How to subset sequences in fasta file based on sequence ID or Name?

Question

I have set of EST sequences in fasta file. Here, how to subset based on sequence ID or name? ``` >gi|296783888|gb|GW992815.1|GW992815 UAS-Mi10 Complementary DNA of mulberry (Morus indica) Morus indica cDNA 5' similar to Putative phosphoribosyltransferase/phosphoribosylanthranilate-like gene from Morus indica, mRNA sequence GCAGCCGTCGGATCGTGAGCGTGATCGCGTGGCTAGTCGGGTTGGCGAAATGGTTGGATGATATCCGGAG GTGGAGGAACCCCATTACCACGGTATTGGTCCACATCTTATATTTAGTGCTTGTTTGGTACCCGGATTTG ATTGTCCCAACCGGGTTTTTATATGTGTTCCTAATCGGTGTATGGTACTATCGGTTTCGGCCCAAGATAC CAGCGGGTATGGATACCCGACTCTCACAAGCTGAAGCGGTTGACCCGGATGAGCTTGATGAGGAATTCGA CACCATACCGAGCTCAAAACCACCCGACATAATCAGGGTCCGGTATGACCGGTTGCGGATATTGGCAGCC CGGGTTCAAACGGTTTTGGGTGATTTTGCAACACAAGGGGAGCGGGTTCAGGCCTTGGTTAGCTGGAGGG ACCCAAGGGCCACAAAATTGTTCATAGGCGTGTGCTTGGCCATAACAATAATTCTCTATGTGGTGCCACC CAAAATGGTTGCCGTGGCACTTGGATTCTACTATTTACGACACCCCATGTTCCGAGACCCCATGCCTCCT GCAAGCTTGAATTTCTTCAGAAGGCTTCCAAGCCTTTCAGACCGCTTTAATGTAGATTAGAATATTATAT GATTATTAGTAGGCCCAA >gi|296783887|gb…

Accepted Answer

For a slightly more heavy-weight solution, if this fits in to the Bioconductor work flow,

```
source("http://bioconductor.org/biocLite.R")
biocLite("Rsamtools")
```

to install the Biostrings and Rsamtools package, then

```
library(Rsamtools)
indexFa("foo.fasta")   # create an index of file 'foo.fasta'
fa = FaFile("foo.fasta")  # reference the fasta file and it's index
```

You can discover the coordinates (names and start / end) of each sequence with

```
gr = as(seqinfo(fa), "GRanges")
```

and query for arbitrary sequences and ranges within sequences by choosing appropriate subsets, e.g., the second sequence and then first sequence in your example

```
getSeq(fa, gr[2:1])
```

or by looking up the coordinates by partial match to the names

```
idx = pmatch("gi|296783888", names(gr))  ## NA's if duplicates or not unique
seq = getSeq(fa, gr[idx])
```

"seq" is a DNAStringSet, and can be manipulated in many ways; see the vignettes available in the package

```
vignette(package="Biostrings")
```

especially the Quick Overview. To save the object to a fasta file 'file.fa' in a directory 'some' relative to the current working directory, use

```
writeXStringSet(seq, "some/file.fa")
```

How to subset sequences in fasta file based on sequence ID or Name?

Solution

Problem