get.oturep sequence names

Commands in mothur
1

Hello,

I’m trying to use get.oturep to recover fasta sequences for my OTUs for use with Arb. However, the fasta file output ends up with these enormous names, and I’m wondering if there’s a simple way to get rid of them; specifically, everything past the OTU number and counts. Example:

MISEQ_31_000000000-AW0EW_1_1101_19671_15407 Otu000001|235327|JP_V4_PCRneg-N10_V4_JP_C_F-N10_V4_JP_D_F-N11_V4_JP_CH_M-N11_V4_JP_C_M-N11_V4_JP_D_M-N11_V4_JP_V_M-N12_V4_JP_CH_M-N12_V4_JP_C_M-N12_V4_JP_D_M-N12_V4_JP_V_M-N13_V4_JP_CH_M-N13_V4_JP_C_M-N13_V4_JP_D_M-N13_V4_JP_V_M-N13_V4_PF_C-N13_V4_PF_CH-N13_V4_PF_V-N14_V4_PF_C-N15_V4_JP_CH_M-N15_V4_JP_C_M-N15_V4_JP_D_M-N15_V4_JP_V_M-N15_V4_PF_CH-N16_V4_JP_C_M-N16_V4_JP_D_M-N16_V4_JP_V_M-N16_V4_PF_C-N16_V4_PF_V-N17_V4_JP_CH_M-N17_V4_JP_C_M-N17_V4_JP_D_M-N17_V4_JP_V_M-N17_V4_PF_C-N17_V4_PF_CH-N17_V4_PF_V-N18_V4_JP_CH_M-N18_V4_JP_C_M-N18_V4_JP_D_M-N19_V4_JP_CH_M-N19_V4_JP_C_M-N19_V4_JP_D_M-N19_V4_JP_V_M-N1_V4_JP_CH_F-N1_V4_JP_C_F-N1_V4_JP_D_F-N1_V4_JP_V_F-N20_V4_JP_CH_M-N20_V4_JP_C_M-N20_V4_JP_D_M-N20_V4_JP_V_M-N21_V4_JP_CH_M-N21_V4_JP_C_M-N21_V4_JP_D_M-N21_V4_JP_V_M-N22_V4_JP_CH_M-N22_V4_JP_C_M-N22_V4_JP_V_M-N2_V4_JP_CH_F-N2_V4_JP_C_F-N2_V4_JP_V_F-N3_V4_JP_CH_F-N3_V4_JP_D_F-N3_V4_JP_V_F-N4_V4_JP_CH_F-N4_V4_JP_C_F-N4_V4_JP_D_F-N4_V4_JP_V_F-N5_V4_JP_CH_F-N5_V4_JP_C_F-N5_V4_JP_V_F-N6_V4_JP_CH_F-N6_V4_JP_C_F-N6_V4_JP_D_F-N6_V4_JP_V_F-N7_V4_JP_CH_F-N7_V4_JP_C_F-N7_V4_JP_D_F-N7_V4_JP_V_F-N7_V4_PF_C-N7_V4_PF_V-N8_V4_JP_CH_F-N8_V4_JP_C_F-N8_V4_JP_D_F-N8_V4_JP_V_F-N8_V4_PF_CH-N8_V4_PF_D-N8_V4_PF_V-N9_V4_JP_CH_F-N9_V4_JP_C_F-N9_V4_JP_D_F-N9_V4_JP_V_F-N9_V4_PF_C-Soil_V4_JP
