extracting organism count with thier corrosponding ID?Text file look-up by columnMerge two lists while...
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extracting organism count with thier corrosponding ID?
Text file look-up by columnMerge two lists while removing duplicatesSelect lines from text file which have ids listed in another fileHow to get the unique count of a particular part of a stringstream editing tools: output what's scrapedExtract data from csvHow to Wget images from CSV, append url and filenames from fields?Using Uniq -c with a regular expression or counting the number of lines removedconditional extracting a columnCounting instances in a variable, then reformatting rows/columns within bash script
.everyoneloves__top-leaderboard:empty,.everyoneloves__mid-leaderboard:empty,.everyoneloves__bot-mid-leaderboard:empty{ margin-bottom:0;
}
I have a file with many column like:
ID1 XP_026389348.1_stearoyl-[acyl-carrier-protein]_9-desaturase,_chloroplastic_[Papaver_somniferum]
ID2 XP_026389348.1_stearoyl-[acyl-carrier-protein]_9-desaturase,_chloroplastic_[Papaver_somniferum]
ID3 XP_026389348.1_stearoyl-[acyl-carrier-protein]_9-desaturase,_chloroplastic_[Papaver_somniferum]
ID4 XP_026389348.1_stearoyl-[acyl-carrier-protein]_9-desaturase,_chloroplastic_[Papaver_somniferum]
ID5 XP_026389348.1_stearoyl-[acyl-carrier-protein]_9-desaturase,_chloroplastic_[Papaver_somniferum]
ID6 XP_022013305.1_60S_ribosomal_protein_L36-2-like_[Helianthus_annuus]
ID7 XP_022033863.1_60S_ribosomal_protein_L36-2-like_[Helianthus_annuus]
ID8 XP_022033864.1_60S_ribosomal_protein_L36-2-like_[Helianthus_annuus]
ID9 XP_022033865.1_60S_ribosomal_protein_L36-2-like_[Helianthus_annuus]
ID10 NP_850400.1_Plant_stearoyl-acyl-carrier-protein_desaturase_family_protein_[Arabidopsis_thaliana]
ID11 XP_015383392.1_60S_ribosomal_protein_L36-3-like_[Citrus_sinensis]
ID12 XP_015383392.1_60S_ribosomal_protein_L36-3-like_[Citrus_sinensis]
ID13 XP_019051818.1_PREDICTED:_stearoyl-[acyl-carrier-protein]_9-desaturase,_chloroplastic_isoform_X2_[Nelumbo_nucifera]
ID14 XP_019051818.1_PREDICTED:_stearoyl-[acyl-carrier-protein]_9-desaturase,_chloroplastic_isoform_X2_[Nelumbo_nucifera]
ID15 XP_019051818.1_PREDICTED:_stearoyl-[acyl-carrier-protein]_9-desaturase,_chloroplastic_isoform_X2_[Nelumbo_nucifera]
ID16 XP_021982111.1_stearoyl-[acyl-carrier-protein]_9-desaturase,_chloroplastic_[Helianthus_annuus]
ID17 NP_001150213.1_uncharacterized_protein_LOC100283843_[Zea_mays]
ID18 XP_027164486.1_stearoyl-[acyl-carrier-protein]_9-desaturase,_chloroplastic_[Coffea_eugenioides]
ID19 XP_009419937.1_PREDICTED:_60S_ribosomal_protein_L36-3-like_[Musa_acuminata]
ID20 XP_020267482.1_60S_ribosomal_protein_L36-2-like_[Asparagus_officinalis]
i want to extract organism name from 2nd column in [ ] , and count them with their respective IDs like :
5 Papaver somniferum ID1
ID2
ID3
ID4
ID5
4 Helianthus annuus ID6
ID7
ID8
ID9
1 Arabidopsis thaliana ID10
2 Citrus sinensis ID11
ID12
3 Nelumbo nucifera ID13
ID14
ID15
1 Helianthus annuus ID16
1 Zea mays ID17
1 Coffea eugenioides ID18
1 Musa acuminata ID19
1 Asparagus officinalis ID20
I have tried something :
cat file | cut -f2 | rev |awk -F "[" '{gsub("]", "");print $1 | "rev"}' | sed '/#/d' | sort |uniq -c| sort -nr
which gives the output:
5 Papaver somniferum
4 Helianthus annuus
1 Arabidopsis thaliana
2 Citrus sinensis
3 Nelumbo nucifera
1 Helianthus annuus
1 Zea mays
1 Coffea eugenioides
1 Musa acuminata
1 Asparagus officinalis
Thankyou.
