Converting a single line fasta transcriptome [no space between sequence and name] to conventional fasta format

Question

[Roelof]

Hi there,

I've been handed a transcriptome containing consensus sequence data contained in a word document. For some reason this person also place each contig entry in the fasta file as a single line with no character separation between name and sequence.

The resulting file looks as follows. I've tried to solve using SeqIO in biopython, but to no avail. My Regex just isn't good enough to separate this. Later on in the file the contig names have vivid descriptions and so a pattern on the names seems to be error prone.

>rmi3_Contig1AAAATATGACAGTCTTTATTCCAGTCTATTTTAGCCAATACAGCACACACAGCTCAAGAAGTTCTTAAAATGACAGTCTAGAAATGACTACAAAGCATTTTCTTTTGCTGGAACTTTGTACAAATACAAGTAATTGTCTAAACAACTAGTTAAATATTGGCTCAAGAATCTGCCGTTCATCATAAAAAACTAGTGACAGAAAGTTGCAGTAAACCGAATAAATTTTCTGACATGCACTACCGCATCAAACGGCGCATGGATTTTATTCTGGAACAATGAGAGCATTGCACACGGCATCTGCTTCTCATGGCGTTCCTGCAAACGTTCGTTTGTGCTACAATTTCGACATTCTCATGCGTGCACTTCAAACTCTTTGTATATTATGCTTGCATATACTCTAAGGAAGCAGCATGTTCGCAGAATGATTTCTAGGAATATGTTCTGAAGGCGAGACATGACAGCGCATCGTATGCTACACACAGATCTGCTTCTGATACTGATTTACCCGGTGACCTTAGTGCTAAATCCCCTTGATATTTCTGCACTGCTCCACAAAAATGCGGGTATATTTTAGCGAGAAGTTGGATTCTGGAACAGAATTTGTGTGCACAGAAGTGTGCGTAGGAACATATGAAAAAAACTAATCTTGTGCGAATACTCGAACGAGTAATACGATATTCGAATTTGTTTCAATTAGAATTTAAATTATTGAAGATTTTGAAGAATCAAAATGAGTGAATAGCTGTGTATGAATCTGAATGTAACCTCCTGTAGAGATAGTTTGGTGGCAGTATAGAAGTATTAAGTTGTGAAAACACCTAACTAGAGGACATCTGCACTGGCACAAAACCTCGCTTCAATTTTAAATGAAATTATCACCCTCACACCGATTAATAATTTTTTTAAGTTTAAAAGCTTGTTACACCGGTTTATATGTCTGACGTATAGAAACTTTTTAAGAGTAACATACTTTACAGGTTATAACTTGCATTTTACCGAAAGTCAAATCCTGCTACTGTTCAAAGTTGTTTTCACTTCTTTTGAACCAATAAAACAAAACAAAAAAGGCACTTGCACGGGCTTTGTTTCAATTTAATAAGATAAATATTGTGCACATTCGTTAGGTGATGACAAATATGCCTATGTTTAAAATAATATTTATAATAAGTGAGATATAATATTTTATTTGATTCAAAATAATTTGACCAAAATTGCTATTCGTTTCAAATTCGCTACGAGCCTAAAATTAACTATTCGCACAAGCGTAAAAAAAAAGTTATTGTTAGATGCATATTGCTATACTGGAGATAGTAAAGCCTGCTTATAAAATATAACACATACTTCCTGGGAACAGGTATATTTTTGTGAAGATCGTGTAGCCTTATATGGTAAAATTTTGGCAAGTGCAGGCTCACATTCACGGTTATTCTTTGAAGCAAAGTAACAAATCCCAACTTGCTGAGCTTGAGCTTCTTCTTTTCTTATTGCACGTCCACATTGGGATCAGAGATGTGATTAGGGGGTTCCTAAGTTCACTTGAAAACTGTCAGGCTCTGGCCATATAATACCTGCTATGGCCAGACCTGTTATATTGTATACCTGTTATTTCCTTTGAGGCACGAAACATCAAATTAACACTAGATGTCCAATAATGCTCAATGCGCAATCTAAAAAACAAAGTTGCAAGAACACTCGCACAGCAAAACGATTTTACTAGGATACTGCGACCAATACAGTTGTCCAAATGCTTTTATACTTTTCTGATAGTTCGAGAAGCGCGCTTTAAGTAGGGAAAGGAATAACAGTAGATTGCAAGATGCGCCTATGGAATTAGGAAGTTCACTTTGCCGTATTTCTTGGTCCATTACCAGCATACCATATGTTTATAAAAAATGCATTGATAATTATGATTTTGCTTGAAAAATTATGACCTAGAAAGATGAAATGGAAGCCGCATATTGTGGGATTCCTAAGAACTGGTTTGCTACGATTCAAAGCATTCTGATGATTTAAAAAATGAAGTGAAAAAAGAATCACGAGAAGGACTAGATGCTTGAACATAATTATGATTTTCGAAACAAGATGCATGCATTGAAAACCCGTGAAATCATTTGTCATGATTTAACAATTTTTTTTCGCAAAATGAAAATGAAGCGTGGACATCAGGACGAGGAGACAAACAATATTCAGATAATATATGTCATCCGATGCTATCCCTGCGATAGATGCCGGCAACATCAGACTTCGGGGTGCCATATTTTGACTTAGTGGGAACGGCAGTTGGGCGGCATCCGGTGAATGCTGCATCATAACGAGATGTTTTTCCAGCAGAACAGGATGACCCCGATGGAGGCGAGCACGGCGGCTGCTGAAAAATCAACCTTGTTGGCGAATGATGGCACGCCCATGTAGTCTTGGACGTTGGCCTTGTCCCATCCGACTACCTCATTTTTGATGCGCTCGTCAAGCCATTTCTCGAGCGGCTCGTAGTACTTCTTTAAGGATGAAGCTGACATCTGCCGCGTGCCAGCCATGATCTCGAGGACATCGGGCCAAGGCTTAGAGCGACCCAGCGACAGTCCCTTCTTGAGGACGTCGCCAGCGTTCTTCTCTCCGTAAATGTCGCATTCATGGAATGGATGATGTTCGTCCACCTTCTTTGCAACTGTGCATAAATGCTCGTGAAACTGGAACTGAAGGATGAACGCCACGAAATATCTCAGGTACGGAACGTGCAAAGCCACGTGGTACTTAGCTCCGCCGTCAAAGAAGGACTCGTTGCGCTTTACCGGAGGTGACACGCCTTGGTATTTTATCCTGTATTCCCAGAACTTCTCGTTCATCTTGTCGAACGGCGTCTCGCCGGTGAATATGGTCCAGCGCCACTTGTCCAACAGGTACCCGAATGGCAAGAAGGCGATCTTGTCAAGTGCCGACATAAGCAGGAGGTCAACAGCATTGTATTTATCCGTTGGTTTCAGCAAGCTAAGCTTTCCGTAATGTGTTTTTGTGGCAACTGAAAGGGCTATCAGATCTCCGACGGCCTCATGGAAACCTTCGTTGGCTCCCTCTTGCAGCAGGACGTGCAGGTGCTTGTACTGCATGTAATACTCGATGTGGCCCATCTCGTGGTGGACAGTGCGCAGTTCCTCGACGCTGGGGTCGGTGCACATCTTTATTCTGAAGTCGTCGCCGTTGTACATGTTCCAGGCGGAGGCGTGACACTGAATCTCTCGGTCTTCGGGCTTTGTAAGGATGGACTTGCTCCAAAACTCGCTGGTCATGTTGTCCAGGCCCAGACTCGTAAAGAAGTCCTCCGCTGCGTGGAACATCTTTTGGGCATCCCATTTCTGTTCCACCATTGTCTTCGAGATATCCAAAGGTTTGTCTTCCATCGTTAGGTGAGGGTATAGTGTGCCCCACTCTTGCGCCCACATGTTCCCTAACAGATGGGCTGGTATCGTGCCATCTTCGGGCAGGCGTCCAGGATAAATCTCCCTGAGCTTCATTCTCACGTAGGCGTGCAGCTTTTTGTACAGCGGAGACAGATCTTCCCACAGTTTGTCGACGATCTCGGTCATGTTTTCCGTCTCGTAGTCACTGAGCCAGGCGCTCTTGATATTGTCGTAACCGTCCAGAGACGCTGCTTCATTGGACAGCTTGATGTAGGGAATGTAGTACTGTTTTATAGCCGGACCAACTGCGTTATGCCATGCCAGCCAAGTTTGCAGTAATTTATCGTAATTGCCAACTTCCTTCATATTCCGGGTGAGATCTGGTTCCAGAGGAAGGTCCTTATCCTTGCCAACGGTCACCTTGGTCGATCCATATATGGCGGCCATCTTCGAACTGAGACTGGTCGCATTCTCAAGCTTGTCGTCGGGAAGAGCTGCCAGGCCAATGGTAGCGACGTGCCTAAATAGTCGTTTGAGCGAATCATTTTTGAAATTGTGCCAGTCGAAACGCTTCGCCGTAATTCCAAACTGCCGCTCCATTTTTGAGACTTCGGTGGAGACCTTATTCGACATGTTTTGGTTGTAATCGGTGATGTTGGAAGCATAGTCCCAACTAGAAGATGAGTCCACGTTGTTAATCGTTGTATATGGGTCATTCAAGCCTTCTATAAAGGCAACGCCCATTGCTTCATCTTTTATCAAGGCTGATACATTCGATAAAGTTGCCAAGTAGGTGTCGAAGTTGTCTGCGGCTGCTGTCGCGTACAGCGCGGTGGCCAGGAGAGCGACGGCCACGAAGCGATCGGCGGCCGACGATCCCGATCGAGCAGCCATGTCGGGCCGTTTCGGTGCGGGTGAAGCTCCGCAGCTGCTCTGGTTTGTTGAGGATGTTGCGCGCGCTCTTCGCTGCTCACCGACGAGAGCGCACTCCG
>rmi3_Contig2CAAGAGCGCATCTGAGCATGCGCACTGGTATGTTTGCAACCCTCTTTACTAGGCCTAGTGCATTTTAACATGGACCCAGAGGGAAGCCGTGAAAGATCCTGAAACTATTTAATTTAGTGCAAAGTTTATTGATTTAGTGTTGTTGCGAGGTGCCTGCAGTTGGCTACAAGCACATTTAGGATCCATGGACAGTACGTCCATAATTACTCAAGTGAACAGAGAAGAGGAACAACTAACAAATTTTCCTCCTGCTGATCGAGTGCCGCCCTCCAGCAGGAAGCCCCGGCAGCGCGGCTTCCTCAACACGCTGCTCTGCTGCTTCGGGAGCAACAACCAAGGCAACAACCCCGTGATTGCCGAGGAAAATGGCCAGTACTCGCCCAAGCTCCAGGGCAAGTACCTGCTGCCACCCGTGCGGCATCAGGATATTCGCAAGATATGCCTCATCATTGACCTCGATGAGACATTGGTCCATAGCTCATTCAAGCCCATCAACAATGCTGACTTCGTGGTGCCTGTAGAGATAGATGGCACGGTGCACCAGGTGTATGTCTTGAAGAGGCCTTATGTGGACGAGTTCTTGCAGCGAGTTGGCGATGCCTACGAATGTGTCTTATTCACAGCCAGCCTTGCAAAGTATGCTGACCCTGTGGCTGACCTGCTGGACAAGTGGGGTGTCTTCCGGGCACGGTTATTCCGAGAGTCTTGTGTCTTCTACCGAGGAAACTATGTCAAGGACCTTGGTAGGCTGGGCCGGGATCTGCGCAGAGTGGTCATAATAGACAACTCACCGGCCTCGTACATCTTCCATCCTGACAATGCAGTACCTGTCAACTCGTGGTTCGATGACATGTCAGACACGGAGCTGCGGGACCTGATGCCATTGTTCGACGAACTGAGCCGTGTCGAGGACGTGTACACGGTGCTGCGCAACTCCAACAACGCGGCTGGCGGTGGCGGCGGCTCTCCGGCCTTCCCTGCACCACTCCTGATGAACGGCAGCGCGGTGGCTTTGCACAACAGCGGTTCCTAGCATTCCGCACAGTGCGGCTTGTGCAATAGCCCCTTCTCCGCCGGCAGTACAAAAGCGCTTACGGGTCCCGTGCTAGTCTCGCCGGCCTACTTAACGTCGGAGGGGGGCTGCCCCTTGTGCCTTGTCTCTTCCGCTCTGGACGAGAGTTTGTATAATAACGGTGTTCCATAATCTCGCCTGTATCATAGATTAAAGACGACTATTTCAGCCTGCAAAA