TAC–GT-AG-GGT----GCG-A-G–C–G–T-T–AA-T-CGG-AA—TT-A–C-T–GG-GC—GT–A–AA-GC-GT-GC----G-CA-G-G-C-G—G–T-TA-T-A-T------AA–G-T-C-A----G-A-T–G–TG–A-AA-TC–C-C-CG-G-G—CT-C-AA----------------C-C-T-G-G-G-A–C-C—T-G–C-A–T-T—T–GA-G-A–C–T–G-T–AT–A-G-C-----------------------------------------------------------------T-A-G-A-G-T–A-----C-GG----TA-G-A–G-G-G-G—GA-T------GG–A–ATT-----C-C-G-C-GT–GT-A-G-CA-GT-G–A-A-A—TG-C-GT-AG–AT-A-TG--------C-G—G-A–G-G-A-AC-A-CC-----GA–T–G–GC-GAA-G–G-C—A------A–T-C-C-C—CTG–G–AC-C-T------G-T-----A-C-T–GA–CG-C—T-C–A-TG–C-A-CG-A–AA-G-C----G-TG–GG-G–AG-C-A-AA-CAGG
MISEQ_31_000000000-AW0EW_1_1113_4167_9419 Otu000002|226099|JP_V4_PCRneg-N10_V4_JP_C_F-N10_V4_JP_D_F-N10_V4_PF_C-N10_V4_PF_CH-N10_V4_PF_D-N10_V4_PF_V-N11_V4_JP_CH_M-N11_V4_JP_C_M-N11_V4_JP_D_M-N11_V4_JP_V_M-N11_V4_PF_C-N11_V4_PF_CH-N11_V4_PF_D-N11_V4_PF_V-N12_V4_JP_CH_M-N12_V4_JP_C_M-N12_V4_JP_D_M-N12_V4_JP_V_M-N12_V4_PF_C-N12_V4_PF_CH-N12_V4_PF_D-N12_V4_PF_V-N13_V4_JP_CH_M-N13_V4_JP_C_M-N13_V4_JP_D_M-N13_V4_JP_V_M-N13_V4_PF_C-N13_V4_PF_CH-N13_V4_PF_D-N13_V4_PF_V-N14_V4_JP_CH_M-N14_V4_JP_C_M-N14_V4_JP_D_M-N14_V4_JP_V_M-N14_V4_PF_C-N14_V4_PF_CH-N15_V4_JP_CH_M-N15_V4_JP_C_M-N15_V4_JP_D_M-N15_V4_JP_V_M-N15_V4_PF_C-N15_V4_PF_CH-N15_V4_PF_D-N15_V4_PF_V-N16_V4_JP_C_M-N16_V4_JP_D_M-N16_V4_JP_V_M-N16_V4_PF_C-N16_V4_PF_CH-N16_V4_PF_D-N16_V4_PF_V-N17_V4_JP_CH_M-N17_V4_JP_C_M-N17_V4_JP_D_M-N17_V4_JP_V_M-N17_V4_PF_C-N17_V4_PF_CH-N17_V4_PF_D-N17_V4_PF_V-N18_V4_JP_CH_M-N18_V4_JP_C_M-N18_V4_JP_D_M-N18_V4_PF_C-N18_V4_PF_CH-N18_V4_PF_D-N18_V4_PF_V-N19_V4_JP_CH_M-N19_V4_JP_C_M-N19_V4_JP_D_M-N19_V4_JP_V_M-N1_V4_JP_CH_F-N1_V4_JP_C_F-N1_V4_JP_D_F-N1_V4_JP_V_F-N1_V4_PF_C-N1_V4_PF_CH-N1_V4_PF_D-N1_V4_PF_V-N20_V4_JP_CH_M-N20_V4_JP_C_M-N20_V4_JP_D_M-N20_V4_JP_V_M-N21_V4_JP_CH_M-N21_V4_JP_C_M-N21_V4_JP_D_M-N21_V4_JP_V_M-N22_V4_JP_CH_M-N22_V4_JP_C_M-N22_V4_JP_V_M-N2_V4_JP_CH_F-N2_V4_JP_C_F-N2_V4_JP_V_F-N2_V4_PF_C-N2_V4_PF_CH-N2_V4_PF_D-N2_V4_PF_V-N3_V4_JP_CH_F-N3_V4_JP_D_F-N3_V4_JP_V_F-N3_V4_PF_C-N3_V4_PF_D-N3_V4_PF_V-N4_V4_JP_CH_F-N4_V4_JP_C_F-N4_V4_JP_D_F-N4_V4_JP_V_F-N4_V4_PF_C-N4_V4_PF_CH-N4_V4_PF_D-N5