bash shell ubuntu bioinformatics
edited 24 mins ago
Kusalananda♦
162k18 gold badges320 silver badges506 bronze badges
asked 1 hour ago
Anjali ChaudharyAnjali Chaudhary
153 bronze badges
add a comment |
I have a file with many column like:
ID1 XP_026389348.1_stearoyl-[acyl-carrier-protein]_9-desaturase,_chloroplastic_[Papaver_somniferum]
ID2 XP_026389348.1_stearoyl-[acyl-carrier-protein]_9-desaturase,_chloroplastic_[Papaver_somniferum]
ID3 XP_026389348.1_stearoyl-[acyl-carrier-protein]_9-desaturase,_chloroplastic_[Papaver_somniferum]
ID4 XP_026389348.1_stearoyl-[acyl-carrier-protein]_9-desaturase,_chloroplastic_[Papaver_somniferum]
ID5 XP_026389348.1_stearoyl-[acyl-carrier-protein]_9-desaturase,_chloroplastic_[Papaver_somniferum]
ID6 XP_022013305.1_60S_ribosomal_protein_L36-2-like_[Helianthus_annuus]
ID7 XP_022033863.1_60S_ribosomal_protein_L36-2-like_[Helianthus_annuus]
ID8 XP_022033864.1_60S_ribosomal_protein_L36-2-like_[Helianthus_annuus]
ID9 XP_022033865.1_60S_ribosomal_protein_L36-2-like_[Helianthus_annuus]
ID10 NP_850400.1_Plant_stearoyl-acyl-carrier-protein_desaturase_family_protein_[Arabidopsis_thaliana]
ID11 XP_015383392.1_60S_ribosomal_protein_L36-3-like_[Citrus_sinensis]
ID12 XP_015383392.1_60S_ribosomal_protein_L36-3-like_[Citrus_sinensis]
ID13 XP_019051818.1_PREDICTED:_stearoyl-[acyl-carrier-protein]_9-desaturase,_chloroplastic_isoform_X2_[Nelumbo_nucifera]
ID14 XP_019051818.1_PREDICTED:_stearoyl-[acyl-carrier-protein]_9-desaturase,_chloroplastic_isoform_X2_[Nelumbo_nucifera]
ID15 XP_019051818.1_PREDICTED:_stearoyl-[acyl-carrier-protein]_9-desaturase,_chloroplastic_isoform_X2_[Nelumbo_nucifera]
ID16 XP_021982111.1_stearoyl-[acyl-carrier-protein]_9-desaturase,_chloroplastic_[Helianthus_annuus]
ID17 NP_001150213.1_uncharacterized_protein_LOC100283843_[Zea_mays]
ID18 XP_027164486.1_stearoyl-[acyl-carrier-protein]_9-desaturase,_chloroplastic_[Coffea_eugenioides]
ID19 XP_009419937.1_PREDICTED:_60S_ribosomal_protein_L36-3-like_[Musa_acuminata]
ID20 XP_020267482.1_60S_ribosomal_protein_L36-2-like_[Asparagus_officinalis]
i want to extract organism name from 2nd column in [ ] , and count them with their respective IDs like :
5 Papaver somniferum ID1
ID2
ID3
ID4
ID5
4 Helianthus annuus ID6
ID7
ID8
ID9
1 Arabidopsis thaliana ID10
2 Citrus sinensis ID11
ID12
3 Nelumbo nucifera ID13
ID14
ID15
1 Helianthus annuus ID16
1 Zea mays ID17
1 Coffea eugenioides ID18
1 Musa acuminata ID19
1 Asparagus officinalis ID20
I have tried something :
cat file | cut -f2 | rev |awk -F "[" '{gsub("]", "");print $1 | "rev"}' | sed '/#/d' | sort |uniq -c| sort -nr
which gives the output:
5 Papaver somniferum
4 Helianthus annuus
1 Arabidopsis thaliana
2 Citrus sinensis
3 Nelumbo nucifera
1 Helianthus annuus
1 Zea mays
1 Coffea eugenioides
1 Musa acuminata
1 Asparagus officinalis
Thankyou.