Anyone know how to convert this into the following

>rmi3_Contig1
AAAATATGACAGTCTTTATTCCAGTCTATTTTAGCCAATACAGCACACACAGCTCAAGAAGTTCTTAAAATGACAGTCTAGAAATGACTACAAAGCATTTTCTTTTGCTGGAACTTTGTACAAATACAAGTAATTGTCTAAACAACTAGTTAAATATTGGCTCAAGAATCTGCCGTTCATCATAAAAAACTAGTGACAGAAAGTTGCAGTAAACCGAATAAATTTTCTGACATGCACTACCGCATCAAACGGCGCATGGATTTTATTCTGGAACAATGAGAGCATTGCACACGGCATCTGCTTCTCATGGCGTTCCTGCAAACGTTCGTTTGTGCTACAATTTCGACATTCTCATGCGTGCACTTCAAACTCTTTGTATATTATGCTTGCATATACTCTAAGGAAGCAGCATGTTCGCAGAATGATTTCTAGGAATATGTTCTGAAGGCGAGACATGACAGCGCATCGTATGCTACACACAGATCTGCTTCTGATACTGATTTACCCGGTGACCTTAGTGCTAAATCCCCTTGATATTTCTGCACTGCTCCACAAAAATGCGGGTATATTTTAGCGAGAAGTTGGATTCTGGAACAGAATTTGTGTGCACAGAAGTGTGCGTAGGAACATATGAAAAAAACTAATCTTGTGCGAATACTCGAACGAGTAATACGATATTCGAATTTGTTTCAATTAGAATTTAAATTATTGAAGATTTTGAAGAATCAAAATGAGTGAATAGCTGTGTATGAATCTGAATGTAACCTCCTGTAGAGATAGTTTGGTGGCAGTATAGAAGTATTAAGTTGTGAAAACACCTAACTAGAGGACATCTGCACTGGCACAAAACCTCGCTTCAATTTTAAATGAAATTATCACCCTCACACCGATTAATAATTTTTTTAAGTTTAAAAGCTTGTTACACCGGTTTATATGTCTGACGTATAGAAACTTTTTAAGAGTAACATACTTTACAGGTTATAACTTGCATTTTACCGAAAGTCAAATCCTGCTACTGTTCAAAGTTGTTTTCACTTCTTTTGAACCAATAAAACAAAACAAAAAAGGCACTTGCACGGGCTTTGTTTCAATTTAATAAGATAAATATTGTGCACATTCGTTAGGTGATGACAAATATGCCTATGTTTAAAATAATATTTATAATAAGTGAGATATAATATTTTATTTGATTCAAAATAATTTGACCAAAATTGCTATTCGTTTCAAATTCGCTACGAGCCTAAAATTAACTATTCGCACAAGCGTAAAAAAAAAGTTATTGTTAGATGCATATTGCTATACTGGAGATAGTAAAGCCTGCTTATAAAATATAACACATACTTCCTGGGAACAGGTATATTTTTGTGAAGATCGTGTAGCCTTATATGGTAAAATTTTGGCAAGTGCAGGCTCACATTCACGGTTATTCTTTGAAGCAAAGTAACAAATCCCAACTTGCTGAGCTTGAGCTTCTTCTTTTCTTATTGCACGTCCACATTGGGATCAGAGATGTGATTAGGGGGTTCCTAAGTTCACTTGAAAACTGTCAGGCTCTGGCCATATAATACCTGCTATGGCCAGACCTGTTATATTGTATACCTGTTATTTCCTTTGAGGCACGAAACATCAAATTAACACTAGATGTCCAATAATGCTCAATGCGCAATCTAAAAAACAAAGTTGCAAGAACACTCGCACAGCAAAACGATTTTACTAGGATACTGCGACCAATACAGTTGTCCAAATGCTTTTATACTTTTCTGATAGTTCGAGAAGCGCGCTTTAAGTAGGGAAAGGAATAACAGTAGATTGCAAGATGCGCCTATGGAATTAGGAAGTTCACTTTGCCGTATTTCTTGGTCCATTACCAGCATACCATATGTTTATAAAAAATGCATTGATAATTATGATTTTGCTTGAAAAATTATGACCTAGAAAGATGAAATGGAAGCCGCATATTGTGGGATTCCTAAGAACTGGTTTGCTACGATTCAAAGCATTCTGATGATTTAAAAAATGAAGTGAAAAAAGAATCACGAGAAGGACTAGATGCTTGAACATAATTATGATTTTCGAAACAAGATGCATGCATTGAAAACCCGTGAAATCATTTGTCATGATTTAACAATTTTTTTTCGCAAAATGAAAATGAAGCGTGGACATCAGGACGAGGAGACAAACAATATTCAGATAATATATGTCATCCGATGCTATCCCTGCGATAGATGCCGGCAACATCAGACTTCGGGGTGCCATATTTTGACTTAGTGGGAACGGCAGTTGGGCGGCATCCGGTGAATGCTGCATCATAACGAGATGTTTTTCCAGCAGAACAGGATGACCCCGATGGAGGCGAGCACGGCGGCTGCTGAAAAATCAACCTTGTTGGCGAATGATGGCACGCCCATGTAGTCTTGGACGTTGGCCTTGTCCCATCCGACTACCTCATTTTTGATGCGCTCGTCAAGCCATTTCTCGAGCGGCTCGTAGTACTTCTTTAAGGATGAAGCTGACATCTGCCGCGTGCCAGCCATGATCTCGAGGACATCGGGCCAAGGCTTAGAGCGACCCAGCGACAGTCCCTTCTTGAGGACGTCGCCAGCGTTCTTCTCTCCGTAAATGTCGCATTCATGGAATGGATGATGTTCGTCCACCTTCTTTGCAACTGTGCATAAATGCTCGTGAAACTGGAACTGAAGGATGAACGCCACGAAATATCTCAGGTACGGAACGTGCAAAGCCACGTGGTACTTAGCTCCGCCGTCAAAGAAGGACTCGTTGCGCTTTACCGGAGGTGACACGCCTTGGTATTTTATCCTGTATTCCCAGAACTTCTCGTTCATCTTGTCGAACGGCGTCTCGCCGGTGAATATGGTCCAGCGCCACTTGTCCAACAGGTACCCGAATGGCAAGAAGGCGATCTTGTCAAGTGCCGACATAAGCAGGAGGTCAACAGCATTGTATTTATCCGTTGGTTTCAGCAAGCTAAGCTTTCCGTAATGTGTTTTTGTGGCAACTGAAAGGGCTATCAGATCTCCGACGGCCTCATGGAAACCTTCGTTGGCTCCCTCTTGCAGCAGGACGTGCAGGTGCTTGTACTGCATGTAATACTCGATGTGGCCCATCTCGTGGTGGACAGTGCGCAGTTCCTCGACGCTGGGGTCGGTGCACATCTTTATTCTGAAGTCGTCGCCGTTGTACATGTTCCAGGCGGAGGCGTGACACTGAATCTCTCGGTCTTCGGGCTTTGTAAGGATGGACTTGCTCCAAAACTCGCTGGTCATGTTGTCCAGGCCCAGACTCGTAAAGAAGTCCTCCGCTGCGTGGAACATCTTTTGGGCATCCCATTTCTGTTCCACCATTGTCTTCGAGATATCCAAAGGTTTGTCTTCCATCGTTAGGTGAGGGTATAGTGTGCCCCACTCTTGCGCCCACATGTTCCCTAACAGATGGGCTGGTATCGTGCCATCTTCGGGCAGGCGTCCAGGATAAATCTCCCTGAGCTTCATTCTCACGTAGGCGTGCAGCTTTTTGTACAGCGGAGACAGATCTTCCCACAGTTTGTCGACGATCTCGGTCATGTTTTCCGTCTCGTAGTCACTGAGCCAGGCGCTCTTGATATTGTCGTAACCGTCCAGAGACGCTGCTTCATTGGACAGCTTGATGTAGGGAATGTAGTACTGTTTTATAGCCGGACCAACTGCGTTATGCCATGCCAGCCAAGTTTGCAGTAATTTATCGTAATTGCCAACTTCCTTCATATTCCGGGTGAGATCTGGTTCCAGAGGAAGGTCCTTATCCTTGCCAACGGTCACCTTGGTCGATCCATATATGGCGGCCATCTTCGAACTGAGACTGGTCGCATTCTCAAGCTTGTCGTCGGGAAGAGCTGCCAGGCCAATGGTAGCGACGTGCCTAAATAGTCGTTTGAGCGAATCATTTTTGAAATTGTGCCAGTCGAAACGCTTCGCCGTAATTCCAAACTGCCGCTCCATTTTTGAGACTTCGGTGGAGACCTTATTCGACATGTTTTGGTTGTAATCGGTGATGTTGGAAGCATAGTCCCAACTAGAAGATGAGTCCACGTTGTTAATCGTTGTATATGGGTCATTCAAGCCTTCTATAAAGGCAACGCCCATTGCTTCATCTTTTATCAAGGCTGATACATTCGATAAAGTTGCCAAGTAGGTGTCGAAGTTGTCTGCGGCTGCTGTCGCGTACAGCGCGGTGGCCAGGAGAGCGACGGCCACGAAGCGATCGGCGGCCGACGATCCCGATCGAGCAGCCATGTCGGGCCGTTTCGGTGCGGGTGAAGCTCCGCAGCTGCTCTGGTTTGTTGAGGATGTTGCGCGCGCTCTTCGCTGCTCACCGACGAGAGCGCACTCCG
>rmi3_Contig2
CAAGAGCGCATCTGAGCATGCGCACTGGTATGTTTGCAACCCTCTTTACTAGGCCTAGTGCATTTTAACATGGACCCAGAGGGAAGCCGTGAAAGATCCTGAAACTATTTAATTTAGTGCAAAGTTTATTGATTTAGTGTTGTTGCGAGGTGCCTGCAGTTGGCTACAAGCACATTTAGGATCCATGGACAGTACGTCCATAATTACTCAAGTGAACAGAGAAGAGGAACAACTAACAAATTTTCCTCCTGCTGATCGAGTGCCGCCCTCCAGCAGGAAGCCCCGGCAGCGCGGCTTCCTCAACACGCTGCTCTGCTGCTTCGGGAGCAACAACCAAGGCAACAACCCCGTGATTGCCGAGGAAAATGGCCAGTACTCGCCCAAGCTCCAGGGCAAGTACCTGCTGCCACCCGTGCGGCATCAGGATATTCGCAAGATATGCCTCATCATTGACCTCGATGAGACATTGGTCCATAGCTCATTCAAGCCCATCAACAATGCTGACTTCGTGGTGCCTGTAGAGATAGATGGCACGGTGCACCAGGTGTATGTCTTGAAGAGGCCTTATGTGGACGAGTTCTTGCAGCGAGTTGGCGATGCCTACGAATGTGTCTTATTCACAGCCAGCCTTGCAAAGTATGCTGACCCTGTGGCTGACCTGCTGGACAAGTGGGGTGTCTTCCGGGCACGGTTATTCCGAGAGTCTTGTGTCTTCTACCGAGGAAACTATGTCAAGGACCTTGGTAGGCTGGGCCGGGATCTGCGCAGAGTGGTCATAATAGACAACTCACCGGCCTCGTACATCTTCCATCCTGACAATGCAGTACCTGTCAACTCGTGGTTCGATGACATGTCAGACACGGAGCTGCGGGACCTGATGCCATTGTTCGACGAACTGAGCCGTGTCGAGGACGTGTACACGGTGCTGCGCAACTCCAACAACGCGGCTGGCGGTGGCGGCGGCTCTCCGGCCTTCCCTGCACCACTCCTGATGAACGGCAGCGCGGTGGCTTTGCACAACAGCGGTTCCTAGCATTCCGCACAGTGCGGCTTGTGCAATAGCCCCTTCTCCGCCGGCAGTACAAAAGCGCTTACGGGTCCCGTGCTAGTCTCGCCGGCCTACTTAACGTCGGAGGGGGGCTGCCCCTTGTGCCTTGTCTCTTCCGCTCTGGACGAGAGTTTGTATAATAACGGTGTTCCATAATCTCGCCTGTATCATAGATTAAAGACGACTATTTCAGCCTGCAAAA

