= '{str=$1; for (i=3; i<=NF; i =3) str=str OFS $i; print str}' | column -t | awk -v ORS='\n\n' '1' > output
which gave:
Danio_rerio transmembrane_protein_129,_E3_ubiquitin_protein_ligase si:zfos-2326c3.2 interleukin_1_receptor_accessory_protein-like_2 family_with_sequence_similarity_199,_X-linked COMM_domain_containing_5 cysteinyl_leukotriene_receptor_1 lysophosphatidic_acid_receptor_4 P2Y_receptor_family_member_10 uncharacterized_protein_K02A2.6-like G_protein-coupled_receptor_174 si:dkey-92i17.2
Danio_rerio cysteinyl_leukotriene_receptor_1 lysophosphatidic_acid_receptor_4 P2Y_receptor_family_member_10 uncharacterized_protein_K02A2.6-like G_protein-coupled_receptor_174 si:dkey-92i17.2
Etheostoma_spectabile integral_membrane_protein_2A-like G_protein-coupled_receptor_174 P2Y_receptor_family_member_10 lysophosphatidic_acid_receptor_4 uncharacterized_LOC116696505 cysteinyl_leukotriene_receptor_1 endothelin_receptor_type_B-like RNA_polymerase_I_and_III_subunit_D synaptobrevin-like_1 microtubule_associated_tumor_suppressor_1a platelet-derived_growth_factor_receptor-like
Pimephales_promelas sulfatase_1 solute_carrier_organic_anion_transporter_family_member_5A1 uncharacterized_si:ch211-51h4.2 TBL1X/Y_related_1a uncharacterized_LOC120475971 cysteinyl_leukotriene_receptor_1 lysophosphatidic_acid_receptor_4 P2Y_receptor_family_member_10 probable_G-protein_coupled_receptor_174 methyltransferase_like_15 kinesin_family_member_18A
However, I want these two to remain together in a single file such that it gives:
Danio_rerio tmem129 si:zfos-2326c3.2 il1rapl2 fam199x commd5 cysltr1 lpar4 p2ry10 LOC101883727 gpr174 si:dkey-92i17.2
Danio_rerio transmembrane_protein_129,_E3_ubiquitin_protein_ligase si:zfos-2326c3.2 interleukin_1_receptor_accessory_protein-like_2 family_with_sequence_similarity_199,_X-linked COMM_domain_containing_5 cysteinyl_leukotriene_receptor_1 lysophosphatidic_acid_receptor_4 P2Y_receptor_family_member_10 uncharacterized_protein_K02A2.6-like G_protein-coupled_receptor_174 si:dkey-92i17.2
Danio_rerio cysltr1 lpar4 p2ry10 LOC101883727 gpr174 si:dkey-92i17.2
Danio_rerio cysteinyl_leukotriene_receptor_1 lysophosphatidic_acid_receptor_4 P2Y_receptor_family_member_10 uncharacterized_protein_K02A2.6-like G_protein-coupled_receptor_174 si:dkey-92i17.2
Etheostoma_spectabile LOC116696506 gpr174 p2ry10 lpar4 LOC116696505 cysltr1 LOC116697110 polr1d sybl1 mtus1a pdgfrl
Etheostoma_spectabile integral_membrane_protein_2A-like G_protein-coupled_receptor_174 P2Y_receptor_family_member_10 lysophosphatidic_acid_receptor_4 uncharacterized_LOC116696505 cysteinyl_leukotriene_receptor_1 endothelin_receptor_type_B-like RNA_polymerase_I_and_III_subunit_D synaptobrevin-like_1 microtubule_associated_tumor_suppressor_1a platelet-derived_growth_factor_receptor-like
Pimephales_promelas sulf1 LOC120475969 si:ch211-51h4.2 tbl1xr1a zgc:113516 cysltr1 lpar4 p2ry10 LOC120475975 mettl15 kif18a
Pimephales_promelas sulfatase_1 solute_carrier_organic_anion_transporter_family_member_5A1 uncharacterized_si:ch211-51h4.2 TBL1X/Y_related_1a uncharacterized_LOC120475971 cysteinyl_leukotriene_receptor_1 lysophosphatidic_acid_receptor_4 P2Y_receptor_family_member_10 probable_G-protein_coupled_receptor_174 methyltransferase_like_15 kinesin_family_member_18A
Let me know in the comments in case of any doubt. Thank you in advance!