bash shell ubuntu bioinformatics
edited 24 mins ago
Kusalananda♦
162k18 gold badges320 silver badges506 bronze badges
asked 1 hour ago
Anjali ChaudharyAnjali Chaudhary
153 bronze badges
add a comment |
I have a file with many column like:
ID1 XP_026389348.1_stearoyl-[acyl-carrier-protein]_9-desaturase,_chloroplastic_[Papaver_somniferum]
ID2 XP_026389348.1_stearoyl-[acyl-carrier-protein]_9-desaturase,_chloroplastic_[Papaver_somniferum]
ID3 XP_026389348.1_stearoyl-[acyl-carrier-protein]_9-desaturase,_chloroplastic_[Papaver_somniferum]
ID4 XP_026389348.1_stearoyl-[acyl-carrier-protein]_9-desaturase,_chloroplastic_[Papaver_somniferum]
ID5 XP_026389348.1_stearoyl-[acyl-carrier-protein]_9-desaturase,_chloroplastic_[Papaver_somniferum]
ID6 XP_022013305.1_60S_ribosomal_protein_L36-2-like_[Helianthus_annuus]
ID7 XP_022033863.1_60S_ribosomal_protein_L36-2-like_[Helianthus_annuus]
ID8 XP_022033864.1_60S_ribosomal_protein_L36-2-like_[Helianthus_annuus]
ID9 XP_022033865.1_60S_ribosomal_protein_L36-2-like_[Helianthus_annuus]
ID10 NP_850400.1_Plant_stearoyl-acyl-carrier-protein_desaturase_family_protein_[Arabidopsis_thaliana]
ID11 XP_015383392.1_60S_ribosomal_protein_L36-3-like_[Citrus_sinensis]
ID12 XP_015383392.1_60S_ribosomal_protein_L36-3-like_[Citrus_sinensis]
ID13 XP_019051818.1_PREDICTED:_stearoyl-[acyl-carrier-protein]_9-desaturase,_chloroplastic_isoform_X2_[Nelumbo_nucifera]
ID14 XP_019051818.1_PREDICTED:_stearoyl-[acyl-carrier-protein]_9-desaturase,_chloroplastic_isoform_X2_[Nelumbo_nucifera]
ID15 XP_019051818.1_PREDICTED:_stearoyl-[acyl-carrier-protein]_9-desaturase,_chloroplastic_isoform_X2_[Nelumbo_nucifera]
ID16 XP_021982111.1_stearoyl-[acyl-carrier-protein]_9-desaturase,_chloroplastic_[Helianthus_annuus]
ID17 NP_001150213.1_uncharacterized_protein_LOC100283843_[Zea_mays]
ID18 XP_027164486.1_stearoyl-[acyl-carrier-protein]_9-desaturase,_chloroplastic_[Coffea_eugenioides]
ID19 XP_009419937.1_PREDICTED:_60S_ribosomal_protein_L36-3-like_[Musa_acuminata]
ID20 XP_020267482.1_60S_ribosomal_protein_L36-2-like_[Asparagus_officinalis]
i want to extract organism name from 2nd column in [ ] , and count them with their respective IDs like :
5 Papaver somniferum ID1
ID2
ID3
ID4
ID5
4 Helianthus annuus ID6
ID7
ID8
ID9
1 Arabidopsis thaliana ID10
2 Citrus sinensis ID11
ID12
3 Nelumbo nucifera ID13
ID14
ID15
1 Helianthus annuus ID16
1 Zea mays ID17
1 Coffea eugenioides ID18
1 Musa acuminata ID19
1 Asparagus officinalis ID20
I have tried something :
cat file | cut -f2 | rev |awk -F "[" '{gsub("]", "");print $1 | "rev"}' | sed '/#/d' | sort |uniq -c| sort -nr
which gives the output:
5 Papaver somniferum
4 Helianthus annuus
1 Arabidopsis thaliana
2 Citrus sinensis
3 Nelumbo nucifera
1 Helianthus annuus
1 Zea mays
1 Coffea eugenioides
1 Musa acuminata
1 Asparagus officinalis
Thankyou.
