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Craig mfa extract #669

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c868068
saving progress
craiglowe Apr 19, 2022
d606aa3
revcomp based on strand
craiglowe Apr 20, 2022
a65a836
comment for fasta copy
craiglowe Apr 20, 2022
d25f55c
remove mention of genes
craiglowe Apr 20, 2022
6c85b27
use bed name for filename
craiglowe Aug 6, 2022
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29 changes: 17 additions & 12 deletions cmd/multiFaExtract/multiFaExtract.go
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Original file line number Diff line number Diff line change
Expand Up @@ -15,30 +15,35 @@ func multiFaExtract(s Settings) {
var ans []fasta.Fasta
records := fasta.Read(s.InFile)
if s.Bed == "" {
if !(s.Start < s.End) {
log.Fatalf("Invalid arguments, start must be lower than end")
}
ans = extractMultiHelper(records, s.Start, s.End)
if s.RemoveGaps {
ans = fasta.RemoveGaps(ans)
}
ans = extractMultiHelper(records, s.Start, s.End, s.RemoveGaps, false)
fasta.Write(s.OutFile, ans)
} else {
bedChan := bed.GoReadToChan(s.Bed)
for b := range bedChan {
ans = extractMultiHelper(records, b.ChromStart, b.ChromEnd)
if s.RemoveGaps {
ans = fasta.RemoveGaps(ans)
ans = extractMultiHelper(records, b.ChromStart, b.ChromEnd, s.RemoveGaps, b.Strand == bed.Negative)
if b.FieldsInitialized >= 4 {
fasta.Write(fmt.Sprintf("%s.fa", b.Name), ans)
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@cshoben cshoben Aug 7, 2022

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Can you help me understand why we would name the output file differently if the fields initialized are less than or equal to 4? I'm assuming it would be to not lose information, but then we do not seem to include the chrom start end anymore?

} else {
fasta.Write(fmt.Sprintf("%s.%d.%d.fa", b.Chrom, b.ChromStart, b.ChromEnd), ans)
}
fasta.Write(fmt.Sprintf("%s.%d.%d.fa", b.Chrom, b.ChromStart, b.ChromEnd), ans)
}
}
}

func extractMultiHelper(records []fasta.Fasta, start int, end int) []fasta.Fasta {
func extractMultiHelper(records []fasta.Fasta, start int, end int, removeGaps bool, revComp bool) []fasta.Fasta {
var ans = make([]fasta.Fasta, len(records))
if !(start < end) {
log.Fatalf("Invalid arguments, start must be lower than end. start=%d end=%d\n", start, end)
}
for i := range records {
ans[i] = fasta.Extract(records[i], fasta.RefPosToAlnPos(records[0], start), fasta.RefPosToAlnPos(records[0], end), records[i].Name)
if revComp {
ans[i] = fasta.Copy(ans[i])
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fasta.ReverseComplement(ans[i])
}
}
if removeGaps {
ans = fasta.RemoveGaps(ans)
}
return ans
}
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9 changes: 9 additions & 0 deletions fasta/modify.go
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Expand Up @@ -5,6 +5,15 @@ import (
"strings"
)

// Copy makes a copy of the fasta struct and the associated slice of dna so that
// modifying one will not also modify the other
func Copy(a Fasta) Fasta {
var ans Fasta
ans = Fasta{a.Name, make([]dna.Base, len(a.Seq))}
copy(ans.Seq, a.Seq)
return ans
}

// Remove fasta record with index i from slice of fasta.
func Remove(slice []Fasta, i int) []Fasta {
return append(slice[:i], slice[i+1:]...)
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