_V4_JP_CH_F-N5_V4_JP_C_F-N5_V4_JP_V_F-N5_V4_PF_C-N5_V4_PF_CH-N5_V4_PF_D-N5_V4_PF_V-N6_V4_JP_CH_F-N6_V4_JP_C_F-N6_V4_JP_D_F-N6_V4_JP_V_F-N6_V4_PF_C-N6_V4_PF_CH-N6_V4_PF_D-N7_V4_JP_CH_F-N7_V4_JP_C_F-N7_V4_JP_D_F-N7_V4_JP_V_F-N7_V4_PF_C-N7_V4_PF_CH-N7_V4_PF_D-N7_V4_PF_V-N8_V4_JP_CH_F-N8_V4_JP_C_F-N8_V4_JP_D_F-N8_V4_JP_V_F-N8_V4_PF_C-N8_V4_PF_CH-N8_V4_PF_V-N9_V4_JP_CH_F-N9_V4_JP_C_F-N9_V4_JP_D_F-N9_V4_JP_V_F-N9_V4_PF_C-N9_V4_PF_CH-N9_V4_PF_D-N9_V4_PF_V-Neg17_18_V4_PF-Neg1_V4_PF-Neg2_V4_PF-Soil_V4_JP-Soil_V4_PF-Water_V4_PF
TAC–GG-AG-GGT----GCA-A-G–C–G–T-T–AT-C-CGG-AT—TT-A–T-T–GG-GT—TT–A–AA-GG-GT-CC----G-TA-G-G-C-G—G–G-CT-A-G-T------AA–G-T-C-A----G-T-G–G–TG–A-AA-TC–T-C-GA-T-G—CT-T-AA----------------C-A-T-C-G-A-A–A-C—T-G–C-C–A-T—T–GA-T-A–C–T–G-C–TA–G-C-C-----------------------------------------------------------------T-T-G-A-G-T–A-----A-GG----TA-G-A–G-G-T-A—GC-T------GG–A–ATA-----A-G-T-A-GT–GT-A-G-CG-GT-G–A-A-A—TG-C-AT-AG–AT-A-TT--------A-C—T-T–A-G-A-AC-A-CC-----AA–T–T–GC-GAA-G–G-C—A------G–G-T-T-A—CCA–T–GT-C-T------T-A-----A-C-T–GA–CG-C—T-G–A-GG–G-A-CG-A–AA-G-C----G-TG–GG-G–AG-C-G-AA-CAGG
MISEQ_31_000000000-AW0EW_1_1102_10783_24000 Otu000003|114487|JP_V4_PCRneg-N10_V4_JP_C_F-N10_V4_JP_D_F-N10_V4_PF_C-N10_V4_PF_CH-N10_V4_PF_D-N10_V4_PF_V-N11_V4_JP_CH_M-N11_V4_JP_C_M-N11_V4_JP_D_M-N11_V4_JP_V_M-N11_V4_PF_C-N11_V4_PF_CH-N11_V4_PF_D-N11_V4_PF_V-N12_V4_JP_CH_M-N12_V4_JP_C_M-N12_V4_JP_D_M-N12_V4_JP_V_M-N12_V4_PF_C-N12_V4_PF_CH-N12_V4_PF_D-N12_V4_PF_V-N13_V4_JP_CH_M-N13_V4_JP_C_M-N13_V4_JP_D_M-N13_V4_JP_V_M-N13_V4_PF_C-N13_V4_PF_CH-N13_V4_PF_D-N13_V4_PF_V-N14_V4_JP_CH_M-N14_V4_JP_C_M-N14_V4_JP_V_M-N14_V4_PF_C-N14_V4_PF_CH-N14_V4_PF_D-N14_V4_PF_V-N15_V4_JP_CH_M-N15_V4_JP_C_M-N15_V4_JP_D_M-N15_V4_JP_V_M-N15_V4_PF_C-N15_V4_PF_CH-N15_V4_PF_D-N15_V4_PF_V-N16_V4_JP_C_M-N16_V4_JP_D_M-N16_V4_JP_V_M-N16_V4_PF_C-N16_V4_PF_CH-N16_V4_PF_D-N16_V4_PF_V-N17_V4_JP_CH_M-N17_V4_JP_C_M-N17_V4_JP_D_M-N17_V4_JP_V_M-N17_V4_PF_C-N17_V4_PF_CH-N17_V4_PF_D-N17_V4_PF_V-N18_V4_JP_CH_M-N18_V4_JP_C_M-N18_V4_JP_D_M-N18_V4_PF_C-N18_V4_PF_CH-N18_V4_PF_D-N18_V4_PF_V-N19_V4_JP_CH_M-N19_V4_JP_C_M-N19_V4_JP_D_M-N19_V4_JP_V_M-N1_V4_JP_CH_F-N1_V4_JP_C_F-N1_V4_JP_D_F-N1_V4_JP_V_F-N1_V4_PF_C-N1_V4_PF_CH-N1_V4_PF_D-N1_V4_PF_V-N20_V4_JP_CH_M-N20_V4_JP_C_M-N20_V4_JP_D_M-N20_V4_JP_V_M-N21_V4_JP_CH_M-N21_V4_JP_C_M-N21_V4_JP_D_M-N21_V4_JP_V_M-N22_V4_JP_CH_M-N22_V4_JP_C_M-N22_V4_JP_V_M-N2_V4_JP_CH_F-N2_V4_JP_C_F-N2_V4_JP_V_F-N2_V4_PF_C-N2_V4_PF_CH-N2_V4_PF_D-N2_V4_PF_V-N3_V4_JP_CH_F-N3_V4_JP_D_F-N3_V4_JP_V_F-N3_V4_PF_C-N3_V4_PF_D-N3_V4_PF_V-N4_V4_JP_CH_F-N4_V4_JP_C_F-N4_V4_JP_D_F-N4_V4_JP_V_F-N4_V4_PF_C-N4_V4_PF_CH-N4_V4_PF_D-N5_V4_JP_CH_F-N5_V4_JP_C_F-N5_V4_JP_V_F-N5_V4_PF_C-N5_V4_PF_CH-N5_V4_PF_D-N5_V4_PF_V-N6_V4_JP_CH_F-N6_V4_JP_C_F-N6_V4_JP_D_F-N6_V4_JP_V_F-N6_V4_PF_C-N6_V4_PF_CH-N6_V4_PF_D-N6_V4_PF_V-N7_V4_JP_CH_F-N7_V4_JP_C_F-N7_V4_JP_D_F-N7_V4_JP_V_F-N7_V4_PF_C-N7_V4_PF_CH-N7_V4_PF_D-N7_V4_PF_V-N8_V4_JP_CH_F-N8_V4_JP_C_F-N8_V4_JP_D_F-N8_V4_JP_V_F-N8_V4_PF_C-N8_V4_PF_CH-N8_V4_PF_D-N8_V4_PF_V-N9_V4_JP_CH_F-N9_V4_JP_C_F-N9_V4_JP_D_F-N9_V4_JP_V_F-N9_V4_PF_C-N9_V4_PF_CH-N9_V4_PF_D-N9_V4_PF_V-Neg11_13_V4_PF-Neg1_V4_PF-Neg5_7_V4_PF-Neg8_10_V4_PF-Soil_V4_JP-Soil_V4_PF
TAC–GT-AG-GGT----GCA-A-G–C–G–T-T–AA-T-CGG-AA—TT-A–C-T–GG-GC—GT–A–AA-GC-GT-GC----G-CA-G-G-C-G—G–C-TT-T-G-C------AA–G-A-C-A----G-A-T–G–TG–A-AA-TC–C-C-CG-G-G—CT-C-AA----------------C-C-T-G-G-G-A–A-C—T-G–C-A–T-T—T–GT-G-A–C–T–G-C–AA–G-G-C-----------------------------------------------------------------T-A-G-A-G-T–A-----C-GG----TA-G-A–G-G-G-G—AG-T------GG–A–ATT-----C-C-G-C-GT–GT-A-G-CA-GT-G–A-A-A—TG-C-GT-AG–AT-A-TG--------C-G—G-A–G-G-A-AC-A-CC-----GA–T–G–GC-GAA-G–G-C—A------G–C-T-C-C—CTG–G–AC-C-T------G-T-----A-C-T–GA–CG-C—T-C–A-TG–C-A-CG-A–AA-G-C----G-TG–GG-G–AG-C-A-AA-CAGG