bash shell ubuntu bioinformatics
edited 24 mins ago
Kusalananda♦
162k18 gold badges320 silver badges506 bronze badges
asked 1 hour ago
Anjali ChaudharyAnjali Chaudhary
153 bronze badges
I have a file with many column like:
ID1 XP_026389348.1_stearoyl-[acyl-carrier-protein]_9-desaturase,_chloroplastic_[Papaver_somniferum]
ID2 XP_026389348.1_stearoyl-[acyl-carrier-protein]_9-desaturase,_chloroplastic_[Papaver_somniferum]
ID3 XP_026389348.1_stearoyl-[acyl-carrier-protein]_9-desaturase,_chloroplastic_[Papaver_somniferum]
ID4 XP_026389348.1_stearoyl-[acyl-carrier-protein]_9-desaturase,_chloroplastic_[Papaver_somniferum]
ID5 XP_026389348.1_stearoyl-[acyl-carrier-protein]_9-desaturase,_chloroplastic_[Papaver_somniferum]
ID6 XP_022013305.1_60S_ribosomal_protein_L36-2-like_[Helianthus_annuus]
ID7 XP_022033863.1_60S_ribosomal_protein_L36-2-like_[Helianthus_annuus]
ID8 XP_022033864.1_60S_ribosomal_protein_L36-2-like_[Helianthus_annuus]
ID9 XP_022033865.1_60S_ribosomal_protein_L36-2-like_[Helianthus_annuus]
ID10 NP_850400.1_Plant_stearoyl-acyl-carrier-protein_desaturase_family_protein_[Arabidopsis_thaliana]
ID11 XP_015383392.1_60S_ribosomal_protein_L36-3-like_[Citrus_sinensis]
ID12 XP_015383392.1_60S_ribosomal_protein_L36-3-like_[Citrus_sinensis]
ID13 XP_019051818.1_PREDICTED:_stearoyl-[acyl-carrier-protein]_9-desaturase,_chloroplastic_isoform_X2_[Nelumbo_nucifera]
ID14 XP_019051818.1_PREDICTED:_stearoyl-[acyl-carrier-protein]_9-desaturase,_chloroplastic_isoform_X2_[Nelumbo_nucifera]
ID15 XP_019051818.1_PREDICTED:_stearoyl-[acyl-carrier-protein]_9-desaturase,_chloroplastic_isoform_X2_[Nelumbo_nucifera]
ID16 XP_021982111.1_stearoyl-[acyl-carrier-protein]_9-desaturase,_chloroplastic_[Helianthus_annuus]
ID17 NP_001150213.1_uncharacterized_protein_LOC100283843_[Zea_mays]
ID18 XP_027164486.1_stearoyl-[acyl-carrier-protein]_9-desaturase,_chloroplastic_[Coffea_eugenioides]
ID19 XP_009419937.1_PREDICTED:_60S_ribosomal_protein_L36-3-like_[Musa_acuminata]
ID20 XP_020267482.1_60S_ribosomal_protein_L36-2-like_[Asparagus_officinalis]
i want to extract organism name from 2nd column in [ ] , and count them with their respective IDs like :
5 Papaver somniferum ID1
ID2
ID3
ID4
ID5
4 Helianthus annuus ID6
ID7
ID8
ID9
1 Arabidopsis thaliana ID10
2 Citrus sinensis ID11
ID12
3 Nelumbo nucifera ID13
ID14
ID15
1 Helianthus annuus ID16
1 Zea mays ID17
1 Coffea eugenioides ID18
1 Musa acuminata ID19
1 Asparagus officinalis ID20
I have tried something :
cat file | cut -f2 | rev |awk -F "[" '{gsub("]", "");print $1 | "rev"}' | sed '/#/d' | sort |uniq -c| sort -nr
which gives the output:
5 Papaver somniferum
4 Helianthus annuus
1 Arabidopsis thaliana
2 Citrus sinensis
3 Nelumbo nucifera
1 Helianthus annuus
1 Zea mays
1 Coffea eugenioides
1 Musa acuminata
1 Asparagus officinalis
Thankyou.
bash shell ubuntu bioinformatics
bash shell ubuntu bioinformatics
edited 24 mins ago
Kusalananda♦
162k18 gold badges320 silver badges506 bronze badges
asked 1 hour ago
Anjali ChaudharyAnjali Chaudhary
153 bronze badges
edited 24 mins ago
Kusalananda♦
162k18 gold badges320 silver badges506 bronze badges
asked 1 hour ago
Anjali ChaudharyAnjali Chaudhary
153 bronze badges
edited 24 mins ago
Kusalananda♦
162k18 gold badges320 silver badges506 bronze badges
edited 24 mins ago
Kusalananda♦
162k18 gold badges320 silver badges506 bronze badges
edited 24 mins ago
Kusalananda♦
162k18 gold badges320 silver badges506 bronze badges
162k18 gold badges320 silver badges506 bronze badges
asked 1 hour ago
Anjali ChaudharyAnjali Chaudhary
153 bronze badges
asked 1 hour ago
Anjali ChaudharyAnjali Chaudhary
153 bronze badges
asked 1 hour ago
Anjali ChaudharyAnjali Chaudhary
153 bronze badges
153 bronze badges
add a comment |
add a comment |
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