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Is there a way to tell efetch to download FASTA records such that record headers include the GI number? For example, a given header would look like this >gi|2248537881|ref|NM_001407571.1| Homo sapiens BRCA1 DNA repair associated (BRCA1), transcript variant 6, mRNA
instead of like this >NM_001407571.1 Homo sapiens BRCA1 DNA repair associated (BRCA1), transcript variant 6, mRNA
The command I'm using is efetch -db nuccore -input accNosRandom.txt -format fasta > seq.fna where accNosRandom.txt contains a list of accession numbers. It results in the non-GI number format.
The text was updated successfully, but these errors were encountered:
GIs were phased out by NCBI a few years ago. While they still remain in the ASN1 records and can be fetched using efetch with the option -format gi they are not exposed in the FASTA files and it does not have an option to include the gi number in FASTA output.
Is there a way to tell
efetch
to download FASTA records such that record headers include the GI number? For example, a given header would look like this>gi|2248537881|ref|NM_001407571.1| Homo sapiens BRCA1 DNA repair associated (BRCA1), transcript variant 6, mRNA
instead of like this
>NM_001407571.1 Homo sapiens BRCA1 DNA repair associated (BRCA1), transcript variant 6, mRNA
The command I'm using is
efetch -db nuccore -input accNosRandom.txt -format fasta > seq.fna
whereaccNosRandom.txt
contains a list of accession numbers. It results in the non-GI number format.The text was updated successfully, but these errors were encountered: