This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Converting .txt into .fasta

I'm new to biopython and I'm just having trouble converting a .txt file into a .fasta file using biopython.

sequence
• 26,889 views • link
updated by GenoMax 16K • | written by trejomarco6 0

You should add a snippet of your file so users can see how it looks and which code is necessary to convert it.

• 0 views • link
written by ATpoint 9.1K 
>NC_048263.2 Setaria viridis chromosome 1, Setaria_viridis_v4.0, whole genome shotgun sequence
ACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAA
ACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAA
CCCTAAACCTAAACCCTAAACCCTAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACC
CTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCTAAACCC

>NC_028450.1 Setaria italica strain Yugu1 chromosome I, Setaria_italica_v2.0, whole genome shotgun sequence
GGTCACAGGAGCCCTAAAACGGCCACACCGGCAACTATTGTCGAAAACGTGGGGGATGGTCCGAAGCCGT
AAAAATGTCTTACAGACCCATGTTCACCCAAGGAAACGTGTGCTATAGGTCACGGGAGCCCGAAAATGGC
CAAACCAGCAATCGGTGTTGAAAACGTGAGGGATGGTTGGATGCCGTGATAATGGCCTCCGGACCCGTTT
TCGGCCAAGAAAACGTGTGCTATAGATCACAGGAGCCCTAAAATAGCCATATTGGTAATCGGTGTCGAAA
ACATGGTGGATGGTCCGATGCCGCGAAAATATCCTCCAAACCTGTGTTCGGCCAAGAAAACATCTGCTAT

>L20582.1 Pennisetum glaucum isolate 85-34 alcohol dehydrogenase 1 (Adh1) gene, partial cds
TTCGGTCATGAGGCTGGAGGGTACGTTCTCTCCCCTGAACCACTTTATTTTGTTAGTGATTGAGCGTCTA
TGTACTTCACGTGTTCATAATTTTTGTTCTTGTGCTTGGATTTATGGTTATCGATGTTGGTCTTTGTTTA
TTGGCTTCACTAGATGCAGATCAATCTGTTAGTGTAGCCTGGATTNCTAGAGACATGTGAAACAGTCGTA
AGAAATAATTTGTCTTGTTTCAAATGGTATATCAATATTAATATGATTGAATATTATGTGTGGATACCAG

>EU075263.1 Eleusine coracana clone RGCFM90 NBS-LRR-like disease resistance protein gene, partial cds
GGGGGGGGGAGAGGTCCGAGATTATCAGGGGAGCTTGTTGGAGAAGATAATCAGGGGTGCGGTGCCGATG
TCAGGGACACAGAGAACAATGAGGGACTCATCGGCCTCCTCAGTTCTGACCTTTCAAAGAGGTTTCTGAT
GGTCTTGGATGACTTGAACAGCCCGGGCATATGGGACAATCTGCTCAAAGATCCGATGGGAGATGGCGTG
GCGAGAGGCAGGATACTGATCACGACAAGGAACGAGGAAGTGGCAACAAGCATGAAGGCAACTGTCCACC
• 0 views • link
updated by GenoMax 16K • | written by Preethika 0

What is your question? This is already a text multi-fasta file in proper format.

• 0 views • link
written by GenoMax 16K

2 answers

FASTA files are plain text files - they simply don't end in .txt for reasons of naming convention. It is likely that renaming a file or copying it into something that ends in .fas would do the trick.

If your text file is in some sequence format other than FASTA - it could be, because most of them are plain text files as well - it would help if you show the first few lines of the file and tell us what is it that you tried in BioPython that didn't work.

• 0 views • link
written by Mensur Dlakic 3.0K

If possible try converting this .txt file to .fasta file using UNIX command line Use awk command
eg.

awk '{ print ">"NR"\n"$0 }' yourfile.txt > yourfasta.fas

check this link for more help https://www.researchgate.net/post/How_to_convert_a_Text_File_to_a_Fasta_Format_File

You may try this or other similar methods in UNIX command line (since you r new to biopython)

• 0 views • link
updated by GenoMax 16K • | written by raavi21198 2

Log in to answer this question.

More posts like this