Thank you,
Patric

2

If you’re using a Linux/Mac computer, you could just use the cut command on the terminal:

cut -f1 input.fasta > outut.fasta
3

This worked very well. Thank you. I added -d"|" flag so I could keep the OTU number, and used “sed” to replace the tab with “_” in the name.

From the terminal:

mothur get.oturep(column=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.dist, list=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.an.unique_list.list, fasta=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta, count=stability.count_table)

Output (with names for my actual samples, not stability.names):

MISEQ_31_000000000-AW0EW_1_1101_19671_15407 Otu000001|235327|JP_V4_PCRneg-N10_V4_JP_C_F-N10_V4_JP_D_F-N11_V4_JP_CH_M-N11_V4_JP_C_M-N11_V4_JP_D_M-N11_V4_JP_V_M-N12_V4_JP_CH_M-N12_V4_JP_C_M-N12_V4_JP_D_M-N12_V4_JP_V_M-N13_V4_JP_CH_M-N13_V4_JP_C_M-N13_V4_JP_D_M-N13_V4_JP_V_M-N13_V4_PF_C-N13_V4_PF_CH-N13_V4_PF_V-N14_V4_PF_C-N15_V4_JP_CH_M-N15_V4_JP_C_M-N15_V4_JP_D_M-N15_V4_JP_V_M-N15_V4_PF_CH-N16_V4_JP_C_M-N16_V4_JP_D_M-N16_V4_JP_V_M-N16_V4_PF_C-N16_V4_PF_V-N17_V4_JP_CH_M-N17_V4_JP_C_M-N17_V4_JP_D_M-N17_V4_JP_V_M-N17_V4_PF_C-N17_V4_PF_CH-N17_V4_PF_V-N18_V4_JP_CH_M-N18_V4_JP_C_M-N18_V4_JP_D_M-N19_V4_JP_CH_M-N19_V4_JP_C_M-N19_V4_JP_D_M-N19_V4_JP_V_M-N1_V4_JP_CH_F-N1_V4_JP_C_F-N1_V4_JP_D_F-N1_V4_JP_V_F-N20_V4_JP_CH_M-N20_V4_JP_C_M-N20_V4_JP_D_M-N20_V4_JP_V_M-N21_V4_JP_CH_M-N21_V4_JP_C_M-N21_V4_JP_D_M-N21_V4_JP_V_M-N22_V4_JP_CH_M-N22_V4_JP_C_M-N22_V4_JP_V_M-N2_V4_JP_CH_F-N2_V4_JP_C_F-N2_V4_JP_V_F-N3_V4_JP_CH_F-N3_V4_JP_D_F-N3_V4_JP_V_F-N4_V4_JP_CH_F-N4_V4_JP_C_F-N4_V4_JP_D_F-N4_V4_JP_V_F-N5_V4_JP_CH_F-N5_V4_JP_C_F-N5_V4_JP_V_F-N6_V4_JP_CH_F-N6_V4_JP_C_F-N6_V4_JP_D_F-N6_V4_JP_V_F-N7_V4_JP_CH_F-N7_V4_JP_C_F-N7_V4_JP_D_F-N7_V4_JP_V_F-N7_V4_PF_C-N7_V4_PF_V-N8_V4_JP_CH_F-N8_V4_JP_C_F-N8_V4_JP_D_F-N8_V4_JP_V_F-N8_V4_PF_CH-N8_V4_PF_D-N8_V4_PF_V-N9_V4_JP_CH_F-N9_V4_JP_C_F-N9_V4_JP_D_F-N9_V4_JP_V_F-N9_V4_PF_C-Soil_V4_JP
TAC–GT-AG-GGT----GCG-A-G–C–G–T-T–AA-T-CGG-AA—TT-A–C-T–GG-GC—GT–A–AA-GC-GT-GC----G-CA-G-G-C-G—G–T-TA-T-A-T------AA–G-T-C-A----G-A-T–G–TG–A-AA-TC–C-C-CG-G-G—CT-C-AA----------------C-C-T-G-G-G-A–C-C—T-G–C-A–T-T—T–GA-G-A–C–T–G-T–AT–A-G-C-----------------------------------------------------------------T-A-G-A-G-T–A-----C-GG----TA-G-A–G-G-G-G—GA-T------GG–A–ATT-----C-C-G-C-GT–GT-A-G-CA-GT-G–A-A-A—TG-C-GT-AG–AT-A-TG--------C-G—G-A–G-G-A-AC-A-CC-----GA–T–G–GC-GAA-G–G-C—A------A–T-C-C-C—CTG–G–AC-C-T------G-T-----A-C-T–GA–CG-C—T-C–A-TG–C-A-CG-A–AA-G-C----G-TG–GG-G–AG-C-A-AA-CAGG