CodePudding user response：
Here is an awk that treats the same key as two blocks if separated by runs of #:
awk '
FNR==1{
f1=$1 OFS $2
f2=$1 OFS $3
next
}
/^#/ && last==$1{next}
/^[^#]/ && last=="#" {
printf("%s\n%s\n\n",f1,f2)
f1=f2=$1
}
{
f1=f1 OFS $2
f2=f2 OFS $3
last=$1
}
END{printf("%s\n%s\n",f1,f2)}
' file
Or with ruby it is easier to deal with runs of # as an additional data element to separate Danio_rerio into two separate blocks:
ruby -e 'blocks=$<.read.split(/^#[\s\S]*?(?=[^#\s])/m)
blocks.map{|s| s.split(/\r?\n/)}.
each{|sl|
tag=sl[0][/^\S /]
f1=sl.map{|ss| ss.split()[1]}.join("\t")
f2=sl.map{|ss| ss.split()[2]}.join("\t")
puts "#{tag}\t#{f1}\n#{tag}\t#{f2}\n\n" }
' file
Either prints:
Danio_rerio tmem129 si:zfos-2326c3.2 il1rapl2 fam199x commd5 cysltr1 lpar4 p2ry10 LOC101883727 gpr174 si:dkey-92i17.2
Danio_rerio transmembrane_protein_129,_E3_ubiquitin_protein_ligase si:zfos-2326c3.2 interleukin_1_receptor_accessory_protein-like_2 family_with_sequence_similarity_199,_X-linked COMM_domain_containing_5 cysteinyl_leukotriene_receptor_1 lysophosphatidic_acid_receptor_4 P2Y_receptor_family_member_10 uncharacterized_protein_K02A2.6-like G_protein-coupled_receptor_174 si:dkey-92i17.2
Danio_rerio cysltr1 lpar4 p2ry10 LOC101883727 gpr174 si:dkey-92i17.2
Danio_rerio cysteinyl_leukotriene_receptor_1 lysophosphatidic_acid_receptor_4 P2Y_receptor_family_member_10 uncharacterized_protein_K02A2.6-like G_protein-coupled_receptor_174 si:dkey-92i17.2
Etheostoma_spectabile LOC116696506 gpr174 p2ry10 lpar4 LOC116696505 cysltr1 LOC116697110 polr1d sybl1 mtus1a pdgfrl
Etheostoma_spectabile integral_membrane_protein_2A-like G_protein-coupled_receptor_174 P2Y_receptor_family_member_10 lysophosphatidic_acid_receptor_4 uncharacterized_LOC116696505 cysteinyl_leukotriene_receptor_1 endothelin_receptor_type_B-like RNA_polymerase_I_and_III_subunit_D synaptobrevin-like_1 microtubule_associated_tumor_suppressor_1a platelet-derived_growth_factor_receptor-like
Pimephales_promelas sulf1 LOC120475969 si:ch211-51h4.2 tbl1xr1a zgc:113516 cysltr1 lpar4 p2ry10 LOC120475975 mettl15 kif18a
Pimephales_promelas sulfatase_1 solute_carrier_organic_anion_transporter_family_member_5A1 uncharacterized_si:ch211-51h4.2 TBL1X/Y_related_1a uncharacterized_LOC120475971 cysteinyl_leukotriene_receptor_1 lysophosphatidic_acid_receptor_4 P2Y_receptor_family_member_10 probable_G-protein_coupled_receptor_174 methyltransferase_like_15 kinesin_family_member_18A