Hopelessly stuck R

[cpad0112]

try:

   $ sed 's/\(.*[0-9]\+\)/\1\n/g' test.fa > new.fa

or

$ sed 's/\(.*Contig[0-9]\+\)/\1\n/g' test.fa

[cpad0112]

with bash: Regex works only if there is 6 letter word (contig in this example), preceded by _ (underscore) and followed by a single number (contig number in this example) (probably works with OP data only):

$ grep -Po '\w*\W\w*[0-9]+(?=[ATGCN]*)|(?<=_\w{6}[0-9]).*' test.fa

>rmi3_Contig1
AAAATATGACAGTCTTTATTCCAGTCTATTTTAGCCAATACAGCACACACAGCTCAAGAAGTTCTTAAAATGACAGTCTAGAAATGACTACAAAGCATTTTCTTTTGCTGGAACTTTGTACAAATACAAGTAATTGTCTAAACAACTAGTTAAATATTGGCTCAAGAATCTGCCGTTCAT............................................................GCTGATACATTCGATAAAGTTGCCAAGTAGGTGTCGAAGTTGTCTGCGGCTGCTGTCGCGTACAGCGCGGTGGCCAGGAGAGCGACGGCCACGAAGCGATCGGCGGCCGACGATCCCGATCGAGCAGCCATGTCGGGCCGTTTCGGTGCGGGTGAAGCTCCGCAGCTGCTCTGGTTTGTTGAGGATGTTGCGCGCGCTCTTCGCTGCTCACCGACGAGAGCGCACTCCG
>rmi3_Contig2
CAAGAGCGCATCTGAGCATGCGCACTGGTATGTTTGCAACCCTCTTTACTAGGCCTAGTGCATTTTAACATGGACCCAGAGGGAAGCCGTGAAAGATCCTGAAACTATTTAATTTAGTGCAAAGTTTATTGATTTAGTGTTGTTGCGAGGTGCCTGCAGTTGGCTACAAGCACATTTAGGATCCATGGACAGTACGTCCATAATTACTCAAGTGAACAGAGAAGAGGAACAACTAACAAATTTTCCTCCTGCTGATCGAGTGCCGCCCTCCAGCAGGAAGCCCCGGCAGCGCGGCTTCCTCAACACGCTGCTCTGCTGCTTCGGGAGCAACAACCAAGGCAACAACCCCGTGATTGCCGAGGAAAATGGCCAGTACTCGCCCAAGCTCCAGGGCAAGTACCTGCTGCCACCCGTGCGGCATCAGGATATTCGCAAGATATGCCTCATCATTGACCTCGATGAGACATTGGTCCATAGCTCATTCAAGCCCATCAACAATGCTGACTTCGTGGTGCCTGTAGAGATAGATGGCACGGTGCACCAGGTGTATGTCTTGAAGAGGCCTTATGTGGACGAGTTCTTGCAGCGAGTTGGCGATGCCTACGAATGTGTCTTATTCACAGCCAGCCTTGCAAAGTATGCTGACCCTGTGGCTGACCTGCTGGACAAGTGGGGTGTCTTCCGGGCACGGTTATTCCGAGAGTCTTGTGTCTTCTACCGAGGAAACTATGTCAAGGACCTTGGTAGGCTGGG

ps: Removed part of contig 1 sequence for 5000 character limit.

Answer 1

[Pierre Lindenbaum]

 sed 's/\([ATGCNatgc]*\)$/ \1/'  input.txt | tr " " "\n"  > out.fa