Remove trump character in fasta file generated during analysis by Mothur

Question

[junseob.kim.83]

Dear All,

What I understand is that trump character like ‘-’ in fasta file does not affect to data analysis, but I want to get the fasta file without trump character.

For example, in final.fasta sequences show like below.

> M04483_123_000000000-CHC2V_1_1104_5572_24823
CC-T–AC–G-G-G-A-G-GC-A-GCAG-T-G-G-G-G-A-A–TA-TT–GC-A-C—AA-T-G-G–GG–GA-A–A-C-C–C-T-G-A-T-G-CA–GC-G–A-C-GCC-G-C-G-T-------G-A-G-T–GA-----------A-G–A–A–G-T-AT-----------TT-CG-------G-T-A----------C-G-T–A—AA-G-C-TC-------------------------TA-TC-A-G–C-AGG----G–A-A–G—A-----------------------------------------A----------------------------AA-------------------------------------------------------------------T-G-A-C-G-----G-T—A-C-CT--------G-A-C-T---------A-A-----------G–AA-----------GC-G–CC-G–G-C-TAA------C–T-A-C–G-T------G-C-CA–G-C-T-G-C–CG-C—GG–TA-AT-------AC—GT-AG-GGG---------GCA-A-G–C–G–T—T–AT-C-CGG-AT–TT-A–C-T–GG-GT—GT–A-----AA-GG-GA-GC-----G-TA-G-A-C-G---------G–C-AG-C-G-C---------------------AA----G-T-C-T----------------------G-G-A–G–TG–A-AA-TG–C-C-GG-G-G-------------CC-C-AA----------C-C-C-C-G-G-G–A-C----T-G–C-T—T–T—G–GA-A-A—C------T–G-T–GC–A-G-C------T-T-G-A-G-T–G—C-GG----GA-G-A-G-G-T-A—AG-T-----GG–A–ATT–C-C-T-A-GT–GT-A-G-CG-GT-G-A-A-A–TG-C-GT-AG–AT-A-TT----------A-G----G-A-G-G-A-AC-A-CC----AG–T-G–GC-GAA-G-G-C–G-G–C-T-T-A–CTG–G–AC-C-G—T-A—A-C-T–GA–CG—T–T-G-A-GG–C-T-CG-A–AA-G-C-G-TG–GG-G–AG-C-A-AA–CA–GG-AT–TA-G-ATA–C-C-C-T–G-GTA–G-T-C

But I want to remove all the ‘-’ character and make single continuous reads like below.

> M04483_123_000000000-CHC2V_1_1104_5572_24823
CCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGGGAAACCCTGATGCAGCGACGCCGCGTGAGTGAAGAAGTATTTCGGTACGTAAAGCTCTATCAGCAGGGAAGAAAATGACGGTACCTGACTAAGAAGCGCCGGCTAACTACGTGCCAGCTGCCGCGGTAATACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCAGCGCAAGTCTGGAGTGAAATGCCGGGGCCCAACCCCGGGACTGCTTTGGAAACTGTGCAGCTTGAGTGCGGGAGAGGTAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACCGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTC

How can I make this happen? I used filter.seqs with trump=- and vetical option in Mothur command, it failed. Is there anyway to do this in Mothur commands or terminal?

Thanks!

[Mensur Dlakic]

I'd understand if you called it a minus symbol or a dash. But a trump character? Where does that come from? At least I got to see some interesting results after googling trump character.

Answer 1

[shenwei356]

sed:

sed '/^[^>]/{s/-//g;}' in.fasta > out.fasta

seqkit:

seqkit replace -s -p "-" in.fasta > out.fasta