mv stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.an.unique_list.unique.rep.fasta stability.repOTU.fasta
cut -d"|" -f1 stability.repOTU.fasta > stability.repOTU.output.fasta
head stability.repOTU.output.fasta

MISEQ_31_000000000-AW0EW_1_1101_19671_15407 Otu000001
TAC–GT-AG-GGT----GCG-A-G–C–G–T-T–AA-T-CGG-AA—TT-A–C-T–GG-GC—GT–A–AA-GC-GT-GC----G-CA-G-G-C-G—G–T-TA-T-A-T------AA–G-T-C-A----G-A-T–G–TG–A-AA-TC–C-C-CG-G-G—CT-C-AA----------------C-C-T-G-G-G-A–C-C—T-G–C-A–T-T—T–GA-G-A–C–T–G-T–AT–A-G-C-----------------------------------------------------------------T-A-G-A-G-T–A-----C-GG----TA-G-A–G-G-G-G—GA-T------GG–A–ATT-----C-C-G-C-GT–GT-A-G-CA-GT-G–A-A-A—TG-C-GT-AG–AT-A-TG--------C-G—G-A–G-G-A-AC-A-CC-----GA–T–G–GC-GAA-G–G-C—A------A–T-C-C-C—CTG–G–AC-C-T------G-T-----A-C-T–GA–CG-C—T-C–A-TG–C-A-CG-A–AA-G-C----G-TG–GG-G–AG-C-A-AA-CAGG

And some options for cleaning up:

sed -i 's/-//g' stability.repOTU.output.fasta
sed -i 's/ /_/g' stability.repOTU.output.fasta
head stability.repOTU.output.fasta

MISEQ_31_000000000AW0EW_1_1101_19671_15407_Otu000001
TACGTAGGGTGCGAGCGTTAATCGGAATTACTGGGCGTAAAGCGTGCGCAGGCGGTTATATAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGACCTGCATTTGAGACTGTATAGCTAGAGTACGGTAGAGGGGGATGGAATTCCGCGTGTAGCAGTGAAATGCGTAGATATGCGGAGGAACACCGATGGCGAAGGCAATCCCCTGGACCTGTACTGACGCTCATGCACGAAAGCGTGGGGAGCAAACAGG