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fasta.md

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FASTAstic

Convert FASTQ to FASTA

 zcat input_file.fastq.gz | awk 'NR%4==1{printf ">%s\n", substr($0,2)}NR%4==2{print}' > output_file.fa

Fasta to tab-delimited

!perl -e '$count=0; $len=0; while(<>) {s/\r?\n//; s/\t/ /g; if (s/^>//) { if ($. != 1) {print "\n"} s/ |$/\t/; $count++; $_ .= "\t";} else {s/ //g; $len += length($_)} print $_;} print "\n"; warn "\nConverted $count FASTA records in $. lines to tabular format\nTotal sequence length: $len\n\n";' /Volumes/web/cnidarian/oyster.v9.fa > /Volumes/web/cnidarian/cgigas_v9_genome01.tab

Tab-delimited to fasta

!awk '{print ">"$1"\n"$2}'

Count bp in fasta Tab-delim (perl)

!perl -e '$col = 2;' -e 'while (<>) { s/\r?\n//; @F = split /\t/, $_; $len = length($F[$col]); print "$_\t$len\n" } warn "\nAdded column with length of column $col for $. lines.\n\n";' /Volumes/web/cnidarian/cgigas_v9_genome01.tab > /Volumes/web/cnidarian/cgigas_v9_genome02.tab

Sequence lengths in FASTA file - tab-delimited (awk)

awk '$0 ~ ">" {print c; c=0;printf substr($0,2,100) "\t"; } $0 !~ ">" {c+=length($0);} END { print c; }' input_file.fasta

Taken from here: http://www.danielecook.com/generate-fasta-sequence-lengths/

Count Number of Sequences in a FASTA File (grep)

 $grep -c '>' path/to/InputFasta/file.fasta

Count Number of Sequences in a FASTA File (awk)

 $awk '/>/ { count++ } END { print count }' path/to/InputFastFile.fasta

Code explanation: />/

  • Tells awk to look for whatever regular expression is between the two slashes. In this instance, a greater-than symbol (which identifies a new sequence entry in a FASTA file).

{ count++ }

  • Tells awk to assign the variable called "count" to the results of counting ("++") all of the greater-than symbols it encounters

END{ print count }

  • Tells awk to print the variable called "count", which is the total number of ">" in our input FASTA file

NOTE: If the sequence IDs of your FASTA file also contain ">", the one-liner listed above will report an inaccurate result. However, as FASTA formatting goes, a ">" should never appear in the file other than as a sequence ID indicator.

Filter FASTA File by Minimum Sequence Length

Just change the number "200" in the code below to your desired minimum sequence length.

$ awk '!/^>/ { next } { getline seq } length(seq) >= 200 { print $0 "\n" seq }' /path/to/InputFastaFile.fasta > /path/to/OutputFastaFile.fasta

Code explanation: !/^>/ {next }
– If a line (i.e. record) begins with a “>”, go to the next line (record). The "!" tells awk to skip the regular expression that immediatley follows. The "^" tells awk that the regular expression it's looking for should only match if it's at the beginning of a line. Finally, the regular expression we're looking for in this example is the ">", which denotes the sequence descriptor portion of FASTA files.
{ getline seq }
– “getline” reads the next record and assigns the entire record to a variable called “seq”
length(seq) >=200
– If the length of the “seq” record is greater than, or equal to, 200 then…
{print $0 "\n" seq>}
– Print all records ($0) of the variable “seq” in the file that matched our conditions, each on a new line (“\n”)